Running as unit: rb-build-amd64_25-49280.service ==================================================================================== Wed Aug 6 06:08:18 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_25) on jenkins, called using "ionos1-amd64 ionos5-amd64" as arguments. Wed Aug 6 06:08:18 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-ZpEP1RAV" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Aug 6 06:08:18 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Wed Aug 6 06:08:18 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-6f9dOe' Wed Aug 6 06:08:18 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Wed Aug 6 06:08:18 UTC 2025 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-eKbxiV' ok, let's check if molmodel is building anywhere yet… ok, molmodel is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of molmodel in trixie on amd64 on jenkins now. 1st build will be done on ionos1-amd64.debian.net. 2nd build will be done on ionos5-amd64.debian.net. ============================================================================= Wed Aug 6 06:08:25 UTC 2025 I: starting to build molmodel/trixie/amd64 on jenkins on '2025-08-06 06:08' Wed Aug 6 06:08:25 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_25/49280/console.log 1754460505 amd64 trixie molmodel Wed Aug 6 06:08:25 UTC 2025 I: Downloading source for trixie/molmodel=3.1.0-4.1 --2025-08-06 06:08:25-- http://deb.debian.org/debian/pool/main/m/molmodel/molmodel_3.1.0-4.1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2238 (2.2K) [text/prs.lines.tag] Saving to: ‘molmodel_3.1.0-4.1.dsc’ 0K .. 100% 248M=0s 2025-08-06 06:08:25 (248 MB/s) - ‘molmodel_3.1.0-4.1.dsc’ saved [2238/2238] --2025-08-06 06:08:25-- http://deb.debian.org/debian/pool/main/m/molmodel/molmodel_3.1.0-4.1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2238 (2.2K) [text/prs.lines.tag] Saving to: ‘molmodel_3.1.0-4.1.dsc’ 0K .. 100% 248M=0s 2025-08-06 06:08:25 (248 MB/s) - ‘molmodel_3.1.0-4.1.dsc’ saved [2238/2238] Wed Aug 6 06:08:25 UTC 2025 I: molmodel_3.1.0-4.1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: molmodel Binary: libsimtkmolmodel-dev, libsimtkmolmodel3.1t64, libsimtkmolmodel-plugins Architecture: any Version: 3.1.0-4.1 Maintainer: Debichem Team Uploaders: Andrius Merkys , Homepage: https://simtk.org/projects/molmodel Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/debichem-team/molmodel Vcs-Git: https://salsa.debian.org/debichem-team/molmodel.git Build-Depends: dpkg-dev (>= 1.22.5), cmake, debhelper-compat (= 13), gemmi-dev, libmmdb2-dev, libopenmm-dev, libopenblas-pthread-dev, libsimbody-dev, tao-pegtl-dev, zlib1g-dev Package-List: libsimtkmolmodel-dev deb libdevel optional arch=any libsimtkmolmodel-plugins deb libs optional arch=any libsimtkmolmodel3.1t64 deb libs optional arch=any Checksums-Sha1: 5ad7cc7f74a13d8b57d5d4cb468aa48f3f67ad75 11118182 molmodel_3.1.0.orig.tar.gz efaae5b5d6d58f308d09b977cac013b9be6b0920 4668 molmodel_3.1.0-4.1.debian.tar.xz Checksums-Sha256: d9fef841ce0b5978a20c0fce77e7f74e2a360576388e564fbe84a15cb53fbedd 11118182 molmodel_3.1.0.orig.tar.gz 9b7b272b68c31804fcc9363601d26d32b0f3d75d82df7dcfda0c8957c6694749 4668 molmodel_3.1.0-4.1.debian.tar.xz Files: 082b507dc0ac23db29b0984b28176c41 11118182 molmodel_3.1.0.orig.tar.gz 5030a4382974e8ede80d8154f14cc268 4668 molmodel_3.1.0-4.1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEpi0s+9ULm1vzYNVLFZ61xO/Id0wFAmXflQIACgkQFZ61xO/I d0xOlRAAqGBiBblkhRenTb3Rl8iXKdltKy/Kd3Gta2oE18ZMlFrxBIW0TYo68w67 wghGg9hMtIrERAicaibg1JO5g8dl2CwX5h+/rxvUqJjwMwhb8GQLrhrRAzbq+7ju lHpACiuzvPWAnw8colgPJaOZZjas5mAuUYPkNZVRE/pqdjx/rhVv0WeXmXrE94f8 BxoN4ILfkDK/mRhNPC1z9FeJpjWXMEhN36hbT0U1zcN8bK6N5nCjZJ/XSPWTsBRR urYkGU2Sbr0APafaCi0I6e73OzBLlA7ZZFv2cz5oRDYTiDklYUhCdKfoKjPq2Yjs k+wrf/NU5gBQfjMo25YWkCEA9iOAtyxCOiYydU7yFV3vY3EG6woBPmew2YUtk31g 4Q/CUO4gy0oDBvu0l6S02Rc/aiK/yk+Q+jYTHMuDfkFyTB0fkj6p6MSvhtyRCPRN z+Qxu0fmRjPmfGOrK9S96/1paEu1qGM/CR//Z6CPWNcPxpugxCDErzCZgJh++fjn oYEKK7ZS9eDpbrZwhZ7di+JHt14gQ3nwgOISiak7j0e3pzUYHrkK/V31OMWly8se aIXUJY6xZDe2SbkuELG5rkuXytnhFZJK2u4zPAGhAgYfdSq095Vz/jBVv0mej6fA lsJGdeyiN0HAha+GQw5ZubxHyMzPY1q+vR4nPm9qXze3cggVhY0= =ejfd -----END PGP SIGNATURE----- Wed Aug 6 06:08:25 UTC 2025 I: Checking whether the package is not for us Wed Aug 6 06:08:25 UTC 2025 I: Starting 1st build on remote node ionos1-amd64.debian.net. Wed Aug 6 06:08:25 UTC 2025 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Wed Aug 6 06:08:25 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Wed Aug 6 06:08:25 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-Q5TIdF' ==================================================================================== Wed Aug 6 06:08:26 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos1-amd64, called using "1 molmodel trixie /srv/reproducible-results/rbuild-debian/r-b-build.dpippO63 3.1.0-4.1" as arguments. Wed Aug 6 06:08:26 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-UcENDdsA" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Aug 6 06:08:26 UTC 2025 I: Downloading source for trixie/molmodel=3.1.0-4.1 Reading package lists... NOTICE: 'molmodel' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/molmodel.git Please use: git clone https://salsa.debian.org/debichem-team/molmodel.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 11.1 MB of source archives. Get:1 http://deb.debian.org/debian trixie/main molmodel 3.1.0-4.1 (dsc) [2238 B] Get:2 http://deb.debian.org/debian trixie/main molmodel 3.1.0-4.1 (tar) [11.1 MB] Get:3 http://deb.debian.org/debian trixie/main molmodel 3.1.0-4.1 (diff) [4668 B] Fetched 11.1 MB in 0s (100 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'molmodel' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/molmodel.git Please use: git clone https://salsa.debian.org/debichem-team/molmodel.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 11.1 MB of source archives. Get:1 http://deb.debian.org/debian trixie/main molmodel 3.1.0-4.1 (dsc) [2238 B] Get:2 http://deb.debian.org/debian trixie/main molmodel 3.1.0-4.1 (tar) [11.1 MB] Get:3 http://deb.debian.org/debian trixie/main molmodel 3.1.0-4.1 (diff) [4668 B] Fetched 11.1 MB in 0s (100 MB/s) Download complete and in download only mode ============================================================================= Building molmodel in trixie on amd64 on ionos1-amd64 now. Date: Wed Aug 6 06:08:26 UTC 2025 Date UTC: Wed Aug 6 06:08:26 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Tue Aug 5 18:08:26 -12 2025 I: pbuilder-time-stamp: 1754460506 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [molmodel_3.1.0-4.1.dsc] I: copying [./molmodel_3.1.0.orig.tar.gz] I: copying [./molmodel_3.1.0-4.1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./molmodel_3.1.0-4.1.dsc: no acceptable signature found dpkg-source: info: extracting molmodel in molmodel-3.1.0 dpkg-source: info: unpacking molmodel_3.1.0.orig.tar.gz dpkg-source: info: unpacking molmodel_3.1.0-4.1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying drop-CMAKE_CXX_STANDARD.patch dpkg-source: info: applying plugin_dir.patch dpkg-source: info: applying f8492b9346dd8a2c32e3aa815294a3248b051d1f.patch dpkg-source: info: applying 968a0af8bc1a224337a3d1e1bd2fec3aec9e3fa1.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3688181/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=40 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='3ce44856bbe44d5b953de42cfcc03334' 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='3688181' PS1='# ' PS2='> ' 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.dpippO63/pbuilderrc_2roa --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.dpippO63/b1 --logfile b1/build.log molmodel_3.1.0-4.1.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3688181/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: dpkg-dev (>= 1.22.5), cmake, debhelper-compat (= 13), gemmi-dev, libmmdb2-dev, libopenmm-dev, libopenblas-pthread-dev, libsimbody-dev, tao-pegtl-dev, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19851 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on gemmi-dev; however: Package gemmi-dev is not installed. pbuilder-satisfydepends-dummy depends on libmmdb2-dev; however: Package libmmdb2-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenmm-dev; however: Package libopenmm-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenblas-pthread-dev; however: Package libopenblas-pthread-dev is not installed. pbuilder-satisfydepends-dummy depends on libsimbody-dev; however: Package libsimbody-dev is not installed. pbuilder-satisfydepends-dummy depends on tao-pegtl-dev; however: Package tao-pegtl-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} freeglut3-dev{a} gemmi-dev{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libbrotli1{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm2{a} libedit2{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgbm1{a} libgfortran5{a} libgl-dev{a} libgl1{a} libgl1-mesa-dri{a} libglu1-mesa{a} libglu1-mesa-dev{a} libglut-dev{a} libglut3.12{a} libglvnd0{a} libglx-dev{a} libglx-mesa0{a} libglx0{a} libgnutls30t64{a} libgssapi-krb5-2{a} libice-dev{a} libice6{a} libidn2-0{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap2{a} libllvm19{a} libmagic-mgc{a} libmagic1t64{a} libmmdb2-0{a} libmmdb2-dev{a} libnghttp2-14{a} libnghttp3-9{a} libopenblas-pthread-dev{a} libopenblas0-pthread{a} libopengl-dev{a} libopengl0{a} libopenmm-dev{a} libopenmm8.1{a} libp11-kit0{a} libpciaccess0{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libsimbody-dev{a} libsimbody3.7{a} libsm-dev{a} libsm6{a} libssh2-1t64{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libvulkan1{a} libwayland-server0{a} libx11-6{a} libx11-data{a} libx11-dev{a} libx11-xcb1{a} libxau-dev{a} libxau6{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxfixes-dev{a} libxfixes3{a} libxi-dev{a} libxi6{a} libxml2{a} libxmu-dev{a} libxmu-headers{a} libxmu6{a} libxshmfence1{a} libxt-dev{a} libxt6t64{a} libxxf86vm1{a} libz3-4{a} m4{a} man-db{a} mesa-libgallium{a} po-debconf{a} procps{a} sensible-utils{a} tao-pegtl-dev{a} uuid-dev{a} x11-common{a} x11proto-dev{a} xorg-sgml-doctools{a} xtrans-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx mesa-vulkan-drivers psmisc publicsuffix wget 0 packages upgraded, 140 newly installed, 0 to remove and 0 not upgraded. Need to get 114 MB of archives. After unpacking 530 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-4 [862 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 cmake-data all 3.31.6-2 [2268 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-2.1 [698 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libarchive13t64 amd64 3.7.4-4 [349 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 27 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-3 [1465 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.14.1-2 [391 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.31.6-2 [12.0 MB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 54 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.2 [919 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.124-2 [8288 B] Get: 67 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.124-2 [39.0 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libx11-xcb1 amd64 2:1.8.12-1 [247 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b4 [19.3 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.124-2 [22.6 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libdrm-intel1 amd64 2.4.124-2 [64.1 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libllvm19 amd64 1:19.1.7-3+b1 [26.0 MB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libsensors-config all 1:3.6.2-2 [16.2 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libsensors5 amd64 1:3.6.2-2 [37.5 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libxshmfence1 amd64 1.3.3-1 [10.9 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 mesa-libgallium amd64 25.0.7-2 [9629 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libwayland-server0 amd64 1.23.1-3 [34.4 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libgbm1 amd64 25.0.7-2 [44.4 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libvulkan1 amd64 1.4.309.0-1 [130 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libgl1-mesa-dri amd64 25.0.7-2 [46.1 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libglx-mesa0 amd64 25.0.7-2 [143 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libglut3.12 amd64 3.4.0-4 [139 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libopengl0 amd64 1.7.0-1+b2 [30.9 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libglu1-mesa amd64 9.0.2-1.1+b3 [184 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 x11proto-dev all 2024.1-1 [603 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libxau-dev amd64 1:1.0.11-1 [23.6 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libxdmcp-dev amd64 1:1.1.5-1 [44.3 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libxcb1-dev amd64 1.17.0-2+b1 [181 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libx11-dev amd64 2:1.8.12-1 [894 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libglx-dev amd64 1.7.0-1+b2 [15.8 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libgl-dev amd64 1.7.0-1+b2 [101 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libopengl-dev amd64 1.7.0-1+b2 [5388 B] Get: 109 http://deb.debian.org/debian trixie/main amd64 libglu1-mesa-dev amd64 9.0.2-1.1+b3 [223 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libxext-dev amd64 2:1.3.4-1+b3 [104 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+24 [217 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.6-1 [37.3 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b2 [188 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libice-dev amd64 2:1.1.1-1 [73.8 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 uuid-dev amd64 2.41-5 [48.8 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libsm-dev amd64 2:1.2.6-1 [39.7 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libxt-dev amd64 1:1.2.1-1.2+b2 [407 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libglut-dev amd64 3.4.0-4 [163 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 freeglut3-dev amd64 3.4.0-4 [53.4 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 tao-pegtl-dev all 3.2.7-1 [69.4 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 gemmi-dev amd64 0.6.5+ds-3 [1137 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libopenblas0-pthread amd64 0.3.29+ds-3 [6740 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-4 [2447 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libopenblas-pthread-dev amd64 0.3.29+ds-3 [5063 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 liblapack-dev amd64 3.12.1-4 [4991 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libmmdb2-0 amd64 2.0.22-1+b2 [342 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libmmdb2-dev amd64 2.0.22-1+b2 [92.9 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libopenmm8.1 amd64 8.1.2+dfsg-11 [1059 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libopenmm-dev amd64 8.1.2+dfsg-11 [346 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libxfixes3 amd64 1:6.0.0-2+b4 [20.2 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libxfixes-dev amd64 1:6.0.0-2+b4 [22.4 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libxi-dev amd64 2:1.8.2-1 [241 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libxmu6 amd64 2:1.1.3-3+b4 [59.0 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libxmu-headers all 2:1.1.3-3 [68.5 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libxmu-dev amd64 2:1.1.3-3+b4 [65.3 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libsimbody3.7 amd64 3.7+dfsg-4 [3363 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libsimbody-dev amd64 3.7+dfsg-4 [2726 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 114 MB in 2s (50.0 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 ... 