Fri Jun 2 07:32:46 UTC 2023 I: starting to build molmodel/bookworm/amd64 on jenkins on '2023-06-02 07:32' Fri Jun 2 07:32:46 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_4/89/console.log Fri Jun 2 07:32:46 UTC 2023 I: Downloading source for bookworm/molmodel=3.1.0-2 --2023-06-02 07:32:47-- http://cdn-fastly.deb.debian.org/debian/pool/main/m/molmodel/molmodel_3.1.0-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2227 (2.2K) [text/prs.lines.tag] Saving to: ‘molmodel_3.1.0-2.dsc’ 0K .. 100% 176M=0s 2023-06-02 07:32:47 (176 MB/s) - ‘molmodel_3.1.0-2.dsc’ saved [2227/2227] Fri Jun 2 07:32:47 UTC 2023 I: molmodel_3.1.0-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: molmodel Binary: libsimtkmolmodel-dev, libsimtkmolmodel3.1, libsimtkmolmodel-plugins Architecture: any Version: 3.1.0-2 Maintainer: Debichem Team Uploaders: Andrius Merkys , Homepage: https://simtk.org/projects/molmodel Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/debichem-team/molmodel Vcs-Git: https://salsa.debian.org/debichem-team/molmodel.git Build-Depends: 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 libsimtkmolmodel3.1 deb libs optional arch=any Checksums-Sha1: 5ad7cc7f74a13d8b57d5d4cb468aa48f3f67ad75 11118182 molmodel_3.1.0.orig.tar.gz 73724f8af94543024126f440f8612b0f88881c58 3548 molmodel_3.1.0-2.debian.tar.xz Checksums-Sha256: d9fef841ce0b5978a20c0fce77e7f74e2a360576388e564fbe84a15cb53fbedd 11118182 molmodel_3.1.0.orig.tar.gz ecc4625872e4acf0cfde4c8caaad543a978852f44c10af029b0fbb8ed286edd2 3548 molmodel_3.1.0-2.debian.tar.xz Files: 082b507dc0ac23db29b0984b28176c41 11118182 molmodel_3.1.0.orig.tar.gz bbc8d13ff160afd99092acab5e645c33 3548 molmodel_3.1.0-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEdyKS9veshfrgQdQe5fQ/nCc08ocFAmOMXcMSHG1lcmt5c0Bk ZWJpYW4ub3JnAAoJEOX0P5wnNPKHLi4QAKUszRP3CqmKj5eSmpptzqvGrq8if6Az LcRqD4BmwbNeZ02uSMPVxcidPsioj9qXWzDJTW2TT1LemizRbaeDn2lADSQiwqRJ Qj0fq8OyEWZAGpDqK+LVZuD8WtrFS5xgRV3WIo5ZeoVFm2nHd7Xzspa/qnmiNN6f Tu+3aTpu7gWuuAMOB0VDPK34d/6GQHgQ2DxciSrumStiJ7WdrOiacgdSQHX7vPJi 7YxNe8ss1BwiH+4dn46gCMzMYrtCmOWr2fnjkX8GtwjAyFE5Z3OkCkgMgjcOxc0G duQSXrgj6xZxQYT885G9J1CbtlyPH3ThZ45nTwH/T3gUEYlaiETlJ75tWpaQAScR EA816ktEmF7rGY/hCl5R+F7ebYr+A81JEq5s+12RYZb+eMrVTVVKuOdX3KpkiPQ8 1be3q+ViVuSvBNcx3VcKRIZM2AtMwMihS1ZTpJOwZUtOiiRg/Oq2IFcfIZx/G3cO RNLqmetWd3y+OI/5onT6ce8e9GqaQqdBc3dmSxIzaijrTejaiVo/L5MsNcT66TgQ 1QZnXfgrlCGdDFTvGaJjo5UFDm7UMvZXjuMvGfX249r4ZbsmrlbtLJDVysEx/eba 6lhFYsx8iNnm+QcSaVS2kTdAzgF7GQadQudqZYnI2UmmJDH6sDQpxQKlE5vaO23s acqflVbCQ0GF =FOfX -----END PGP SIGNATURE----- Fri Jun 2 07:32:47 UTC 2023 I: Checking whether the package is not for us Fri Jun 2 07:32:47 UTC 2023 I: Starting 1st build on remote node ionos15-amd64.debian.net. Fri Jun 2 07:32:47 UTC 2023 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Fri Jun 2 07:38:18 UTC 2023 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jul 4 01:55:51 -12 2024 I: pbuilder-time-stamp: 1720101351 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] tar: ./usr/share/doc/adduser/examples/adduser.local.conf.examples/skel: time stamp 2025-08-04 08:27:04 is 34237851.926488366 s in the future tar: ./usr/share/doc/adduser/examples/adduser.local.conf.examples/skel.other: time stamp 2025-08-04 08:27:04 is 34237851.926253221 s in the future tar: ./usr/share/doc/adduser/examples/adduser.local.conf.examples: time stamp 2025-08-04 08:27:04 is 34237851.926227437 s in the future tar: ./usr/share/doc/adduser/examples: time stamp 2025-08-04 08:27:04 is 34237851.926204992 s in the future tar: ./usr/share/doc/adduser: time stamp 2025-08-04 08:27:04 is 34237851.926183265 s in the future tar: ./usr/share/locale/ca/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34237851.722825298 s in the future tar: ./usr/share/locale/cs/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34237851.704612098 s in the future tar: ./usr/share/locale/da/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34237851.686455505 s in the future tar: ./usr/share/locale/de/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34237851.66667198 s in the future tar: ./usr/share/locale/es/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34237851.638035015 s in the future tar: ./usr/share/locale/eu/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34237851.63279408 s in the future tar: ./usr/share/locale/fr/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34237851.597784351 s in the future tar: ./usr/share/locale/gl/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34237851.590883807 s in the future tar: ./usr/share/locale/hu/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34237851.579082123 s in the future tar: ./usr/share/locale/it/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34237851.558622481 s in the future tar: ./usr/share/locale/ja/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34237851.538352198 s in the future tar: ./usr/share/locale/ko/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34237851.525263738 s in the future tar: ./usr/share/locale/nb/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34237851.513042553 s in the future tar: ./usr/share/locale/nl/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34237851.494130843 s in the future tar: ./usr/share/locale/pl/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34237851.476781686 s in the future tar: ./usr/share/locale/pt/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34237851.453433483 s in the future tar: ./usr/share/locale/pt_BR/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34237851.427034671 s in the future tar: ./usr/share/locale/ru/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34237851.370257498 s in the future tar: ./usr/share/locale/sk/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34237851.360442858 s in the future tar: ./usr/share/locale/sv/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34237851.330115171 s in the future tar: ./usr/share/locale/uk/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34237851.29646823 s in the future tar: ./usr/share/locale/vi/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34237851.277896212 s in the future tar: ./usr/share/locale/zh_CN/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34237851.26118974 s in the future tar: ./usr/share/man/de/man5: time stamp 2025-08-04 08:27:04 is 34237851.011568913 s in the future tar: ./usr/share/man/fr/man5: time stamp 2025-08-04 08:27:04 is 34237851.001318626 s in the future tar: ./usr/share/man/man5: time stamp 2025-08-04 08:27:04 is 34237850.989301146 s in the future tar: ./usr/share/man/nl/man5: time stamp 2025-08-04 08:27:04 is 34237850.976001646 s in the future tar: ./usr/share/man/nl/man8: time stamp 2025-08-04 08:27:04 is 34237850.974853545 s in the future tar: ./usr/share/man/pt/man5: time stamp 2025-08-04 08:27:04 is 34237850.968629798 s in the future tar: ./usr/share/man/pt/man8: time stamp 2025-08-04 08:27:04 is 34237850.967479467 s in the future tar: ./usr/share/perl5/Debian: time stamp 2025-08-04 08:27:04 is 34237850.605342631 s in the future tar: ./var/lib/dpkg/info/adduser.list: time stamp 2025-08-04 08:27:04 is 34237842.427193184 s in the future tar: ./usr/sbin: time stamp 2025-08-04 08:27:04 is 34237842.23572607 s in the future tar: ./usr/share/man/man8: time stamp 2025-08-04 08:27:04 is 34237842.234712136 s in the future tar: ./usr/share/man/fr/man8: time stamp 2025-08-04 08:27:04 is 34237842.234658732 s in the future tar: ./usr/share/man/de/man8: time stamp 2025-08-04 08:27:04 is 34237842.234594065 s in the future 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_3.1.0-2.dsc] I: copying [./molmodel_3.1.0.orig.tar.gz] I: copying [./molmodel_3.1.0-2.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Dec 3 20:43:47 2022 -12 gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 gpgv: issuer "merkys@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./molmodel_3.1.0-2.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_3.1.0-2.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1711909/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='6c2bddab234a45d5bea2a746b36fc521' 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='1711909' 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.XpsqAnvW/pbuilderrc_Wvqw --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.XpsqAnvW/b1 --logfile b1/build.log molmodel_3.1.0-2.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://85.184.249.68:3128' I: uname -a Linux ionos15-amd64 6.1.0-0.deb11.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.20-2~bpo11+1 (2023-04-23) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 2023 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 2023 more -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 2023 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/1711909/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: 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 ... 19591 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} libarchive13{a} libbrotli1{a} libbsd0{a} libcurl4{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} libelf1{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} libice-dev{a} libice6{a} libicu72{a} libjsoncpp25{a} liblapack-dev{a} liblapack3{a} libldap-2.5-0{a} libllvm15{a} libmagic-mgc{a} libmagic1{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} libopenmm7.7{a} libpciaccess0{a} libpipeline1{a} libproc2-0{a} libpsl5{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} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libuv1{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} libxt6{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 libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget 0 packages upgraded, 142 newly installed, 0 to remove and 0 not upgraded. Need to get 106 MB of archives. After unpacking 489 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 libproc2-0 amd64 2:4.0.2-3 [62.8 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 procps amd64 2:4.0.2-3 [709 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libarchive13 amd64 3.6.2-1 [343 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-10 [386 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libjsoncpp25 amd64 1.9.5-4 [78.6 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 librhash0 amd64 1.4.3-3 [134 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libuv1 amd64 1.44.2-1 [140 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 cmake-data