Mon May 13 09:50:11 UTC 2024 I: starting to build molmodel/trixie/amd64 on jenkins on '2024-05-13 09:49' Mon May 13 09:50:11 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_7/20863/console.log Mon May 13 09:50:11 UTC 2024 I: Downloading source for trixie/molmodel=3.1.0-4.1 --2024-05-13 09:50:11-- 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% 286M=0s 2024-05-13 09:50:11 (286 MB/s) - ‘molmodel_3.1.0-4.1.dsc’ saved [2238/2238] Mon May 13 09:50:11 UTC 2024 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----- Mon May 13 09:50:11 UTC 2024 I: Checking whether the package is not for us Mon May 13 09:50:11 UTC 2024 I: Starting 1st build on remote node ionos11-amd64.debian.net. Mon May 13 09:50:11 UTC 2024 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Mon May 13 09:59:35 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun May 12 21:50:14 -12 2024 I: pbuilder-time-stamp: 1715593814 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 gpgv: Signature made Wed Feb 28 20:18:10 2024 gpgv: using RSA key A62D2CFBD50B9B5BF360D54B159EB5C4EFC8774C gpgv: Can't check signature: No public key 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/3267390/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='ed0df8413ee946af8d59b14981f05900' 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='3267390' 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.qI2Ya58z/pbuilderrc_8wlT --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.qI2Ya58z/b1 --logfile b1/build.log molmodel_3.1.0-4.1.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 10 11:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3267390/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 ... 19699 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} libbsd0{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libegl-dev{a} libegl-mesa0{a} libegl1{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgbm1{a} libgfortran5{a} libgl-dev{a} libgl1{a} libgl1-mesa-dev{a} libgl1-mesa-dri{a} libglapi-mesa{a} libgles-dev{a} libgles1{a} libgles2{a} libglu1-mesa{a} libglu1-mesa-dev{a} libglut-dev{a} libglut3.12{a} libglvnd-core-dev{a} libglvnd-dev{a} libglvnd0{a} libglx-dev{a} libglx-mesa0{a} libglx0{a} libgssapi-krb5-2{a} libice-dev{a} libice6{a} libicu72{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-2.5-0{a} libllvm17t64{a} libmagic-mgc{a} libmagic1t64{a} libmmdb2-0{a} libmmdb2-dev{a} libnghttp2-14{a} libopenblas-pthread-dev{a} libopenblas0-pthread{a} libopengl-dev{a} libopengl0{a} libopenmm-dev{a} libopenmm8.0t64{a} libpciaccess0{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} libpthread-stubs0-dev{a} librhash0{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} libsub-override-perl{a} libtool{a} libuchardet0{a} libuv1t64{a} libvulkan1{a} libwayland-client0{a} libwayland-server0{a} libx11-6{a} libx11-data{a} libx11-dev{a} libx11-xcb1{a} libxau-dev{a} libxau6{a} libxcb-dri2-0{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} po-debconf{a} procps{a} sensible-utils{a} tao-pegtl-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 lynx mesa-vulkan-drivers psmisc publicsuffix wget 0 packages upgraded, 149 newly installed, 0 to remove and 0 not upgraded. Need to get 113 MB of archives. After unpacking 531 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libarchive13t64 amd64 3.7.2-2 [346 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1~rc2-1 [22.6 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 26 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.7.1-5 [441 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libjsoncpp25 amd64 1.9.5-6+b2 [81.9 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 librhash0 amd64 1.4.3-3+b1 [132 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.48.0-1.1 [147 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 cmake-data all 3.29.2-2 [2167 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.29.2-2 [10.7 MB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 49 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libglvnd0 amd64 1.7.0-1+b1 [56.3 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.120-2 [7688 B] Get: 63 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libglapi-mesa amd64 24.0.6-1+b1 [36.6 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libx11-xcb1 amd64 2:1.8.7-1+b1 [232 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libxcb-dri2-0 amd64 1.15-1 [107 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libxcb-dri3-0 amd64 1.15-1 [107 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libxcb-glx0 amd64 1.15-1 [122 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libxcb-present0 amd64 1.15-1 [105 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libxcb-randr0 amd64 1.15-1 [117 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libxcb-sync1 amd64 1.15-1 [109 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libxcb-xfixes0 amd64 1.15-1 [109 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libxfixes3 amd64 1:6.0.0-2+b1 [20.3 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libxshmfence1 amd64 1.3-1+b1 [8852 B] Get: 77 http://deb.debian.org/debian trixie/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libvulkan1 amd64 1.3.280.0-1 [123 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libdrm-intel1 amd64 2.4.120-2 [62.7 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libdrm-nouveau2 amd64 2.4.120-2 [19.3 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libdrm-radeon1 amd64 2.4.120-2 [22.2 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20230828-1+b1 [93.5 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libllvm17t64 amd64 1:17.0.6-12 [23.7 