19851 files and directories currently installed.) Preparing to unpack .../000-libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-9_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-9) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.4-9_amd64.deb ... Unpacking procps (2:4.0.4-9) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../005-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.23.1-2_amd64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../008-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../009-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../010-bsdextrautils_2.41-5_amd64.deb ... Unpacking bsdextrautils (2.41-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../011-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../012-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../013-m4_1.4.19-8_amd64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../014-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../015-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../016-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../017-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package cmake-data. Preparing to unpack .../018-cmake-data_3.31.6-2_all.deb ... Unpacking cmake-data (3.31.6-2) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../019-libxml2_2.12.7+dfsg+really2.9.14-2.1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Selecting previously unselected package libarchive13t64:amd64. Preparing to unpack .../020-libarchive13t64_3.7.4-4_amd64.deb ... Unpacking libarchive13t64:amd64 (3.7.4-4) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../021-libbrotli1_1.1.0-2+b7_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b7) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../022-libkrb5support0_1.21.3-5_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-5) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../023-libcom-err2_1.47.2-3+b3_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2-3+b3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../024-libk5crypto3_1.21.3-5_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-5) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../025-libkeyutils1_1.6.3-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../026-libkrb5-3_1.21.3-5_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../027-libgssapi-krb5-2_1.21.3-5_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-5) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../028-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libidn2-0:amd64. Preparing to unpack .../029-libidn2-0_2.3.8-2_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.8-2) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../030-libsasl2-modules-db_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../031-libsasl2-2_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libldap2:amd64. Preparing to unpack .../032-libldap2_2.6.10+dfsg-1_amd64.deb ... Unpacking libldap2:amd64 (2.6.10+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../033-libnghttp2-14_1.64.0-1.1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.64.0-1.1) ... Selecting previously unselected package libnghttp3-9:amd64. Preparing to unpack .../034-libnghttp3-9_1.8.0-1_amd64.deb ... Unpacking libnghttp3-9:amd64 (1.8.0-1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../035-libpsl5t64_0.21.2-1.1+b1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1+b1) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../036-libffi8_3.4.8-2_amd64.deb ... Unpacking libffi8:amd64 (3.4.8-2) ... Selecting previously unselected package libp11-kit0:amd64. Preparing to unpack .../037-libp11-kit0_0.25.5-3_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6:amd64. Preparing to unpack .../038-libtasn1-6_4.20.0-2_amd64.deb ... 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Setting up autotools-dev (20240727.1) ... Setting up libz3-4:amd64 (4.13.3-1) ... Setting up libx11-data (2:1.8.12-1) ... Setting up libxcb-sync1:amd64 (1.17.0-2+b1) ... Setting up libjsoncpp26:amd64 (1.9.6-3) ... Setting up uuid-dev:amd64 (2.41-5) ... Setting up libproc2-0:amd64 (2:4.0.4-9) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up libmmdb2-dev (2.0.22-1+b2) ... Setting up autopoint (0.23.1-2) ... Setting up libsensors5:amd64 (1:3.6.2-2) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Setting up libgfortran5:amd64 (14.2.0-19) ... Setting up libvulkan1:amd64 (1.4.309.0-1) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:amd64 (1.8.0-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.4.8-2) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libxshmfence1:amd64 (1.3.3-1) ... Setting up libxcb-randr0:amd64 (1.17.0-2+b1) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-9) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up libx11-6:amd64 (2:1.8.12-1) ... Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up cmake-data (3.31.6-2) ... Setting up librhash1:amd64 (1.4.5-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libglu1-mesa:amd64 (9.0.2-1.1+b3) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libopengl-dev:amd64 (1.7.0-1+b2) ... Setting up libopenmm8.1 (8.1.2+dfsg-11) ... Setting up libdrm-common (2.4.124-2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Setting up libldap2:amd64 (2.6.10+dfsg-1) ... Setting up tao-pegtl-dev (3.2.7-1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up x11proto-dev (2024.1-1) ... Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up libxcb-dri3-0:amd64 (1.17.0-2+b1) ... Setting up libllvm19:amd64 (1:19.1.7-3+b1) ... Setting up libwayland-server0:amd64 (1.23.1-3) ... Setting up libx11-xcb1:amd64 (2:1.8.12-1) ... Setting up libice6:amd64 (2:1.1.1-1) ... Setting up gettext (0.23.1-2) ... Setting up libopenblas0-pthread:amd64 (0.3.29+ds-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-x86_64-linux-gnu) in auto mode Setting up libxau-dev:amd64 (1:1.0.11-1) ... Setting up libice-dev:amd64 (2:1.1.1-1) ... Setting up libtool (2.5.4-4) ... Setting up gemmi-dev (0.6.5+ds-3) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up libidn2-0:amd64 (2.3.8-2) ... Setting up libopenmm-dev (8.1.2+dfsg-11) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libxdmcp-dev:amd64 (1:1.1.5-1) ... Setting up libxfixes3:amd64 (1:6.0.0-2+b4) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up libdrm2:amd64 (2.4.124-2) ... Setting up groff-base (1.23.0-9) ... Setting up libsm6:amd64 (2:1.2.6-1) ... Setting up libarchive13t64:amd64 (3.7.4-4) ... Setting up libdrm-amdgpu1:amd64 (2.4.124-2) ... Setting up libgnutls30t64:amd64 (3.8.9-3) ... Setting up libopenblas-pthread-dev:amd64 (0.3.29+ds-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/x86_64-linux-gnu/libopenblas.so (libopenblas.so-x86_64-linux-gnu) in auto mode Setting up liblapack3:amd64 (3.12.1-4) ... Setting up libxcb1-dev:amd64 (1.17.0-2+b1) ... Setting up libxi6:amd64 (2:1.8.2-1) ... Setting up libsm-dev:amd64 (2:1.2.6-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libdrm-intel1:amd64 (2.4.124-2) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libx11-dev:amd64 (2:1.8.12-1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxfixes-dev:amd64 (1:6.0.0-2+b4) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2+b2) ... Setting up liblapack-dev:amd64 (3.12.1-4) ... Setting up libxext-dev:amd64 (2:1.3.4-1+b3) ... Setting up libxi-dev:amd64 (2:1.8.2-1) ... Setting up mesa-libgallium:amd64 (25.0.7-2) ... Setting up libxmu-headers (2:1.1.3-3) ... Setting up libxmu6:amd64 (2:1.1.3-3+b4) ... Setting up libcurl4t64:amd64 (8.14.1-2) ... Setting up libgbm1:amd64 (25.0.7-2) ... Setting up libgl1-mesa-dri:amd64 (25.0.7-2) ... Setting up debhelper (13.24.2) ... Setting up libxt-dev:amd64 (1:1.2.1-1.2+b2) ... Setting up cmake (3.31.6-2) ... Setting up libglx-mesa0:amd64 (25.0.7-2) ... Setting up libglx0:amd64 (1.7.0-1+b2) ... Setting up libxmu-dev:amd64 (2:1.1.3-3+b4) ... Setting up libgl1:amd64 (1.7.0-1+b2) ... Setting up libglut3.12:amd64 (3.4.0-4) ... Setting up libsimbody3.7:amd64 (3.7+dfsg-4) ... Setting up libglx-dev:amd64 (1.7.0-1+b2) ... Setting up libgl-dev:amd64 (1.7.0-1+b2) ... Setting up libglu1-mesa-dev:amd64 (9.0.2-1.1+b3) ... Setting up libglut-dev:amd64 (3.4.0-4) ... Setting up freeglut3-dev:amd64 (3.4.0-4) ... Setting up libsimbody-dev:amd64 (3.7+dfsg-4) ... Processing triggers for libc-bin (2.41-11) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... 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 dpkg-buildpackage: info: source package molmodel dpkg-buildpackage: info: source version 3.1.0-4.1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Benjamin Drung dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/molmodel-3.1.0' dh_auto_configure -- -DBUILD_EXAMPLES=OFF -DBUILD_TESTING=OFF cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DBUILD_EXAMPLES=OFF -DBUILD_TESTING=OFF .. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found OpenMM: /usr/include -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") CMake Warning (dev) at CMakeLists.txt:277 (INCLUDE): Policy CMP0145 is not set: The Dart and FindDart modules are removed. Run "cmake --help-policy CMP0145" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at /usr/share/cmake-3.31/Modules/Dart.cmake:47 (message): Policy CMP0145 is not set: The Dart and FindDart modules are removed. Run "cmake --help-policy CMP0145" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:277 (INCLUDE) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Configuring done (0.7s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED -- 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 -j40 "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 make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' make -f CMakeFiles/SimTKmolmodel.dir/build.make CMakeFiles/SimTKmolmodel.dir/depend make[3]: Entering directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/molmodel-3.1.0 /build/reproducible-path/molmodel-3.1.0 /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu/CMakeFiles/SimTKmolmodel.dir/DependInfo.cmake "--color=" 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/Compound.cpp.o [ 6%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/BondGeometry.cpp.o [ 9%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/AtomSubsystem.cpp.o [ 18%] 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/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 [ 21%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/PDBReader.cpp.o [ 21%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/CompoundSystem.cpp.o [ 25%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/MolecularMechanicsSystem.cpp.o [ 25%] 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/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 [ 31%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/DuMMForceFieldSubsystemRep.cpp.o [ 31%] 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 -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 [ 37%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/PeriodicVmdReporter.cpp.o [ 37%] 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/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 /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 /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" 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CXX object CMakeFiles/SimTKmolmodel.dir/src/Biotype.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/PeriodicVmdReporter.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/PeriodicVmdReporter.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/PeriodicVmdReporter.cpp.o -c 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-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 /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 [ 90%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMUtilities.cpp.o [ 90%] 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 -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 /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 /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/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 /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 /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/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 /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 /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/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 > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/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/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 > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/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/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 > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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/cpuObcInterface.h:34, from /build/reproducible-path/molmodel-3.1.0/src/gbsa/cpuObcInterface.cpp:25: /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: /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 > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/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/CpuObc.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 > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/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/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] 163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/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/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 > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/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: /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 > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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: /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/DuMMForceFieldSubsystem.cpp:43: /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 > { | ^~~~~~~~~~~~~~~ /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++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/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 struct std::iterator' is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath: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 | ^~~~~~~~ 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 struct std::iterator' is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath: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 struct std::iterator' is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath: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 | ^~~~~~~~ [ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libSimTKsimbody.so.3.7 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libSimTKmath.so.3.7 /usr/lib/x86_64-linux-gnu/libSimTKcommon.so.3.7 /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lpthread -lrt -ldl -lm /usr/bin/cmake -E cmake_symlink_library libSimTKmolmodel.so.3.1 libSimTKmolmodel.so.3.1 libSimTKmolmodel.so make[3]: Leaving directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' [ 93%] Built target SimTKmolmodel make -f OpenMMPlugin/CMakeFiles/OpenMMPlugin_shared.dir/build.make OpenMMPlugin/CMakeFiles/OpenMMPlugin_shared.dir/depend make[3]: Entering directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/molmodel-3.1.0 /build/reproducible-path/molmodel-3.1.0/OpenMMPlugin /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu/OpenMMPlugin /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu/OpenMMPlugin/CMakeFiles/OpenMMPlugin_shared.