all 3.25.1-1 [2026 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 cmake amd64 3.25.1-1 [8692 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 43 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 libglvnd0 amd64 1.6.0-1 [51.8 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2 [292 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2 [759 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libdrm-common all 2.4.114-1 [7112 B] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libdrm2 amd64 2.4.114-1+b1 [37.5 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libglapi-mesa amd64 22.3.6-1+deb12u1 [35.7 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 libx11-xcb1 amd64 2:1.8.4-2 [192 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri2-0 amd64 1.15-1 [107 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri3-0 amd64 1.15-1 [107 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libxcb-glx0 amd64 1.15-1 [122 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 libxcb-present0 amd64 1.15-1 [105 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 libxcb-randr0 amd64 1.15-1 [117 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libxcb-sync1 amd64 1.15-1 [109 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 libxcb-xfixes0 amd64 1.15-1 [109 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 libxfixes3 amd64 1:6.0.0-2 [22.7 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get: 71 http://deb.debian.org/debian bookworm/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 libdrm-amdgpu1 amd64 2.4.114-1+b1 [20.9 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 libpciaccess0 amd64 0.17-2 [51.4 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 libdrm-intel1 amd64 2.4.114-1+b1 [64.0 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 libdrm-nouveau2 amd64 2.4.114-1+b1 [19.1 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libdrm-radeon1 amd64 2.4.114-1+b1 [21.8 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 libz3-4 amd64 4.8.12-3.1 [7216 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 libllvm15 amd64 1:15.0.6-4+b1 [23.1 MB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 libsensors-config all 1:3.6.0-7.1 [14.3 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 libsensors5 amd64 1:3.6.0-7.1 [34.2 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 libgl1-mesa-dri amd64 22.3.6-1+deb12u1 [7239 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 libglx-mesa0 amd64 22.3.6-1+deb12u1 [147 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 libglx0 amd64 1.6.0-1 [34.4 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 libgl1 amd64 1.6.0-1 [88.4 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 libxi6 amd64 2:1.8-1+b1 [84.2 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 libglut3.12 amd64 3.4.0-1 [139 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 x11proto-dev all 2022.1-1 [599 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 libxau-dev amd64 1:1.0.9-1 [22.9 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 libxdmcp-dev amd64 1:1.1.2-3 [42.2 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 libpthread-stubs0-dev amd64 0.4-1 [5344 B] Get: 94 http://deb.debian.org/debian bookworm/main amd64 libxcb1-dev amd64 1.15-1 [181 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 libx11-dev amd64 2:1.8.4-2 [836 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 libglx-dev amd64 1.6.0-1 [15.3 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 libgl-dev amd64 1.6.0-1 [100 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 libglvnd-core-dev amd64 1.6.0-1 [12.9 kB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 libwayland-server0 amd64 1.21.0-1 [35.9 kB] Get: 100 http://deb.debian.org/debian bookworm/main amd64 libgbm1 amd64 22.3.6-1+deb12u1 [38.0 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 libwayland-client0 amd64 1.21.0-1 [28.3 kB] Get: 102 http://deb.debian.org/debian bookworm/main amd64 libegl-mesa0 amd64 22.3.6-1+deb12u1 [114 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 libegl1 amd64 1.6.0-1 [33.7 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 libegl-dev amd64 1.6.0-1 [19.1 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 libgles1 amd64 1.6.0-1 [11.7 kB] Get: 106 http://deb.debian.org/debian bookworm/main amd64 libgles2 amd64 1.6.0-1 [16.8 kB] Get: 107 http://deb.debian.org/debian bookworm/main amd64 libgles-dev amd64 1.6.0-1 [50.4 kB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 libopengl0 amd64 1.6.0-1 [30.6 kB] Get: 109 http://deb.debian.org/debian bookworm/main amd64 libopengl-dev amd64 1.6.0-1 [4936 B] Get: 110 http://deb.debian.org/debian bookworm/main amd64 libglvnd-dev amd64 1.6.0-1 [4692 B] Get: 111 http://deb.debian.org/debian bookworm/main amd64 libgl1-mesa-dev amd64 22.3.6-1+deb12u1 [14.5 kB] Get: 112 http://deb.debian.org/debian bookworm/main amd64 libglu1-mesa amd64 9.0.2-1.1 [178 kB] Get: 113 http://deb.debian.org/debian bookworm/main amd64 libglu1-mesa-dev amd64 9.0.2-1.1 [216 kB] Get: 114 http://deb.debian.org/debian bookworm/main amd64 libxext-dev amd64 2:1.3.4-1+b1 [107 kB] Get: 115 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 116 http://deb.debian.org/debian