MB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libsensors-config all 1:3.6.0-9 [14.6 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libsensors5 amd64 1:3.6.0-9 [34.6 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libgl1-mesa-dri amd64 24.0.6-1+b1 [8279 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libglx-mesa0 amd64 24.0.6-1+b1 [151 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libglx0 amd64 1.7.0-1+b1 [35.0 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libgl1 amd64 1.7.0-1+b1 [89.8 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.1-1 [79.0 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libglut3.12 amd64 3.4.0-1+b1 [139 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 x11proto-dev all 2024.1-1 [603 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libxau-dev amd64 1:1.0.9-1+b1 [21.3 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libxdmcp-dev amd64 1:1.1.2-3+b1 [40.8 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libpthread-stubs0-dev amd64 0.4-1+b1 [5348 B] Get: 101 http://deb.debian.org/debian trixie/main amd64 libxcb1-dev amd64 1.15-1 [181 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libx11-dev amd64 2:1.8.7-1+b1 [875 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libglx-dev amd64 1.7.0-1+b1 [15.8 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libgl-dev amd64 1.7.0-1+b1 [101 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libglvnd-core-dev amd64 1.7.0-1+b1 [13.4 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libwayland-server0 amd64 1.22.0-2.1+b1 [33.0 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libgbm1 amd64 24.0.6-1+b1 [41.0 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libwayland-client0 amd64 1.22.0-2.1+b1 [25.7 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libegl-mesa0 amd64 24.0.6-1+b1 [119 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libegl1 amd64 1.7.0-1+b1 [34.3 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libegl-dev amd64 1.7.0-1+b1 [19.5 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libgles1 amd64 1.7.0-1+b1 [12.2 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libgles2 amd64 1.7.0-1+b1 [17.3 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libgles-dev amd64 1.7.0-1+b1 [50.8 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libopengl0 amd64 1.7.0-1+b1 [31.1 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libopengl-dev amd64 1.7.0-1+b1 [5380 B] Get: 117 http://deb.debian.org/debian trixie/main amd64 libglvnd-dev amd64 1.7.0-1+b1 [5144 B] Get: 118 http://deb.debian.org/debian trixie/main amd64 libgl1-mesa-dev amd64 24.0.6-1+b1 [17.2 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libglu1-mesa amd64 9.0.2-1.1+b1 [180 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libglu1-mesa-dev amd64 9.0.2-1.1+b1 [219 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libxext-dev amd64 2:1.3.4-1+b1 [107 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.0.10-1+b1 [56.7 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.3-1+b1 [33.6 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libice-dev amd64 2:1.0.10-1+b1 [64.8 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libsm-dev amd64 2:1.2.3-1+b1 [36.1 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libxt-dev amd64 1:1.2.1-1.2 [406 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libglut-dev amd64 3.4.0-1+b1 [163 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 freeglut3-dev amd64 3.4.0-1+b1 [53.4 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 gemmi-dev amd64 0.6.4+ds-1 [1115 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14-20240330-1 [836 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libopenblas0-pthread amd64 0.3.27+ds-2 [6813 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libopenblas-pthread-dev amd64 0.3.27+ds-2 [4780 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 liblapack-dev amd64 3.12.0-3 [4880 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libmmdb2-0 amd64 2.0.22-1+b1 [341 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libmmdb2-dev amd64 2.0.22-1+b1 [92.9 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libopenmm8.0t64 amd64 8.0.0+dfsg-6.1 [1018 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libopenmm-dev amd64 8.0.0+dfsg-6.1 [338 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libxfixes-dev amd64 1:6.0.0-2+b1 [22.3 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libxi-dev amd64 2:1.8.1-1 [241 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 libxmu6 amd64 2:1.1.3-3+b2 [58.7 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libxmu-headers all 2:1.1.3-3 [68.5 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libxmu-dev amd64 2:1.1.3-3+b2 [65.1 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libsimbody3.7 amd64 3.7+dfsg-3 [3230 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libsimbody-dev amd64 3.7+dfsg-3 [2727 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 tao-pegtl-dev all 3.2.7-1 [69.4 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Fetched 113 MB in 4s (29.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0: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 ... 