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' make -f OpenMMPlugin/CMakeFiles/OpenMMPlugin_shared.dir/build.make OpenMMPlugin/CMakeFiles/OpenMMPlugin_shared.dir/build make[3]: Entering directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' [ 96%] Building CXX object OpenMMPlugin/CMakeFiles/OpenMMPlugin_shared.dir/OpenMMPlugin.cpp.o cd /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu/OpenMMPlugin && /usr/bin/c++ -DOpenMMPlugin_shared_EXPORTS -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -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=\"\" -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 OpenMMPlugin/CMakeFiles/OpenMMPlugin_shared.dir/OpenMMPlugin.cpp.o -MF CMakeFiles/OpenMMPlugin_shared.dir/OpenMMPlugin.cpp.o.d -o CMakeFiles/OpenMMPlugin_shared.dir/OpenMMPlugin.cpp.o -c /build/reproducible-path/molmodel-3.1.0/OpenMMPlugin/OpenMMPlugin.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/OpenMMPlugin/OpenMMPlugin.cpp:43: /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 > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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/OpenMMPlugin/OpenMMPlugin.cpp:41: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [100%] Linking CXX shared library libOpenMMPlugin.so cd /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu/OpenMMPlugin && /usr/bin/cmake -E cmake_link_script CMakeFiles/OpenMMPlugin_shared.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 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'/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-x86_64-linux-gnu && make -j40 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 make[2]: Entering directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1 -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/doc/api/Molmodel/html -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/doc/MolmodelAPI.html -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/Molmodel.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/SimTKmolmodel.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/AtomSubsystem.h -- Installing: 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/build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Exceptions.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/GrinPointer.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Ions.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Ligands.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Linkage.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/MassCenterMotionRemover.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/MolecularMechanicsSystem.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/NA.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/NoseHooverThermostat.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/PDBReader.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Pdb.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/PeriodicPdbWriter.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/PeriodicVmdReporter.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Protein.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/RNA.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/RiboseMobilizer.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Superpose.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/VanDerWaalsForce.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/VanderWallSphere.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/VelocityRescalingThermostat.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/VmdConnection.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/VoxelHash.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Water.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/bondGeometry.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/common.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/units.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/doc/MolmodelUsersGuide.pdf -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/molmodel/MolmodelConfig.cmake -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/molmodel/MolmodelConfigVersion.cmake -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/molmodel/MolmodelTargets.cmake -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/molmodel/MolmodelTargets-none.cmake -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/molmodel.pc -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/molmodel/plugins/libOpenMMPlugin.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/molmodel/plugins/libOpenMMPlugin.so" to "" make[1]: Leaving directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' dh_install dh_installdocs dh_installchangelogs dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 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 _ZN5gemmi16assign_subchainsERNS_9StructureEbb 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 _ZN5gemmi8GzStream4getcEv 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 _ZN5gemmi12MaybeGzipped24get_uncompressing_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 _ZN5gemmi15change_ccd_codeERNS_9StructureERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_ 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 _ZN5gemmi8GzStream4getsEPci 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 _ZN5gemmi19remove_entity_typesERNS_9StructureE 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 dh_builddeb 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' 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) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration 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/3688181 and its subdirectories I: Current time: Tue Aug 5 18:11:05 -12 2025 I: pbuilder-time-stamp: 1754460665 Wed Aug 6 06:11:05 UTC 2025 I: Signing ./b1/molmodel_3.1.0-4.1_amd64.buildinfo as molmodel_3.1.0-4.1_amd64.buildinfo.asc Wed Aug 6 06:11:05 UTC 2025 I: Signed ./b1/molmodel_3.1.0-4.1_amd64.buildinfo as ./b1/molmodel_3.1.0-4.1_amd64.buildinfo.asc Wed Aug 6 06:11:05 UTC 2025 - build #1 for molmodel/trixie/amd64 on ionos1-amd64 done. Starting cleanup. All cleanup done. Wed Aug 6 06:11:05 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-UcENDdsA, removing. /srv/reproducible-results/rbuild-debian/r-b-build.dpippO63: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Aug 6 06:11 b1 drwxr-xr-x 2 jenkins jenkins 4096 Aug 6 06:08 b2 -rw-r--r-- 1 jenkins jenkins 2238 Feb 28 2024 molmodel_3.1.0-4.1.dsc -rw------- 1 jenkins jenkins 3351 Aug 6 06:08 rbuildlog.1tolR3I /srv/reproducible-results/rbuild-debian/r-b-build.dpippO63/b1: total 16596 -rw-r--r-- 1 jenkins jenkins 131118 Aug 6 06:11 build.log -rw-r--r-- 1 jenkins jenkins 1863392 Aug 6 06:11 libsimtkmolmodel-dev_3.1.0-4.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 578316 Aug 6 06:11 libsimtkmolmodel-plugins-dbgsym_3.1.0-4.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 19316 Aug 6 06:11 libsimtkmolmodel-plugins_3.1.0-4.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 13674860 Aug 6 06:11 libsimtkmolmodel3.1t64-dbgsym_3.1.0-4.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 671152 Aug 6 06:11 libsimtkmolmodel3.1t64_3.1.0-4.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 4668 Aug 6 06:11 molmodel_3.1.0-4.1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2238 Aug 6 06:11 molmodel_3.1.0-4.1.dsc -rw-r--r-- 1 jenkins jenkins 9379 Aug 6 06:11 molmodel_3.1.0-4.1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 10261 Aug 6 06:11 molmodel_3.1.0-4.1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2743 Aug 6 06:11 molmodel_3.1.0-4.1_amd64.changes -rw-r--r-- 1 jenkins jenkins 1260 Aug 6 06:11 molmodel_3.1.0-4.1_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.dpippO63/b2: total 0 Wed Aug 6 06:11:06 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Aug 5 18:08:26 -12 2025 I: pbuilder-time-stamp: 1754460506 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [molmodel_3.1.0-4.1.dsc] I: copying [./molmodel_3.1.0.orig.tar.gz] I: copying [./molmodel_3.1.0-4.1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./molmodel_3.1.0-4.1.dsc: no acceptable signature found dpkg-source: info: extracting molmodel in molmodel-3.1.0 dpkg-source: info: unpacking molmodel_3.1.0.orig.tar.gz dpkg-source: info: unpacking molmodel_3.1.0-4.1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying drop-CMAKE_CXX_STANDARD.patch dpkg-source: info: applying plugin_dir.patch dpkg-source: info: applying f8492b9346dd8a2c32e3aa815294a3248b051d1f.patch dpkg-source: info: applying 968a0af8bc1a224337a3d1e1bd2fec3aec9e3fa1.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3688181/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=40 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='3ce44856bbe44d5b953de42cfcc03334' 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='3688181' PS1='# ' PS2='> ' 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.dpippO63/pbuilderrc_2roa --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.dpippO63/b1 --logfile b1/build.log molmodel_3.1.0-4.1.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3688181/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: dpkg-dev (>= 1.22.5), cmake, debhelper-compat (= 13), gemmi-dev, libmmdb2-dev, libopenmm-dev, libopenblas-pthread-dev, libsimbody-dev, tao-pegtl-dev, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19851 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on gemmi-dev; however: Package gemmi-dev is not installed. pbuilder-satisfydepends-dummy depends on libmmdb2-dev; however: Package libmmdb2-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenmm-dev; however: Package libopenmm-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenblas-pthread-dev; however: Package libopenblas-pthread-dev is not installed. pbuilder-satisfydepends-dummy depends on libsimbody-dev; however: Package libsimbody-dev is not installed. pbuilder-satisfydepends-dummy depends on tao-pegtl-dev; however: Package tao-pegtl-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} freeglut3-dev{a} gemmi-dev{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libbrotli1{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm2{a} libedit2{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgbm1{a} libgfortran5{a} libgl-dev{a} libgl1{a} libgl1-mesa-dri{a} libglu1-mesa{a} libglu1-mesa-dev{a} libglut-dev{a} libglut3.12{a} libglvnd0{a} libglx-dev{a} libglx-mesa0{a} libglx0{a} libgnutls30t64{a} libgssapi-krb5-2{a} libice-dev{a} libice6{a} libidn2-0{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap2{a} libllvm19{a} libmagic-mgc{a} libmagic1t64{a} libmmdb2-0{a} libmmdb2-dev{a} libnghttp2-14{a} libnghttp3-9{a} libopenblas-pthread-dev{a} libopenblas0-pthread{a} libopengl-dev{a} libopengl0{a} libopenmm-dev{a} libopenmm8.1{a} libp11-kit0{a} libpciaccess0{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libsimbody-dev{a} libsimbody3.7{a} libsm-dev{a} libsm6{a} libssh2-1t64{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libvulkan1{a} libwayland-server0{a} libx11-6{a} libx11-data{a} libx11-dev{a} libx11-xcb1{a} libxau-dev{a} libxau6{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxfixes-dev{a} libxfixes3{a} libxi-dev{a} libxi6{a} libxml2{a} libxmu-dev{a} libxmu-headers{a} libxmu6{a} libxshmfence1{a} libxt-dev{a} libxt6t64{a} libxxf86vm1{a} libz3-4{a} m4{a} man-db{a} mesa-libgallium{a} po-debconf{a} procps{a} sensible-utils{a} tao-pegtl-dev{a} uuid-dev{a} x11-common{a} x11proto-dev{a} xorg-sgml-doctools{a} xtrans-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx mesa-vulkan-drivers psmisc publicsuffix wget 0 packages upgraded, 140 newly installed, 0 to remove and 0 not upgraded. Need to get 114 MB of archives. After unpacking 530 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-4 [862 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 cmake-data all 3.31.6-2 [2268 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-2.1 [698 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libarchive13t64 amd64 3.7.4-4 [349 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 27 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-3 [1465 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.14.1-2 [391 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.31.6-2 [12.0 MB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 54 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.2 [919 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.124-2 [8288 B] Get: 67 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.124-2 [39.0 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libx11-xcb1 amd64 2:1.8.12-1 [247 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b4 [19.3 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.124-2 [22.6 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libdrm-intel1 amd64 2.4.124-2 [64.1 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libllvm19 amd64 1:19.1.7-3+b1 [26.0 MB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libsensors-config all 1:3.6.2-2 [16.2 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libsensors5 amd64 1:3.6.2-2 [37.5 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libxshmfence1 amd64 1.3.3-1 [10.9 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 mesa-libgallium amd64 25.0.7-2 [9629 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libwayland-server0 amd64 1.23.1-3 [34.4 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libgbm1 amd64 25.0.7-2 [44.4 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libvulkan1 amd64 1.4.309.0-1 [130 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libgl1-mesa-dri amd64 25.0.7-2 [46.1 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libglx-mesa0 amd64 25.0.7-2 [143 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libglut3.12 amd64 3.4.0-4 [139 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libopengl0 amd64 1.7.0-1+b2 [30.9 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libglu1-mesa amd64 9.0.2-1.1+b3 [184 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 x11proto-dev all 2024.1-1 [603 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libxau-dev amd64 1:1.0.11-1 [23.6 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libxdmcp-dev amd64 1:1.1.5-1 [44.3 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libxcb1-dev amd64 1.17.0-2+b1 [181 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libx11-dev