bookworm/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get: 117 http://deb.debian.org/debian bookworm/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get: 118 http://deb.debian.org/debian bookworm/main amd64 libxt6 amd64 1:1.2.1-1.1 [186 kB] Get: 119 http://deb.debian.org/debian bookworm/main amd64 libice-dev amd64 2:1.0.10-1 [67.1 kB] Get: 120 http://deb.debian.org/debian bookworm/main amd64 libsm-dev amd64 2:1.2.3-1 [38.0 kB] Get: 121 http://deb.debian.org/debian bookworm/main amd64 libxt-dev amd64 1:1.2.1-1.1 [405 kB] Get: 122 http://deb.debian.org/debian bookworm/main amd64 libglut-dev amd64 3.4.0-1 [163 kB] Get: 123 http://deb.debian.org/debian bookworm/main amd64 freeglut3-dev amd64 3.4.0-1 [53.1 kB] Get: 124 http://deb.debian.org/debian bookworm/main amd64 gemmi-dev amd64 0.5.7+ds-2+b1 [404 kB] Get: 125 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get: 126 http://deb.debian.org/debian bookworm/main amd64 libopenblas0-pthread amd64 0.3.21+ds-4 [6709 kB] Get: 127 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get: 128 http://deb.debian.org/debian bookworm/main amd64 libopenblas-pthread-dev amd64 0.3.21+ds-4 [4971 kB] Get: 129 http://deb.debian.org/debian bookworm/main amd64 liblapack-dev amd64 3.11.0-2 [4631 kB] Get: 130 http://deb.debian.org/debian bookworm/main amd64 libmmdb2-0 amd64 2.0.22-1 [338 kB] Get: 131 http://deb.debian.org/debian bookworm/main amd64 libmmdb2-dev amd64 2.0.22-1 [92.9 kB] Get: 132 http://deb.debian.org/debian bookworm/main amd64 libopenmm7.7 amd64 7.7.0+dfsg-9+b1 [856 kB] Get: 133 http://deb.debian.org/debian bookworm/main amd64 libopenmm-dev amd64 7.7.0+dfsg-9+b1 [327 kB] Get: 134 http://deb.debian.org/debian bookworm/main amd64 libxfixes-dev amd64 1:6.0.0-2 [24.7 kB] Get: 135 http://deb.debian.org/debian bookworm/main amd64 libxi-dev amd64 2:1.8-1+b1 [246 kB] Get: 136 http://deb.debian.org/debian bookworm/main amd64 libxmu6 amd64 2:1.1.3-3 [60.1 kB] Get: 137 http://deb.debian.org/debian bookworm/main amd64 libxmu-headers all 2:1.1.3-3 [68.5 kB] Get: 138 http://deb.debian.org/debian bookworm/main amd64 libxmu-dev amd64 2:1.1.3-3 [65.9 kB] Get: 139 http://deb.debian.org/debian bookworm/main amd64 libsimbody3.7 amd64 3.7+dfsg-3 [3230 kB] Get: 140 http://deb.debian.org/debian bookworm/main amd64 libsimbody-dev amd64 3.7+dfsg-3 [2727 kB] Get: 141 http://deb.debian.org/debian bookworm/main amd64 tao-pegtl-dev all 3.2.7-1 [69.4 kB] Get: 142 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Fetched 106 MB in 2s (63.6 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 ... 19591 files and directories currently installed.) Preparing to unpack .../000-libproc2-0_2%3a4.0.2-3_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../001-procps_2%3a4.0.2-3_amd64.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../003-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../004-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../005-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../006-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../007-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../008-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/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_3.1.0-2_source.changes dpkg-buildpackage: info: source package molmodel dpkg-buildpackage: info: source version 3.1.0-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys 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/molmodel-3.1.0' dh_auto_configure -- -DBUILD_EXAMPLES=OFF -DBUILD_TESTING=OFF cd obj-x86_64-linux-gnu && 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 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- 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 "1.2.13") -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Configuring done -- Generating done 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/molmodel-3.1.0/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/molmodel-3.1.0' dh_auto_build cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/molmodel-3.1.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/molmodel-3.1.0 -B/build/molmodel-3.1.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/molmodel-3.1.0/obj-x86_64-linux-gnu/CMakeFiles /build/molmodel-3.1.0/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/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/molmodel-3.1.0/obj-x86_64-linux-gnu' cd /build/molmodel-3.1.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/molmodel-3.1.0 /build/molmodel-3.1.0 /build/molmodel-3.1.0/obj-x86_64-linux-gnu /build/molmodel-3.1.0/obj-x86_64-linux-gnu /build/molmodel-3.1.0/obj-x86_64-linux-gnu/CMakeFiles/SimTKmolmodel.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/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/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/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/About.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/About.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/About.cpp.o -c /build/molmodel-3.1.0/src/About.cpp [ 6%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/BondGeometry.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/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/BondGeometry.