19699 files and directories currently installed.) Preparing to unpack .../000-libproc2-0_2%3a4.0.4-4_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-4) ... Selecting previously unselected package procps. Preparing to unpack .../001-procps_2%3a4.0.4-4_amd64.deb ... Unpacking procps (2:4.0.4-4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../003-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../004-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../005-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../006-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../007-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../008-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../009-bsdextrautils_2.40-8_amd64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../010-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../011-man-db_2.12.1-1_amd64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../012-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../013-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../014-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../015-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../016-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../017-libicu72_72.1-4+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-4+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../018-libxml2_2.9.14+dfsg-1.3+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package libarchive13t64:amd64. Preparing to unpack .../019-libarchive13t64_3.7.2-2_amd64.deb ... Unpacking libarchive13t64:amd64 (3.7.2-2) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../020-libbrotli1_1.1.0-2+b3_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b3) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../021-libkrb5support0_1.20.1-6+b1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../022-libcom-err2_1.47.1~rc2-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1~rc2-1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../023-libk5crypto3_1.20.1-6+b1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../024-libkeyutils1_1.6.3-3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../025-libkrb5-3_1.20.1-6+b1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../026-libgssapi-krb5-2_1.20.1-6+b1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../027-libsasl2-modules-db_2.1.28+dfsg1-6_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../028-libsasl2-2_2.1.28+dfsg1-6_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../029-libldap-2.5-0_2.5.17+dfsg-1_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../030-libnghttp2-14_1.61.0-1+b1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.61.0-1+b1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../031-libpsl5t64_0.21.2-1.1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../032-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../033-libssh2-1t64_1.11.0-4.1+b2_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Selecting previously unselected package libcurl4t64:amd64. Preparing to unpack .../034-libcurl4t64_8.7.1-5_amd64.deb ... Unpacking libcurl4t64:amd64 (8.7.1-5) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../035-libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package libjsoncpp25:amd64. Preparing to unpack .../036-libjsoncpp25_1.9.5-6+b2_amd64.deb ... Unpacking libjsoncpp25:amd64 (1.9.5-6+b2) ... Selecting previously unselected package librhash0:amd64. Preparing to unpack .../037-librhash0_1.4.3-3+b1_amd64.deb ... Unpacking librhash0:amd64 (1.4.3-3+b1) ... Selecting previously unselected package libuv1t64:amd64. Preparing to unpack .../038-libuv1t64_1.48.0-1.1_amd64.deb ... Unpacking libuv1t64:amd64 (1.48.0-1.1) ... Selecting previously unselected package cmake-data. Preparing to unpack .../039-cmake-data_3.29.2-2_all.deb ... Unpacking cmake-data (3.29.2-2) ... Selecting previously unselected package cmake. Preparing to unpack .../040-cmake_3.29.2-2_amd64.deb ... Unpacking cmake (3.29.2-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../041-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../042-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../043-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../044-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../045-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../046-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../047-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../048-libelf1t64_0.191-1+b1_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../049-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package gettext. 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Setting up cmake-data (3.29.2-2) ... Setting up libkrb5-3:amd64 (1.20.1-6+b1) ... Setting up libglu1-mesa:amd64 (9.0.2-1.1+b1) ... Setting up libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Setting up libopengl-dev:amd64 (1.7.0-1+b1) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up libdrm-common (2.4.120-2) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up tao-pegtl-dev (3.2.7-1) ... Setting up libopenmm8.0t64 (8.0.0+dfsg-6.1) ... Setting up libwayland-client0:amd64 (1.22.0-2.1+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up x11proto-dev (2024.1-1) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libice6:amd64 (2:1.0.10-1+b1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-14+b1) ... Setting up libopenblas0-pthread:amd64 (0.3.27+ds-2) ... 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 libxcb-xfixes0:amd64 (1.15-1) ... Setting up libxau-dev:amd64 (1:1.0.9-1+b1) ... Setting up libice-dev:amd64 (2:1.0.10-1+b1) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-glx0:amd64 (1.15-1) ... Setting up libedit2:amd64 (3.1-20230828-1+b1) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libopenmm-dev (8.0.0+dfsg-6.1) ... Setting up libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libxcb-present0:amd64 (1.15-1) ... Setting up dh-autoreconf (20) ... Setting up libxdmcp-dev:amd64 (1:1.1.2-3+b1) ... Setting up libllvm17t64:amd64 (1:17.0.6-12) ... Setting up libxcb-sync1:amd64 (1.15-1) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up libxcb-dri2-0:amd64 (1.15-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libdrm2:amd64 (2.4.120-2) ... Setting up groff-base (1.23.0-4) ... Setting up libxcb-randr0:amd64 (1.15-1) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libsm6:amd64 (2:1.2.3-1+b1) ... Setting up libarchive13t64:amd64 (3.7.2-2) ... Setting up libdrm-amdgpu1:amd64 (2.4.120-2) ... Setting up libopenblas-pthread-dev:amd64 (0.3.27+ds-2) ... 