amd64 2:1.8.12-1 [894 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libglx-dev amd64 1.7.0-1+b2 [15.8 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libgl-dev amd64 1.7.0-1+b2 [101 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libopengl-dev amd64 1.7.0-1+b2 [5388 B] Get: 109 http://deb.debian.org/debian trixie/main amd64 libglu1-mesa-dev amd64 9.0.2-1.1+b3 [223 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libxext-dev amd64 2:1.3.4-1+b3 [104 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+24 [217 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.6-1 [37.3 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b2 [188 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libice-dev amd64 2:1.1.1-1 [73.8 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 uuid-dev amd64 2.41-5 [48.8 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libsm-dev amd64 2:1.2.6-1 [39.7 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libxt-dev amd64 1:1.2.1-1.2+b2 [407 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libglut-dev amd64 3.4.0-4 [163 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 freeglut3-dev amd64 3.4.0-4 [53.4 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 tao-pegtl-dev all 3.2.7-1 [69.4 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 gemmi-dev amd64 0.6.5+ds-3 [1137 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libopenblas0-pthread amd64 0.3.29+ds-3 [6740 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-4 [2447 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libopenblas-pthread-dev amd64 0.3.29+ds-3 [5063 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 liblapack-dev amd64 3.12.1-4 [4991 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libmmdb2-0 amd64 2.0.22-1+b2 [342 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libmmdb2-dev amd64 2.0.22-1+b2 [92.9 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libopenmm8.1 amd64 8.1.2+dfsg-11 [1059 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libopenmm-dev amd64 8.1.2+dfsg-11 [346 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libxfixes3 amd64 1:6.0.0-2+b4 [20.2 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libxfixes-dev amd64 1:6.0.0-2+b4 [22.4 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libxi-dev amd64 2:1.8.2-1 [241 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libxmu6 amd64 2:1.1.3-3+b4 [59.0 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libxmu-headers all 2:1.1.3-3 [68.5 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libxmu-dev amd64 2:1.1.3-3+b4 [65.3 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libsimbody3.7 amd64 3.7+dfsg-4 [3363 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libsimbody-dev amd64 3.7+dfsg-4 [2726 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 114 MB in 2s (50.0 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 ... 19851 files and directories currently installed.) Preparing to unpack .../000-libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-9_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-9) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.4-9_amd64.deb ... Unpacking procps (2:4.0.4-9) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../005-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.23.1-2_amd64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../008-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../009-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../010-bsdextrautils_2.41-5_amd64.deb ... Unpacking bsdextrautils (2.41-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../011-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../012-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../013-m4_1.4.19-8_amd64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../014-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../015-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../016-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../017-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package cmake-data. Preparing to unpack .../018-cmake-data_3.31.6-2_all.deb ... Unpacking cmake-data (3.31.6-2) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../019-libxml2_2.12.7+dfsg+really2.9.14-2.1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Selecting previously unselected package libarchive13t64:amd64. Preparing to unpack .../020-libarchive13t64_3.7.4-4_amd64.deb ... Unpacking libarchive13t64:amd64 (3.7.4-4) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../021-libbrotli1_1.1.0-2+b7_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b7) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../022-libkrb5support0_1.21.3-5_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-5) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../023-libcom-err2_1.47.2-3+b3_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2-3+b3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../024-libk5crypto3_1.21.3-5_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-5) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../025-libkeyutils1_1.6.3-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../026-libkrb5-3_1.21.3-5_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../027-libgssapi-krb5-2_1.21.3-5_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-5) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../028-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libidn2-0:amd64. Preparing to unpack .../029-libidn2-0_2.3.8-2_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.8-2) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../030-libsasl2-modules-db_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../031-libsasl2-2_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libldap2:amd64. Preparing to unpack .../032-libldap2_2.6.10+dfsg-1_amd64.deb ... 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Setting up autotools-dev (20240727.1) ... Setting up libz3-4:amd64 (4.13.3-1) ... Setting up libx11-data (2:1.8.12-1) ... Setting up libxcb-sync1:amd64 (1.17.0-2+b1) ... Setting up libjsoncpp26:amd64 (1.9.6-3) ... Setting up uuid-dev:amd64 (2.41-5) ... Setting up libproc2-0:amd64 (2:4.0.4-9) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up libmmdb2-dev (2.0.22-1+b2) ... Setting up autopoint (0.23.1-2) ... Setting up libsensors5:amd64 (1:3.6.2-2) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Setting up libgfortran5:amd64 (14.2.0-19) ... Setting up libvulkan1:amd64 (1.4.309.0-1) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:amd64 (1.8.0-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.4.8-2) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libxshmfence1:amd64 (1.3.3-1) ... Setting up libxcb-randr0:amd64 (1.17.0-2+b1) ... 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Setting up libllvm19:amd64 (1:19.1.7-3+b1) ... Setting up libwayland-server0:amd64 (1.23.1-3) ... Setting up libx11-xcb1:amd64 (2:1.8.12-1) ... Setting up libice6:amd64 (2:1.1.1-1) ... Setting up gettext (0.23.1-2) ... Setting up libopenblas0-pthread:amd64 (0.3.29+ds-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-x86_64-linux-gnu) in auto mode Setting up libxau-dev:amd64 (1:1.0.11-1) ... Setting up libice-dev:amd64 (2:1.1.1-1) ... Setting up libtool (2.5.4-4) ... Setting up gemmi-dev (0.6.5+ds-3) ... 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Setting up libopenblas-pthread-dev:amd64 (0.3.29+ds-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/x86_64-linux-gnu/libopenblas.so (libopenblas.so-x86_64-linux-gnu) in auto mode Setting up liblapack3:amd64 (3.12.1-4) ... Setting up libxcb1-dev:amd64 (1.17.0-2+b1) ... Setting up libxi6:amd64 (2:1.8.2-1) ... Setting up libsm-dev:amd64 (2:1.2.6-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libdrm-intel1:amd64 (2.4.124-2) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libx11-dev:amd64 (2:1.8.12-1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxfixes-dev:amd64 (1:6.0.0-2+b4) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2+b2) ... Setting up liblapack-dev:amd64 (3.12.1-4) ... Setting up libxext-dev:amd64 (2:1.3.4-1+b3) ... Setting up libxi-dev:amd64 (2:1.8.2-1) ... Setting up mesa-libgallium:amd64 (25.0.7-2) ... Setting up libxmu-headers (2:1.1.3-3) ... Setting up libxmu6:amd64 (2:1.1.3-3+b4) ... Setting up libcurl4t64:amd64 (8.14.1-2) ... Setting up libgbm1:amd64 (25.0.7-2) ... Setting up libgl1-mesa-dri:amd64 (25.0.7-2) ... Setting up debhelper (13.24.2) ... Setting up libxt-dev:amd64 (1:1.2.1-1.2+b2) ... Setting up cmake (3.31.6-2) ... Setting up libglx-mesa0:amd64 (25.0.7-2) ... Setting up libglx0:amd64 (1.7.0-1+b2) ... Setting up libxmu-dev:amd64 (2:1.1.3-3+b4) ... Setting up libgl1:amd64 (1.7.0-1+b2) ... Setting up libglut3.12:amd64 (3.4.0-4) ... Setting up libsimbody3.7:amd64 (3.7+dfsg-4) ... Setting up libglx-dev:amd64 (1.7.0-1+b2) ... Setting up libgl-dev:amd64 (1.7.0-1+b2) ... Setting up libglu1-mesa-dev:amd64 (9.0.2-1.1+b3) ... Setting up libglut-dev:amd64 (3.4.0-4) ... Setting up freeglut3-dev:amd64 (3.4.0-4) ... Setting up libsimbody-dev:amd64 (3.7+dfsg-4) ... Processing triggers for libc-bin (2.41-11) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... 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 dpkg-buildpackage: info: source package molmodel dpkg-buildpackage: info: source version 3.1.0-4.1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Benjamin Drung dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/molmodel-3.1.0' dh_auto_configure -- -DBUILD_EXAMPLES=OFF -DBUILD_TESTING=OFF cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DBUILD_EXAMPLES=OFF -DBUILD_TESTING=OFF .. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found OpenMM: /usr/include -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") CMake Warning (dev) at CMakeLists.txt:277 (INCLUDE): Policy CMP0145 is not set: The Dart and FindDart modules are removed. Run "cmake --help-policy CMP0145" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at /usr/share/cmake-3.31/Modules/Dart.cmake:47 (message): Policy CMP0145 is not set: The Dart and FindDart modules are removed. Run "cmake --help-policy CMP0145" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:277 (INCLUDE) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Configuring done (0.7s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED -- 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 -j40 "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 make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' make -f CMakeFiles/SimTKmolmodel.dir/build.make CMakeFiles/SimTKmolmodel.dir/depend make[3]: Entering directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/molmodel-3.1.0 /build/reproducible-path/molmodel-3.1.0 /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu/CMakeFiles/SimTKmolmodel.dir/DependInfo.cmake "--color=" 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/Compound.cpp.o [ 6%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/BondGeometry.cpp.o [ 9%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/AtomSubsystem.cpp.o [ 18%] 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/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 [ 21%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/PDBReader.cpp.o [ 21%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/CompoundSystem.cpp.o [ 25%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/MolecularMechanicsSystem.cpp.o [ 25%] 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/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 [ 31%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/DuMMForceFieldSubsystemRep.cpp.o [ 31%] 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 -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 [ 37%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/PeriodicVmdReporter.cpp.o [ 37%] 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/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 /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" 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CXX object CMakeFiles/SimTKmolmodel.dir/src/Biotype.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/PeriodicVmdReporter.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/PeriodicVmdReporter.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/PeriodicVmdReporter.cpp.o -c 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-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 [ 81%] 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=\"\" 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-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 [ 84%] 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 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-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 [ 90%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMUtilities.cpp.o [ 90%] 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\" 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-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 /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/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 /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 /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/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 /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 /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/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 > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/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/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 > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/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/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 > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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/cpuObcInterface.h:34, from /build/reproducible-path/molmodel-3.1.0/src/gbsa/cpuObcInterface.cpp:25: /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: /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 > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/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/CpuObc.