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/BondGeometry.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/BondGeometry.cpp.o -c /build/molmodel-3.1.0/src/BondGeometry.cpp [ 9%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Biotype.cpp.o [ 12%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/AtomSubsystem.cpp.o [ 15%] 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/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/AtomSubsystem.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/AtomSubsystem.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/AtomSubsystem.cpp.o -c /build/molmodel-3.1.0/src/AtomSubsystem.cpp /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/Biotype.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/Biotype.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/Biotype.cpp.o -c /build/molmodel-3.1.0/src/Biotype.cpp /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/Compound.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/Compound.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/Compound.cpp.o -c /build/molmodel-3.1.0/src/Compound.cpp [ 18%] 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/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/CompoundSystem.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/CompoundSystem.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/CompoundSystem.cpp.o -c /build/molmodel-3.1.0/src/CompoundSystem.cpp [ 21%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/DuMMForceFieldSubsystem.cpp.o /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp [ 25%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Element.cpp.o [ 28%] 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/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/molmodel-3.1.0/src/Element.cpp /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -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/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.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/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/MolecularMechanicsSystem.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/MolecularMechanicsSystem.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/MolecularMechanicsSystem.cpp.o -c /build/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/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/PDBReader.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/PDBReader.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/PDBReader.cpp.o -c /build/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/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/Pdb.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/Pdb.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/Pdb.cpp.o -c /build/molmodel-3.1.0/src/Pdb.cpp [ 40%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/PeriodicVmdReporter.cpp.o /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/PeriodicVmdReporter.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/PeriodicVmdReporter.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/PeriodicVmdReporter.cpp.o -c /build/molmodel-3.1.0/src/PeriodicVmdReporter.cpp [ 43%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Representation.cpp.o /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/Representation.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/Representation.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/Representation.cpp.o -c /build/molmodel-3.1.0/src/Representation.cpp [ 46%] 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/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/TinkerAmber99.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/TinkerAmber99.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/TinkerAmber99.cpp.o -c /build/molmodel-3.1.0/src/TinkerAmber99.cpp [ 50%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/RiboseMobilizer.cpp.o /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/RiboseMobilizer.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/RiboseMobilizer.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/RiboseMobilizer.cpp.o -c /build/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/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/VanderWallSphere.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/VanderWallSphere.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/VanderWallSphere.cpp.o -c /build/molmodel-3.1.0/src/VanderWallSphere.cpp [ 56%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/VelocityRescalingThermostat.cpp.o /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/VelocityRescalingThermostat.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/VelocityRescalingThermostat.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/VelocityRescalingThermostat.cpp.o -c /build/molmodel-3.1.0/src/VelocityRescalingThermostat.cpp [ 59%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/VmdConnection.cpp.o /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/VmdConnection.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/VmdConnection.