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 libxcb-dri3-0:amd64 (1.15-1) ... Setting up libx11-xcb1:amd64 (2:1.8.7-1+b1) ... Setting up liblapack3:amd64 (3.12.0-3) ... Setting up libdrm-nouveau2:amd64 (2.4.120-2) ... Setting up libxcb1-dev:amd64 (1.15-1) ... Setting up libcurl4t64:amd64 (8.7.1-5) ... Setting up libgbm1:amd64 (24.0.6-1+b1) ... Setting up libsm-dev:amd64 (2:1.2.3-1+b1) ... Setting up libdrm-radeon1:amd64 (2.4.120-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libdrm-intel1:amd64 (2.4.120-2) ... Setting up libgl1-mesa-dri:amd64 (24.0.6-1+b1) ... Setting up libx11-dev:amd64 (2:1.8.7-1+b1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up libegl-mesa0:amd64 (24.0.6-1+b1) ... Setting up libxfixes3:amd64 (1:6.0.0-2+b1) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2) ... Setting up liblapack-dev:amd64 (3.12.0-3) ... Setting up libxext-dev:amd64 (2:1.3.4-1+b1) ... Setting up libegl1:amd64 (1.7.0-1+b1) ... Setting up cmake (3.29.2-2) ... Setting up libxmu-headers (2:1.1.3-3) ... Setting up libxmu6:amd64 (2:1.1.3-3+b2) ... Setting up libglx-mesa0:amd64 (24.0.6-1+b1) ... Setting up libxi6:amd64 (2:1.8.1-1) ... Setting up libglx0:amd64 (1.7.0-1+b1) ... Setting up debhelper (13.15.3) ... Setting up libxfixes-dev:amd64 (1:6.0.0-2+b1) ... Setting up libgl1:amd64 (1.7.0-1+b1) ... Setting up libxt-dev:amd64 (1:1.2.1-1.2) ... Setting up libglut3.12:amd64 (3.4.0-1+b1) ... Setting up libsimbody3.7:amd64 (3.7+dfsg-3) ... Setting up libglx-dev:amd64 (1.7.0-1+b1) ... Setting up libxi-dev:amd64 (2:1.8.1-1) ... Setting up libgl-dev:amd64 (1.7.0-1+b1) ... Setting up libegl-dev:amd64 (1.7.0-1+b1) ... Setting up libxmu-dev:amd64 (2:1.1.3-3+b2) ... Setting up libglu1-mesa-dev:amd64 (9.0.2-1.1+b1) ... Setting up libgles-dev:amd64 (1.7.0-1+b1) ... Setting up libglvnd-dev:amd64 (1.7.0-1+b1) ... Setting up libgl1-mesa-dev:amd64 (24.0.6-1+b1) ... Setting up libglut-dev:amd64 (3.4.0-1+b1) ... Setting up freeglut3-dev:amd64 (3.4.0-1+b1) ... Setting up libsimbody-dev:amd64 (3.7+dfsg-3) ... Processing triggers for libc-bin (2.38-10) ... 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 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 13.2.0 -- The CXX compiler identification is GNU 13.2.0 -- 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") 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-3.29/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 (4.6s) -- 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 -j20 "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 /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 [ 6%] 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/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 [ 9%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/DuMMForceFieldSubsystem.cpp.o [ 12%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Compound.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 [ 15%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/DuMMForceFieldSubsystemRep.cpp.o /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/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/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 [ 18%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/BondGeometry.cpp.o [ 21%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/AtomSubsystem.cpp.o /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/AtomSubsystem.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/AtomSubsystem.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/AtomSubsystem.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/AtomSubsystem.cpp [ 25%] 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/BondGeometry.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/BondGeometry.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/BondGeometry.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/BondGeometry.cpp [ 28%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Element.cpp.o /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -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/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 [ 31%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/MolecularMechanicsSystem.cpp.o [ 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/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 /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 [ 37%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Pdb.cpp.o /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -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 [ 40%] 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/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 [ 43%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/PeriodicVmdReporter.cpp.o /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -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 [ 46%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/RiboseMobilizer.cpp.o [ 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/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 [ 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/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 [ 56%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/VmdConnection.cpp.o [ 59%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/VelocityRescalingThermostat.cpp.o /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/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 /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/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 [ 62%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuImplicitSolvent.cpp.o /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuImplicitSolvent.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuImplicitSolvent.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuImplicitSolvent.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.cpp [ 65%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuObc.cpp.o /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuObc.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuObc.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuObc.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/gbsa/CpuObc.cpp 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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /usr/include/c++/13/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++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 68%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/ImplicitSolventParameters.cpp.o /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/ImplicitSolventParameters.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/ImplicitSolventParameters.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/ImplicitSolventParameters.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/gbsa/ImplicitSolventParameters.cpp [ 71%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/ObcParameters.cpp.o /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 [ 75%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMCommon.cpp.o /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMCommon.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMCommon.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMCommon.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.cpp 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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /usr/include/c++/13/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++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 78%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMLog.cpp.o /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMLog.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMLog.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMLog.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMLog.cpp In file included from /build/reproducible-path/molmodel-3.1.0/src/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++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, 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++/13/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/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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /usr/include/c++/13/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++/13/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++/13/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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /usr/include/c++/13/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++/13/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++/13/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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /usr/include/c++/13/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++/13/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++/13/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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /usr/include/c++/13/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++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 81%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMUtilities.cpp.o /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMUtilities.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMUtilities.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMUtilities.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp [ 84%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/cpuObcInterface.cpp.o /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 [ 87%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/imd.cpp.o /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/imd.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/imd.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/imd.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/imd.cpp [ 90%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/vmdsock.cpp.o /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/vmdsock.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/vmdsock.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/vmdsock.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/vmdsock.cpp In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.cpp:25: /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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /usr/include/c++/13/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++/13/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++/13/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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /usr/include/c++/13/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++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/molmodel-3.1.0/src/CompoundAtom.h:36, from /build/reproducible-path/molmodel-3.1.0/src/CompoundRep.h:42, from /build/reproducible-path/molmodel-3.1.0/src/CompoundSystem.cpp:3: /build/reproducible-path/molmodel-3.1.0/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, 