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 > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/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/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] 163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/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/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 > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/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: /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 > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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: /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/DuMMForceFieldSubsystem.cpp:43: /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 > { | ^~~~~~~~~~~~~~~ /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++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/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 struct std::iterator' is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath: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 | ^~~~~~~~ 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 struct std::iterator' is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath: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 struct std::iterator' is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath: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 | ^~~~~~~~ [ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libSimTKsimbody.so.3.7 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libSimTKmath.so.3.7 /usr/lib/x86_64-linux-gnu/libSimTKcommon.so.3.7 /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lpthread -lrt -ldl -lm /usr/bin/cmake -E cmake_symlink_library libSimTKmolmodel.so.3.1 libSimTKmolmodel.so.3.1 libSimTKmolmodel.so make[3]: Leaving directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' [ 93%] Built target SimTKmolmodel make -f OpenMMPlugin/CMakeFiles/OpenMMPlugin_shared.dir/build.make OpenMMPlugin/CMakeFiles/OpenMMPlugin_shared.dir/depend make[3]: Entering directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/molmodel-3.1.0 /build/reproducible-path/molmodel-3.1.0/OpenMMPlugin /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu/OpenMMPlugin /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu/OpenMMPlugin/CMakeFiles/OpenMMPlugin_shared.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' make -f OpenMMPlugin/CMakeFiles/OpenMMPlugin_shared.dir/build.make OpenMMPlugin/CMakeFiles/OpenMMPlugin_shared.dir/build make[3]: Entering directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' [ 96%] Building CXX object OpenMMPlugin/CMakeFiles/OpenMMPlugin_shared.dir/OpenMMPlugin.cpp.o cd /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu/OpenMMPlugin && /usr/bin/c++ -DOpenMMPlugin_shared_EXPORTS -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -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=\"\" -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 OpenMMPlugin/CMakeFiles/OpenMMPlugin_shared.dir/OpenMMPlugin.cpp.o -MF CMakeFiles/OpenMMPlugin_shared.dir/OpenMMPlugin.cpp.o.d -o CMakeFiles/OpenMMPlugin_shared.dir/OpenMMPlugin.cpp.o -c /build/reproducible-path/molmodel-3.1.0/OpenMMPlugin/OpenMMPlugin.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/OpenMMPlugin/OpenMMPlugin.cpp:43: /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 > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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/OpenMMPlugin/OpenMMPlugin.cpp:41: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [100%] Linking CXX shared library libOpenMMPlugin.so cd /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu/OpenMMPlugin && /usr/bin/cmake -E cmake_link_script CMakeFiles/OpenMMPlugin_shared.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 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'/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-x86_64-linux-gnu && make -j40 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 make[2]: Entering directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1 -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/doc/api/Molmodel/html -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/doc/MolmodelAPI.html -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/Molmodel.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/SimTKmolmodel.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/AtomSubsystem.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Biotype.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Clonable.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Compound.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/CompoundModeler.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/CompoundSystem.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/DNA.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/DuMMForceFieldSubsystem.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Element.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Exceptions.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/GrinPointer.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Ions.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Ligands.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Linkage.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/MassCenterMotionRemover.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/MolecularMechanicsSystem.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/NA.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/NoseHooverThermostat.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/PDBReader.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Pdb.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/PeriodicPdbWriter.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/PeriodicVmdReporter.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Protein.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/RNA.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/RiboseMobilizer.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Superpose.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/VanDerWaalsForce.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/VanderWallSphere.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/VelocityRescalingThermostat.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/VmdConnection.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/VoxelHash.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Water.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/bondGeometry.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/common.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/units.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/doc/MolmodelUsersGuide.pdf -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/molmodel/MolmodelConfig.cmake -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/molmodel/MolmodelConfigVersion.cmake -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/molmodel/MolmodelTargets.cmake -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/molmodel/MolmodelTargets-none.cmake -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/molmodel.pc -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/molmodel/plugins/libOpenMMPlugin.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/molmodel/plugins/libOpenMMPlugin.so" to "" make[1]: Leaving directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' dh_install dh_installdocs dh_installchangelogs dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 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 _ZN5gemmi16assign_subchainsERNS_9StructureEbb 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 _ZN5gemmi8GzStream4getcEv 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 _ZN5gemmi12MaybeGzipped24get_uncompressing_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 _ZN5gemmi15change_ccd_codeERNS_9StructureERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_ 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 _ZN5gemmi8GzStream4getsEPci 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 _ZN5gemmi19remove_entity_typesERNS_9StructureE 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 dh_builddeb 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' 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) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration 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/3688181 and its subdirectories I: Current time: Tue Aug 5 18:11:05 -12 2025 I: pbuilder-time-stamp: 1754460665 Wed Aug 6 06:11:06 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Wed Aug 6 06:11:06 UTC 2025 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Wed Aug 6 06:11:06 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Wed Aug 6 06:11:06 UTC 2025 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-DejX41' ==================================================================================== Tue Sep 8 12:34:07 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos5-amd64, called using "2 molmodel trixie /srv/reproducible-results/rbuild-debian/r-b-build.dpippO63 3.1.0-4.1" as arguments. Tue Sep 8 12:34:07 UTC 2026 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-wbYSCY7W" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Sep 8 12:34:07 UTC 2026 I: Downloading source for trixie/molmodel=3.1.0-4.1 Reading package lists... NOTICE: 'molmodel' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/molmodel.git Please use: git clone https://salsa.debian.org/debichem-team/molmodel.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 11.1 MB of source archives. Get:1 http://deb.debian.org/debian trixie/main molmodel 3.1.0-4.1 (dsc) [2238 B] Get:2 http://deb.debian.org/debian trixie/main molmodel 3.1.0-4.1 (tar) [11.1 MB] Get:3 http://deb.debian.org/debian trixie/main molmodel 3.1.0-4.1 (diff) [4668 B] Fetched 11.1 MB in 0s (80.2 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'molmodel' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/molmodel.git Please use: git clone https://salsa.debian.org/debichem-team/molmodel.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 11.1 MB of source archives. Get:1 http://deb.debian.org/debian trixie/main molmodel 3.1.0-4.1 (dsc) [2238 B] Get:2 http://deb.debian.org/debian trixie/main molmodel 3.1.0-4.1 (tar) [11.1 MB] Get:3 http://deb.debian.org/debian trixie/main molmodel 3.1.0-4.1 (diff) [4668 B] Fetched 11.1 MB in 0s (80.2 MB/s) Download complete and in download only mode ============================================================================= Re-Building molmodel in trixie on amd64 on ionos5-amd64 now. Date: Tue Sep 8 12:34:08 UTC 2026 Date UTC: Tue Sep 8 12:34:08 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.dpippO63 + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.dpippO63/pbuilderrc_UXSn + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' molmodel = debian-installer -o molmodel = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' molmodel = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo 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.dpippO63/pbuilderrc_UXSn --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.dpippO63/b2 --logfile b2/build.log molmodel_3.1.0-4.1.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Wed Sep 9 02:34:08 +14 2026 I: pbuilder-time-stamp: 1788870848 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [molmodel_3.1.0-4.1.dsc] I: copying [./molmodel_3.1.0.orig.tar.gz] I: copying [./molmodel_3.1.0-4.1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./molmodel_3.1.0-4.1.dsc: no acceptable signature found dpkg-source: info: extracting molmodel in molmodel-3.1.0 dpkg-source: info: unpacking molmodel_3.1.0.orig.tar.gz dpkg-source: info: unpacking molmodel_3.1.0-4.1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying drop-CMAKE_CXX_STANDARD.patch dpkg-source: info: applying plugin_dir.patch dpkg-source: info: applying f8492b9346dd8a2c32e3aa815294a3248b051d1f.patch dpkg-source: info: applying 968a0af8bc1a224337a3d1e1bd2fec3aec9e3fa1.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1101360/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Sep 8 12:34 /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/1101360/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1101360/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=d229bad98ea24b6aa9071d39fab01e29 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=1101360 PS4='+ ' 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.dpippO63/pbuilderrc_UXSn --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.dpippO63/b2 --logfile b2/build.log molmodel_3.1.0-4.1.dsc' SUDO_GID=110 SUDO_UID=105 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 i-capture-the-hostname 6.12.33+deb12-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.33-1~bpo12+1 (2025-07-09) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1101360/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: dpkg-dev (>= 1.22.5), cmake, debhelper-compat (= 13), gemmi-dev, libmmdb2-dev, libopenmm-dev, libopenblas-pthread-dev, libsimbody-dev, tao-pegtl-dev, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19851 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on gemmi-dev; however: Package gemmi-dev is not installed. pbuilder-satisfydepends-dummy depends on libmmdb2-dev; however: Package libmmdb2-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenmm-dev; however: Package libopenmm-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenblas-pthread-dev; however: Package libopenblas-pthread-dev is not installed. pbuilder-satisfydepends-dummy depends on libsimbody-dev; however: Package libsimbody-dev is not installed. pbuilder-satisfydepends-dummy depends on tao-pegtl-dev; however: Package tao-pegtl-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} freeglut3-dev{a} gemmi-dev{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libbrotli1{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm2{a} libedit2{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgbm1{a} libgfortran5{a} libgl-dev{a} libgl1{a} libgl1-mesa-dri{a} libglu1-mesa{a} libglu1-mesa-dev{a} libglut-dev{a} libglut3.12{a} libglvnd0{a} libglx-dev{a} libglx-mesa0{a} libglx0{a} libgnutls30t64{a} libgssapi-krb5-2{a} libice-dev{a} libice6{a} libidn2-0{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap2{a} libllvm19{a} libmagic-mgc{a} libmagic1t64{a} libmmdb2-0{a} libmmdb2-dev{a} libnghttp2-14{a} libnghttp3-9{a} libopenblas-pthread-dev{a} libopenblas0-pthread{a} libopengl-dev{a} libopengl0{a} libopenmm-dev{a} libopenmm8.1{a} libp11-kit0{a} libpciaccess0{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libsimbody-dev{a} libsimbody3.7{a} libsm-dev{a} libsm6{a} libssh2-1t64{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libvulkan1{a} libwayland-server0{a} libx11-6{a} libx11-data{a} libx11-dev{a} libx11-xcb1{a} libxau-dev{a} libxau6{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxfixes-dev{a} libxfixes3{a} libxi-dev{a} libxi6{a} libxml2{a} libxmu-dev{a} libxmu-headers{a} libxmu6{a} libxshmfence1{a} libxt-dev{a} libxt6t64{a} libxxf86vm1{a} libz3-4{a} m4{a} man-db{a} mesa-libgallium{a} po-debconf{a} procps{a} sensible-utils{a} tao-pegtl-dev{a} uuid-dev{a} x11-common{a} x11proto-dev{a} xorg-sgml-doctools{a} xtrans-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx mesa-vulkan-drivers psmisc publicsuffix wget 0 packages upgraded, 140 newly installed, 0 to remove and 0 not upgraded. Need to get 114 MB of archives. After unpacking 530 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-4 [862 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 cmake-data all 3.31.6-2 [2268 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-2.1 [698 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libarchive13t64 amd64 3.7.4-4 [349 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 27 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-3 [1465 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.14.1-2 [391 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.31.6-2 [12.0 MB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 54 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.2 [919 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.124-2 [8288 B] Get: 67 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.124-2 [39.0 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libx11-xcb1 amd64 2:1.8.12-1 [247 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b4 [19.3 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.124-2 [22.6 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libdrm-intel1 amd64 2.4.124-2 [64.1 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libllvm19 amd64 1:19.1.7-3+b1 [26.0 MB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libsensors-config all 1:3.6.2-2 [16.2 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libsensors5 amd64 1:3.6.2-2 [37.5 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libxshmfence1 amd64 1.3.3-1 [10.9 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 mesa-libgallium amd64 25.0.7-2 [9629 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libwayland-server0 amd64 1.23.1-3 [34.4 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libgbm1 amd64 25.0.7-2 [44.4 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libvulkan1 amd64 1.4.309.0-1 [130 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libgl1-mesa-dri amd64 25.0.7-2 [46.1 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libglx-mesa0 amd64 25.0.7-2 [143 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libglut3.12 amd64 3.4.0-4 [139 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libopengl0 amd64 1.7.0-1+b2 [30.9 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libglu1-mesa amd64 9.0.2-1.1+b3 [184 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 x11proto-dev all 2024.1-1 [603 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libxau-dev amd64 1:1.0.11-1 [23.6 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libxdmcp-dev amd64 1:1.1.5-1 [44.3 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libxcb1-dev amd64 1.17.0-2+b1 [181 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libx11-dev amd64 2:1.8.12-1 [894 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libglx-dev amd64 1.7.0-1+b2 [15.8 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libgl-dev amd64 1.7.0-1+b2 [101 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libopengl-dev amd64 1.7.0-1+b2 [5388 B] Get: 109 http://deb.debian.org/debian trixie/main amd64 libglu1-mesa-dev amd64 9.0.2-1.1+b3 [223 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libxext-dev amd64 2:1.3.4-1+b3 [104 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+24 [217 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.6-1 [37.3 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b2 [188 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libice-dev amd64 2:1.1.1-1 [73.8 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 uuid-dev amd64 2.41-5 [48.8 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libsm-dev amd64 2:1.2.6-1 [39.7 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libxt-dev amd64 1:1.2.1-1.2+b2 [407 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libglut-dev amd64 3.4.0-4 [163 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 freeglut3-dev amd64 3.4.0-4 [53.4 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 tao-pegtl-dev all 3.2.7-1 [69.4 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 gemmi-dev amd64 0.6.5+ds-3 [1137 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libopenblas0-pthread amd64 0.3.29+ds-3 [6740 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-4 [2447 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libopenblas-pthread-dev amd64 0.3.29+ds-3 [5063 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 liblapack-dev amd64 3.12.1-4 [4991 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libmmdb2-0 amd64 2.0.22-1+b2 [342 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libmmdb2-dev amd64 2.0.22-1+b2 [92.9 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libopenmm8.1 amd64 8.1.2+dfsg-11 [1059 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libopenmm-dev amd64 8.1.2+dfsg-11 [346 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libxfixes3 amd64 1:6.0.0-2+b4 [20.2 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libxfixes-dev amd64 1:6.0.0-2+b4 [22.4 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libxi-dev amd64 2:1.8.2-1 [241 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libxmu6 amd64 2:1.1.3-3+b4 [59.0 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libxmu-headers all 2:1.1.3-3 [68.5 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libxmu-dev amd64 2:1.1.3-3+b4 [65.3 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libsimbody3.7 amd64 3.7+dfsg-4 [3363 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libsimbody-dev amd64 3.7+dfsg-4 [2726 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 114 MB in 6s (18.3 MB/s) Preconfiguring packages ... 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Setting up libopenblas-pthread-dev:amd64 (0.3.29+ds-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/x86_64-linux-gnu/libopenblas.so (libopenblas.so-x86_64-linux-gnu) in auto mode Setting up liblapack3:amd64 (3.12.1-4) ... Setting up libxcb1-dev:amd64 (1.17.0-2+b1) ... Setting up libxi6:amd64 (2:1.8.2-1) ... Setting up libsm-dev:amd64 (2:1.2.6-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libdrm-intel1:amd64 (2.4.124-2) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libx11-dev:amd64 (2:1.8.12-1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxfixes-dev:amd64 (1:6.0.0-2+b4) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2+b2) ... Setting up liblapack-dev:amd64 (3.12.1-4) ... Setting up libxext-dev:amd64 (2:1.3.4-1+b3) ... Setting up libxi-dev:amd64 (2:1.8.2-1) ... Setting up mesa-libgallium:amd64 (25.0.7-2) ... Setting up libxmu-headers (2:1.1.3-3) ... Setting up libxmu6:amd64 (2:1.1.3-3+b4) ... Setting up libcurl4t64:amd64 (8.14.1-2) ... Setting up libgbm1:amd64 (25.0.7-2) ... Setting up libgl1-mesa-dri:amd64 (25.0.7-2) ... Setting up debhelper (13.24.2) ... Setting up libxt-dev:amd64 (1:1.2.1-1.2+b2) ... Setting up cmake (3.31.6-2) ... Setting up libglx-mesa0:amd64 (25.0.7-2) ... Setting up libglx0:amd64 (1.7.0-1+b2) ... Setting up libxmu-dev:amd64 (2:1.1.3-3+b4) ... Setting up libgl1:amd64 (1.7.0-1+b2) ... Setting up libglut3.12:amd64 (3.4.0-4) ... Setting up libsimbody3.7:amd64 (3.7+dfsg-4) ... Setting up libglx-dev:amd64 (1.7.0-1+b2) ... Setting up libgl-dev:amd64 (1.7.0-1+b2) ... Setting up libglu1-mesa-dev:amd64 (9.0.2-1.1+b3) ... Setting up libglut-dev:amd64 (3.4.0-4) ... Setting up freeglut3-dev:amd64 (3.4.0-4) ... Setting up libsimbody-dev:amd64 (3.7+dfsg-4) ... Processing triggers for libc-bin (2.41-11) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/1101360/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/1101360/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 dpkg-buildpackage: info: source changed by Benjamin Drung dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/molmodel-3.1.0' dh_auto_configure -- -DBUILD_EXAMPLES=OFF -DBUILD_TESTING=OFF cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DBUILD_EXAMPLES=OFF -DBUILD_TESTING=OFF .. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found OpenMM: /usr/include -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") CMake Warning (dev) at CMakeLists.txt:277 (INCLUDE): Policy CMP0145 is not set: The Dart and FindDart modules are removed. Run "cmake --help-policy CMP0145" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at /usr/share/cmake-3.31/Modules/Dart.cmake:47 (message): Policy CMP0145 is not set: The Dart and FindDart modules are removed. Run "cmake --help-policy CMP0145" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:277 (INCLUDE) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Configuring done (0.6s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED -- 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 -j42 "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 make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' make -f CMakeFiles/SimTKmolmodel.dir/build.make CMakeFiles/SimTKmolmodel.dir/depend make[3]: Entering directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/molmodel-3.1.0 /build/reproducible-path/molmodel-3.1.0 /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu/CMakeFiles/SimTKmolmodel.dir/DependInfo.cmake "--color=" 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/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/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 [ 9%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Biotype.cpp.o [ 15%] 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/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/DuMMForceFieldSubsystem.cpp.o [ 18%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/DuMMForceFieldSubsystemRep.cpp.o [ 21%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Compound.cpp.o [ 25%] 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/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 [ 28%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/CompoundSystem.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/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 [ 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 -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 [ 34%] 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 -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 /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 /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/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 /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 [ 43%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/PeriodicVmdReporter.cpp.o [ 43%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/BondGeometry.cpp.o [ 43%] 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 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-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/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 [ 46%] 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [ 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/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 [ 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/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++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" 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-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 /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/VmdConnection.cpp.o [ 59%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/VelocityRescalingThermostat.cpp.o [ 65%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuObc.cpp.o [ 65%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuImplicitSolvent.cpp.o [ 68%] 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 -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 /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 [ 71%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/ImplicitSolventParameters.cpp.o [ 78%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMCommon.cpp.o [ 78%] 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 -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 [ 81%] 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/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 [ 84%] 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 -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 [ 87%] 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/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 /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/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 /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/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 [ 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/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 /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 /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: /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 > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/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: /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 > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/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/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 > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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/cpuObcInterface.h:34, from /build/reproducible-path/molmodel-3.1.0/src/gbsa/cpuObcInterface.cpp:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/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/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 > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/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/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] 163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/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/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 > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/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/CpuObc.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 > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/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/DuMMForceFieldSubsystem.cpp:43: /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 > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/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 struct std::iterator' is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath: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 | ^~~~~~~~ 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/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 struct std::iterator' is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath: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 struct std::iterator' is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath: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 | ^~~~~~~~ [ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libSimTKsimbody.so.3.7 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libSimTKmath.so.3.7 /usr/lib/x86_64-linux-gnu/libSimTKcommon.so.3.7 /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lpthread -lrt -ldl -lm /usr/bin/cmake -E cmake_symlink_library libSimTKmolmodel.so.3.1 libSimTKmolmodel.so.3.1 libSimTKmolmodel.so make[3]: Leaving directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' [ 93%] Built target SimTKmolmodel make -f OpenMMPlugin/CMakeFiles/OpenMMPlugin_shared.dir/build.make OpenMMPlugin/CMakeFiles/OpenMMPlugin_shared.dir/depend make[3]: Entering directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/molmodel-3.1.0 /build/reproducible-path/molmodel-3.1.0/OpenMMPlugin /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu/OpenMMPlugin /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu/OpenMMPlugin/CMakeFiles/OpenMMPlugin_shared.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' make -f OpenMMPlugin/CMakeFiles/OpenMMPlugin_shared.dir/build.make OpenMMPlugin/CMakeFiles/OpenMMPlugin_shared.dir/build make[3]: Entering directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' [ 96%] Building CXX object OpenMMPlugin/CMakeFiles/OpenMMPlugin_shared.dir/OpenMMPlugin.cpp.o cd /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu/OpenMMPlugin && /usr/bin/c++ -DOpenMMPlugin_shared_EXPORTS -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -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=\"\" -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 OpenMMPlugin/CMakeFiles/OpenMMPlugin_shared.dir/OpenMMPlugin.cpp.o -MF CMakeFiles/OpenMMPlugin_shared.dir/OpenMMPlugin.cpp.o.d -o CMakeFiles/OpenMMPlugin_shared.dir/OpenMMPlugin.cpp.o -c /build/reproducible-path/molmodel-3.1.0/OpenMMPlugin/OpenMMPlugin.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/OpenMMPlugin/OpenMMPlugin.cpp:43: /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 > { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /usr/include/c++/14/complex:45, 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/OpenMMPlugin/OpenMMPlugin.cpp:41: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [100%] Linking CXX shared library libOpenMMPlugin.so cd /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu/OpenMMPlugin && /usr/bin/cmake -E cmake_link_script CMakeFiles/OpenMMPlugin_shared.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -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 -Wl,--dependency-file=CMakeFiles/OpenMMPlugin_shared.dir/link.d -Wl,-z,relro -shared -Wl,-soname,libOpenMMPlugin.so -o libOpenMMPlugin.so CMakeFiles/OpenMMPlugin_shared.dir/OpenMMPlugin.cpp.o -Wl,-rpath,/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu: ../libSimTKmolmodel.so.3.1 /usr/lib/x86_64-linux-gnu/libSimTKsimbody.so.3.7 /usr/lib/x86_64-linux-gnu/libOpenMM.so /usr/lib/x86_64-linux-gnu/libSimTKmath.so.3.7 /usr/lib/x86_64-linux-gnu/libSimTKcommon.so.3.7 /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lpthread -lrt -ldl -lm make[3]: Leaving directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' [100%] Built target OpenMMPlugin_shared make[2]: Leaving directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-x86_64-linux-gnu && make -j42 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 make[2]: Entering directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1 -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/doc/api/Molmodel/html -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/doc/MolmodelAPI.html -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/Molmodel.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/SimTKmolmodel.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/AtomSubsystem.h -- Installing: 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/build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Exceptions.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/GrinPointer.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Ions.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Ligands.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Linkage.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/MassCenterMotionRemover.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/MolecularMechanicsSystem.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/NA.h -- Installing: 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/build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Superpose.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/VanDerWaalsForce.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/VanderWallSphere.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/VelocityRescalingThermostat.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/VmdConnection.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/VoxelHash.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Water.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/bondGeometry.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/common.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/units.h -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/doc/MolmodelUsersGuide.pdf -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/molmodel/MolmodelConfig.cmake -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/molmodel/MolmodelConfigVersion.cmake -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/molmodel/MolmodelTargets.cmake -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/molmodel/MolmodelTargets-none.cmake -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/molmodel.pc -- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/molmodel/plugins/libOpenMMPlugin.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/molmodel/plugins/libOpenMMPlugin.so" to "" make[1]: Leaving directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' dh_install dh_installdocs dh_installchangelogs dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 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 _ZN5gemmi19remove_entity_typesERNS_9StructureE used by debian/libsimtkmolmodel3.1t64/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1 found in none of 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libraries dpkg-shlibdeps: warning: symbol _ZN5gemmi8GzStream4getsEPci 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 _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 _ZN5gemmi16assign_subchainsERNS_9StructureEbb 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 _ZN5gemmi15change_ccd_codeERNS_9StructureERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_ 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 dh_builddeb dpkg-deb: building package 'libsimtkmolmodel-plugins-dbgsym' in '../libsimtkmolmodel-plugins-dbgsym_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 'libsimtkmolmodel-dev' in '../libsimtkmolmodel-dev_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' in '../libsimtkmolmodel-plugins_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) dpkg-source --after-build . 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/1101360/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1101360/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/1101360 and its subdirectories I: Current time: Wed Sep 9 02:36:41 +14 2026 I: pbuilder-time-stamp: 1788871001 + false + set +x Tue Sep 8 12:36:41 UTC 2026 I: Signing ./b2/molmodel_3.1.0-4.1_amd64.buildinfo as molmodel_3.1.0-4.1_amd64.buildinfo.asc Tue Sep 8 12:36:41 UTC 2026 I: Signed ./b2/molmodel_3.1.0-4.1_amd64.buildinfo as ./b2/molmodel_3.1.0-4.1_amd64.buildinfo.asc Tue Sep 8 12:36:41 UTC 2026 - build #2 for molmodel/trixie/amd64 on ionos5-amd64 done. Starting cleanup. All cleanup done. Tue Sep 8 12:36:41 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-wbYSCY7W, removing. /srv/reproducible-results/rbuild-debian/r-b-build.dpippO63: total 148 drwxr-xr-x 2 jenkins jenkins 4096 Aug 6 06:11 b1 drwxr-xr-x 2 jenkins jenkins 4096 Aug 6 06:13 b2 -rw-r--r-- 1 jenkins jenkins 2238 Feb 28 2024 molmodel_3.1.0-4.1.dsc -rw------- 1 jenkins jenkins 134755 Aug 6 06:11 rbuildlog.1tolR3I /srv/reproducible-results/rbuild-debian/r-b-build.dpippO63/b1: total 16632 -rw-r--r-- 1 jenkins jenkins 131118 Aug 6 06:11 build.log -rw-r--r-- 1 jenkins jenkins 1863392 Aug 6 06:11 libsimtkmolmodel-dev_3.1.0-4.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 578316 Aug 6 06:11 libsimtkmolmodel-plugins-dbgsym_3.1.0-4.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 19316 Aug 6 06:11 libsimtkmolmodel-plugins_3.1.0-4.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 13674860 Aug 6 06:11 libsimtkmolmodel3.1t64-dbgsym_3.1.0-4.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 671152 Aug 6 06:11 libsimtkmolmodel3.1t64_3.1.0-4.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 4668 Aug 6 06:11 molmodel_3.1.0-4.1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2238 Aug 6 06:11 molmodel_3.1.0-4.1.dsc -rw-r--r-- 1 jenkins jenkins 9379 Aug 6 06:11 molmodel_3.1.0-4.1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 10261 Aug 6 06:11 molmodel_3.1.0-4.1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2743 Aug 6 06:11 molmodel_3.1.0-4.1_amd64.changes -rw-r--r-- 1 jenkins jenkins 1260 Aug 6 06:11 molmodel_3.1.0-4.1_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.dpippO63/b2: total 16596 -rw-r--r-- 1 jenkins jenkins 133063 Aug 6 06:13 build.log -rw-r--r-- 1 jenkins jenkins 1863392 Aug 6 06:13 libsimtkmolmodel-dev_3.1.0-4.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 578316 Aug 6 06:13 libsimtkmolmodel-plugins-dbgsym_3.1.0-4.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 19316 Aug 6 06:13 libsimtkmolmodel-plugins_3.1.0-4.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 13674860 Aug 6 06:13 libsimtkmolmodel3.1t64-dbgsym_3.1.0-4.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 671152 Aug 6 06:13 libsimtkmolmodel3.1t64_3.1.0-4.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 4668 Aug 6 06:13 molmodel_3.1.0-4.1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2238 Aug 6 06:13 molmodel_3.1.0-4.1.dsc -rw-r--r-- 1 jenkins jenkins 9392 Aug 6 06:13 molmodel_3.1.0-4.1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 10274 Aug 6 06:13 molmodel_3.1.0-4.1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2743 Aug 6 06:13 molmodel_3.1.0-4.1_amd64.changes -rw-r--r-- 1 jenkins jenkins 1260 Aug 6 06:13 molmodel_3.1.0-4.1_source.changes Wed Aug 6 06:13:42 UTC 2025 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Wed Aug 6 06:13:43 UTC 2025 I: molmodel_3.1.0-4.1_amd64.changes: Format: 1.8 Date: Wed, 28 Feb 2024 20:17:19 +0000 Source: molmodel Binary: libsimtkmolmodel-dev libsimtkmolmodel-plugins libsimtkmolmodel-plugins-dbgsym libsimtkmolmodel3.1t64 libsimtkmolmodel3.1t64-dbgsym Architecture: amd64 Version: 3.1.0-4.1 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Benjamin Drung Description: libsimtkmolmodel-dev - C++ API for creating molecular models for SimTK (development file libsimtkmolmodel-plugins - Plugins for C++ API for creating molecular models for SimTK libsimtkmolmodel3.1t64 - C++ API for creating molecular models for SimTK Closes: 1062945 Changes: molmodel (3.1.0-4.1) unstable; urgency=medium . * Non-maintainer upload. * Rename libraries for 64-bit time_t transition. Closes: #1062945 Checksums-Sha1: c2399785aff6f150adfd5c047c57451e83ddfe17 1863392 libsimtkmolmodel-dev_3.1.0-4.1_amd64.deb 8895532a32c355ddaf3437c0bd55aa56afa9e435 578316 libsimtkmolmodel-plugins-dbgsym_3.1.0-4.1_amd64.deb f91d0bb12d80bce157e9f3b08ac2295bdc0d016b 19316 libsimtkmolmodel-plugins_3.1.0-4.1_amd64.deb a30df8f60154215e35a45cfab478c09ab06f1749 13674860 libsimtkmolmodel3.1t64-dbgsym_3.1.0-4.1_amd64.deb 0f6c45a8526950ed896d2bb6377321c1a4141f05 671152 libsimtkmolmodel3.1t64_3.1.0-4.1_amd64.deb 14329fce47e8170e7dc874323d6297ac556761f7 9379 molmodel_3.1.0-4.1_amd64.buildinfo Checksums-Sha256: 7ae3445587e6d0af980605960512efdb4718f890629f773cfb6145ef37d4e351 1863392 libsimtkmolmodel-dev_3.1.0-4.1_amd64.deb 799342524524ce564f9cd8ac026fa5fad441f6b01a91a5fcd1b24e7b45976035 578316 libsimtkmolmodel-plugins-dbgsym_3.1.0-4.1_amd64.deb 7277980e0015b26bf40f8f266822d0c49c04b27986aef594b83b58e305d2523f 19316 libsimtkmolmodel-plugins_3.1.0-4.1_amd64.deb 8d47841987fcb7abb80e8b190216e0480a41163552f77ef15a53526ef962d3b2 13674860 libsimtkmolmodel3.1t64-dbgsym_3.1.0-4.1_amd64.deb 07337ca6507c6cddd26d1d7cfc707f027b3ede856db4cad1e2c64427f3806e1b 671152 libsimtkmolmodel3.1t64_3.1.0-4.1_amd64.deb 2dadb663c1bd591a514a9e625863be54fccdd62d643fe1cfa4c0d3a29b7c7438 9379 molmodel_3.1.0-4.1_amd64.buildinfo Files: 5c84738c96b3e71d9a0fd58c4200ed35 1863392 libdevel optional libsimtkmolmodel-dev_3.1.0-4.1_amd64.deb b0fbafa3e415d4913c96a1230b5787e7 578316 debug optional libsimtkmolmodel-plugins-dbgsym_3.1.0-4.1_amd64.deb 1785b0385a0326ebca9647ba50a002dd 19316 libs optional libsimtkmolmodel-plugins_3.1.0-4.1_amd64.deb 8d29d1ac63595eaa4f354d85ac252828 13674860 debug optional libsimtkmolmodel3.1t64-dbgsym_3.1.0-4.1_amd64.deb 3077825a7747fa54ed62c7887abb18f7 671152 libs optional libsimtkmolmodel3.1t64_3.1.0-4.1_amd64.deb cdbb1a1b8eb27cb8f5162fcf253c87ed 9379 libs optional molmodel_3.1.0-4.1_amd64.buildinfo removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/molmodel_3.1.0-4.1.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/molmodel_3.1.0-4.1.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/molmodel_3.1.0-4.1.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/molmodel_3.1.0-4.1.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/amd64/molmodel_3.1.0-4.1_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/molmodel_3.1.0-4.1.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-08-06 06:11:06.155166642 +0000 +++ b2/build.log 2025-08-06 06:13:42.527361670 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Aug 5 18:08:26 -12 2025 -I: pbuilder-time-stamp: 1754460506 +I: Current time: Wed Sep 9 02:34:08 +14 2026 +I: pbuilder-time-stamp: 1788870848 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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/3688181/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1101360/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Sep 8 12:34 /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/1101360/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1101360/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=40 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='3ce44856bbe44d5b953de42cfcc03334' - 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='3688181' - PS1='# ' - PS2='> ' + INVOCATION_ID=d229bad98ea24b6aa9071d39fab01e29 + 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=1101360 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.dpippO63/pbuilderrc_2roa --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.dpippO63/b1 --logfile b1/build.log molmodel_3.1.0-4.1.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.dpippO63/pbuilderrc_UXSn --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.dpippO63/b2 --logfile b2/build.log molmodel_3.1.0-4.1.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.33+deb12-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.33-1~bpo12+1 (2025-07-09) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3688181/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1101360/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -264,7 +296,7 @@ Get: 138 http://deb.debian.org/debian trixie/main amd64 libsimbody3.7 amd64 3.7+dfsg-4 [3363 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libsimbody-dev amd64 3.7+dfsg-4 [2726 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 114 MB in 2s (50.0 MB/s) +Fetched 114 MB in 6s (18.3 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 ... 