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++/13/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++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, 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++/13/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/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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /usr/include/c++/13/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++/13/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++/13/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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /usr/include/c++/13/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++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 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,-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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /usr/include/c++/13/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++/13/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++/13/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,-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 -j20 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: 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 _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 _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 _ZN5gemmi16assign_subchainsERNS_9StructureEbb 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 'libsimtkmolmodel3.1t64' in '../libsimtkmolmodel3.1t64_3.1.0-4.1_amd64.deb'. dpkg-deb: building package 'libsimtkmolmodel-plugins-dbgsym' in '../libsimtkmolmodel-plugins-dbgsym_3.1.0-4.1_amd64.deb'. dpkg-deb: building package 'libsimtkmolmodel-dev' in '../libsimtkmolmodel-dev_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 'libsimtkmolmodel3.1t64-dbgsym' in '../libsimtkmolmodel3.1t64-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/3267390 and its subdirectories I: Current time: Sun May 12 21:59:34 -12 2024 I: pbuilder-time-stamp: 1715594374 Mon May 13 09:59:36 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Mon May 13 09:59:36 UTC 2024 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Mon May 13 10:01:40 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Mon May 13 10:01:40 UTC 2024 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: 691cd8bf09c6cfab80895c92b04cb00bc7f87e00 1863396 libsimtkmolmodel-dev_3.1.0-4.1_amd64.deb a1ffc68873650ec31ec1206fce20af7ee49385a4 572356 libsimtkmolmodel-plugins-dbgsym_3.1.0-4.1_amd64.deb ea84eb13c781027d6bfa7f953af53be93af96421 19760 libsimtkmolmodel-plugins_3.1.0-4.1_amd64.deb cbb8890e0525c0ab7122790a779b9d618613e591 13316084 libsimtkmolmodel3.1t64-dbgsym_3.1.0-4.1_amd64.deb 579c3c692db9f079b3def99e14cbf6ed8ca6871f 671496 libsimtkmolmodel3.1t64_3.1.0-4.1_amd64.deb 34c0257660b0e061dcf4c719e58ec9c4de728e7a 10002 molmodel_3.1.0-4.1_amd64.buildinfo Checksums-Sha256: caa22b333029a9e5b6b731e637cf4a2ba2b5a98f93b1f0441a8b19087c9c1903 1863396 libsimtkmolmodel-dev_3.1.0-4.1_amd64.deb 5431c146073f551dfdfa785df3d4158ef660da8b414fba153d4d7b4e20e0775f 572356 libsimtkmolmodel-plugins-dbgsym_3.1.0-4.1_amd64.deb 82ece0f940231aea439fa5dce52e29bee82269a279f6970a122b1017d27db79d 19760 libsimtkmolmodel-plugins_3.1.0-4.1_amd64.deb d46614cdabb9b0b3b3e041782944e65f6caaccdd2aa87a65bc13672c2b15f356 13316084 libsimtkmolmodel3.1t64-dbgsym_3.1.0-4.1_amd64.deb 3cd14fd0fcd5d2483caf10064f03b5317718d14824f197664a1140dbb7533f63 671496 libsimtkmolmodel3.1t64_3.1.0-4.1_amd64.deb bc580c74362aaf56a75bbda54851a4a0373325d2cdeda39a5daeeadac8f1577c 10002 molmodel_3.1.0-4.1_amd64.buildinfo Files: 8fb77ce8508bf743c1a92433c418159b 1863396 libdevel optional libsimtkmolmodel-dev_3.1.0-4.1_amd64.deb 53af52fa26b107142b0770d53056b331 572356 debug optional libsimtkmolmodel-plugins-dbgsym_3.1.0-4.1_amd64.deb 86b36481e8b42e11fcd0a08208fd3fec 19760 libs optional libsimtkmolmodel-plugins_3.1.0-4.1_amd64.deb 13731200b633dd07df06cf454a000c23 13316084 debug optional libsimtkmolmodel3.1t64-dbgsym_3.1.0-4.1_amd64.deb 5af4d8ff4defd00826707286b084dbe8 671496 libs optional libsimtkmolmodel3.1t64_3.1.0-4.1_amd64.deb 75397920f3cbb10d0b74d2be150099e2 10002 libs optional molmodel_3.1.0-4.1_amd64.buildinfo Mon May 13 10:01:42 UTC 2024 I: diffoscope 266 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_7-20863.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.qI2Ya58z/molmodel_3.1.0-4.1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.qI2Ya58z/molmodel_3.1.0-4.1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.qI2Ya58z/molmodel_3.1.0-4.1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.qI2Ya58z/b1/molmodel_3.1.0-4.1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.qI2Ya58z/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 abc.DotChangesFile ## main (total time: 0.523s) 0.523s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.185s) 0.185s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 842ms CPU time consumed: 841ms Mon May 13 10:01:43 UTC 2024 I: diffoscope 266 found no differences in the changes files, and a .buildinfo file also exists. Mon May 13 10:01:43 UTC 2024 I: molmodel from trixie built successfully and reproducibly on amd64. Mon May 13 10:01:45 UTC 2024 I: Submitting .buildinfo files to external archives: Mon May 13 10:01:45 UTC 2024 I: Submitting 12K b1/molmodel_3.1.0-4.1_amd64.buildinfo.asc Mon May 13 10:01:46 UTC 2024 I: Submitting 12K b2/molmodel_3.1.0-4.1_amd64.buildinfo.asc Mon May 13 10:01:46 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon May 13 10:01:46 UTC 2024 I: Done submitting .buildinfo files. Mon May 13 10:01:46 UTC 2024 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'