19851 files and directories currently installed.) @@ -847,7 +879,11 @@ 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/1101360/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1101360/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 @@ -895,7 +931,7 @@ This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) --- Configuring done (0.7s) +-- Configuring done (0.6s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -908,7 +944,7 @@ -- 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 -j40 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/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 @@ -920,66 +956,65 @@ 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/Compound.cpp.o -[ 6%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/BondGeometry.cpp.o -[ 9%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/AtomSubsystem.cpp.o -[ 18%] 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/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 -[ 21%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/PDBReader.cpp.o -[ 21%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/CompoundSystem.cpp.o -[ 25%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/MolecularMechanicsSystem.cpp.o -[ 25%] 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/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 -[ 31%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/DuMMForceFieldSubsystemRep.cpp.o -[ 31%] 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 -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 -[ 37%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/PeriodicVmdReporter.cpp.o -[ 37%] 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/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 +[ 3%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/About.cpp.o +[ 6%] 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 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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 -[ 40%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Pdb.cpp.o +[ 9%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Biotype.cpp.o +[ 15%] 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/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/DuMMForceFieldSubsystem.cpp.o +[ 18%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/DuMMForceFieldSubsystemRep.cpp.o +[ 21%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Compound.cpp.o +[ 25%] 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/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 +[ 28%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/CompoundSystem.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/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 +[ 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 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-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 +/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY 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-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 +[ 43%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/PeriodicVmdReporter.cpp.o +[ 43%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/BondGeometry.cpp.o +[ 43%] 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/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 -[ 50%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/VanderWallSphere.cpp.o -[ 50%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/RiboseMobilizer.cpp.o -[ 50%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Biotype.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/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 +[ 46%] 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +[ 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/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 +[ 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 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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 -[ 53%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/VmdConnection.cpp.o -[ 56%] 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/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 -[ 62%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/cpuObcInterface.cpp.o -[ 62%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/VelocityRescalingThermostat.cpp.o -[ 65%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/ImplicitSolventParameters.cpp.o -[ 68%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/ObcParameters.cpp.o -[ 71%] 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 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-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 -/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 -[ 78%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMCommon.cpp.o -[ 81%] 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/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 -[ 81%] 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/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 +/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/VmdConnection.cpp.o +[ 59%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/VelocityRescalingThermostat.cpp.o +[ 65%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuObc.cpp.o +[ 65%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuImplicitSolvent.cpp.o +[ 68%] 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 -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 -[ 84%] 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/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 -/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 -[ 90%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMUtilities.cpp.o -[ 90%] 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 -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 +[ 71%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/ImplicitSolventParameters.cpp.o +[ 78%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMCommon.cpp.o +[ 78%] 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 -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 +[ 81%] 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 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-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 +[ 87%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMUtilities.cpp.o +/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" 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-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 /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/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 +[ 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/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 /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 /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/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/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 > { | ^~~~~~~~~~~~~~~ @@ -1003,7 +1038,8 @@ /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/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 > { | ^~~~~~~~~~~~~~~ @@ -1027,8 +1063,7 @@ /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/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/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 > { | ^~~~~~~~~~~~~~~ @@ -1072,8 +1107,14 @@ /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: +/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++/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/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 > { | ^~~~~~~~~~~~~~~ @@ -1097,13 +1138,7 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/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++/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/CpuObc.cpp:26: +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] 163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > { | ^~~~~~~~~~~~~~~ @@ -1127,7 +1162,8 @@ /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/CpuImplicitSolvent.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 > { | ^~~~~~~~~~~~~~~ @@ -1151,7 +1187,7 @@ /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/ImplicitSolventParameters.cpp:25: +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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > { | ^~~~~~~~~~~~~~~ @@ -1177,7 +1213,7 @@ | ^~~~~~~~~~~~~~~ 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: + 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > { | ^~~~~~~~~~~~~~~ @@ -1192,22 +1228,37 @@ 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/DuMMForceFieldSubsystem.cpp:40: /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/DuMMForceFieldSubsystem.cpp:43: -/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 > { - | ^~~~~~~~~~~~~~~ /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++/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 struct std::iterator' is deprecated [-Wdeprecated-declarations] + 180 | : public std::iterator > + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath: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 + | ^~~~~~~~ +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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > { + | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, @@ -1219,7 +1270,7 @@ 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/DuMMForceFieldSubsystemRep.cpp:38: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1229,21 +1280,6 @@ /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 struct std::iterator' is deprecated [-Wdeprecated-declarations] - 180 | : public std::iterator > - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath: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 - | ^~~~~~~~ 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: @@ -1331,7 +1367,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - cd obj-x86_64-linux-gnu && make -j40 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 -j42 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 @@ -1409,25 +1445,25 @@ diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 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 _ZN5gemmi19remove_entity_typesERNS_9StructureE 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 _ZN5gemmi16assign_subchainsERNS_9StructureEbb 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 _ZN5gemmi8GzStream4getcEv 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 _ZN5gemmi12MaybeGzipped24get_uncompressing_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 _ZN5gemmi15change_ccd_codeERNS_9StructureERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_ 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 _ZN5gemmi8GzStream4getcEv 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 _ZN5gemmi8GzStream4getsEPci 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 _ZN5gemmi19remove_entity_typesERNS_9StructureE 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 _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 _ZN5gemmi16assign_subchainsERNS_9StructureEbb 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 _ZN5gemmi15change_ccd_codeERNS_9StructureERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_ 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 dh_builddeb -dpkg-deb: building package 'libsimtkmolmodel-dev' in '../libsimtkmolmodel-dev_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 'libsimtkmolmodel3.1t64' in '../libsimtkmolmodel3.1t64_3.1.0-4.1_amd64.deb'. +dpkg-deb: building package 'libsimtkmolmodel-dev' in '../libsimtkmolmodel-dev_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' 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) @@ -1435,12 +1471,14 @@ 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/1101360/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1101360/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/3688181 and its subdirectories -I: Current time: Tue Aug 5 18:11:05 -12 2025 -I: pbuilder-time-stamp: 1754460665 +I: removing directory /srv/workspace/pbuilder/1101360 and its subdirectories +I: Current time: Wed Sep 9 02:36:41 +14 2026 +I: pbuilder-time-stamp: 1788871001 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/molmodel_3.1.0-4.1.diff: 90.1% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/molmodel_3.1.0-4.1.diff.gz b2/build.log: 87.7% -- replaced with stdout Compressing the 1st log... b1/build.log: 88.1% -- replaced with stdout Wed Aug 6 06:13:43 UTC 2025 I: diffoscope 303 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_molmodel_trixie_amd64_1754460823 + touch /var/log/reproducible-builds/diffoscope_stamp_molmodel_trixie_amd64_1754460823 + RESULT=0 + systemd-run '--description=diffoscope on molmodel/3.1.0-4.1 in trixie/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_25-49280 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.dpippO63 --run-session -c jenkins-reproducible-trixie-diffoscope-d08a722f-4d82-41bf-8a31-9444d6aa6b6d -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.dpippO63/dbd-tmp-cwiTr7c ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.dpippO63/molmodel_3.1.0-4.1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.dpippO63/molmodel_3.1.0-4.1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.dpippO63/molmodel_3.1.0-4.1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.dpippO63/b1/molmodel_3.1.0-4.1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.dpippO63/b2/molmodel_3.1.0-4.1_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_25-49280.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.dpippO63/molmodel_3.1.0-4.1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.dpippO63/molmodel_3.1.0-4.1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.dpippO63/molmodel_3.1.0-4.1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.dpippO63/b1/molmodel_3.1.0-4.1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.dpippO63/b2/molmodel_3.1.0-4.1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 155ms CPU time consumed: 157ms _ _ _ _ __ ___ ___ | |_ __ ___ ___ __| | ___| | | '_ ` _ \ / _ \| | '_ ` _ \ / _ \ / _` |/ _ \ | | | | | | | (_) | | | | | | | (_) | (_| | __/ | |_| |_| |_|\___/|_|_| |_| |_|\___/ \__,_|\___|_| Wed Aug 6 06:13:44 UTC 2025 I: diffoscope 303 found no differences in the changes files, and a .buildinfo file also exists. Wed Aug 6 06:13:44 UTC 2025 I: molmodel from trixie built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-08-06 06:13:44] INFO: Starting at 2025-08-06 06:13:44.579873 [2025-08-06 06:13:44] INFO: Generating the pages of 1 package(s) [2025-08-06 06:13:44] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/amd64/molmodel didn't produce a buildlog, even though it has been built. [2025-08-06 06:13:44] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/armhf/molmodel_3.1.0-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/armhf/molmodel_3.1.0-2.diff.gz is missing [2025-08-06 06:13:44] INFO: Finished at 2025-08-06 06:13:44.810964, took: 0:00:00.231093 Wed Aug 6 06:13:44 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/amd64/molmodel.html Wed Aug 6 06:13:44 UTC 2025 I: Removing signed molmodel_3.1.0-4.1_amd64.buildinfo.asc files: removed './b1/molmodel_3.1.0-4.1_amd64.buildinfo.asc' removed './b2/molmodel_3.1.0-4.1_amd64.buildinfo.asc' 1754460824 amd64 trixie molmodel Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/molmodel_3.1.0-4.1.rbuild.log: 86.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/molmodel_3.1.0-4.1.rbuild.log.gz [2025-08-06 06:13:45] INFO: Starting at 2025-08-06 06:13:45.083352 [2025-08-06 06:13:45] INFO: Generating the pages of 1 package(s) [2025-08-06 06:13:45] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/armhf/molmodel_3.1.0-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/armhf/molmodel_3.1.0-2.diff.gz is missing [2025-08-06 06:13:45] INFO: Finished at 2025-08-06 06:13:45.296920, took: 0:00:00.213571 All cleanup done. Wed Aug 6 06:13:45 UTC 2025 - total duration: 0h 5m 26s. Wed Aug 6 06:13:45 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-ZpEP1RAV, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 5min 26.912s CPU time consumed: 4.702s