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/VmdConnection.cpp.o -c /build/molmodel-3.1.0/src/VmdConnection.cpp In file included from /build/molmodel-3.1.0/src/AtomSubsystem.cpp:1: /build/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++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, 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/molmodel-3.1.0/./include/molmodel/internal/AtomSubsystem.h:4: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/molmodel-3.1.0/src/gbsa/ObcParameters.h:28, from /build/molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:50, from /build/molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:40: /build/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /usr/include/c++/12/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/molmodel-3.1.0/./include/molmodel/internal/common.h:40, from /build/molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:38: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/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++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 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/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuImplicitSolvent.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuImplicitSolvent.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuImplicitSolvent.cpp.o -c /build/molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.cpp In file included from /build/molmodel-3.1.0/src/gbsa/ObcParameters.h:28, from /build/molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:50, from /build/molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:43: /build/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /usr/include/c++/12/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/molmodel-3.1.0/./include/molmodel/internal/common.h:40, from /build/molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:40: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/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++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 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/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuObc.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuObc.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuObc.cpp.o -c /build/molmodel-3.1.0/src/gbsa/CpuObc.cpp In file included from /build/molmodel-3.1.0/src/CompoundAtom.h:36, from /build/molmodel-3.1.0/src/CompoundRep.h:42, from /build/molmodel-3.1.0/src/CompoundSystem.cpp:3: /build/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++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, 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/molmodel-3.1.0/./include/molmodel/internal/CompoundSystem.h:4, from /build/molmodel-3.1.0/src/CompoundSystem.cpp:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 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/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/ImplicitSolventParameters.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/ImplicitSolventParameters.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/ImplicitSolventParameters.cpp.o -c /build/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/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/ObcParameters.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/ObcParameters.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/ObcParameters.cpp.o -c /build/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/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMCommon.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMCommon.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMCommon.cpp.o -c /build/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.cpp In file included from /build/molmodel-3.1.0/src/CompoundAtom.h:36, from /build/molmodel-3.1.0/src/CompoundRep.h:42, from /build/molmodel-3.1.0/src/Compound.cpp:45: /build/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++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, 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/molmodel-3.1.0/src/Compound.cpp:32: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/molmodel-3.1.0/src/gbsa/CpuObc.cpp:26: /build/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /usr/include/c++/12/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/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:28: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/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++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.cpp:25: /build/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /usr/include/c++/12/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/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:28: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/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++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/molmodel-3.1.0/src/gbsa/ImplicitSolventParameters.cpp:25: /build/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /usr/include/c++/12/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/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:28: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/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++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.cpp:25: /build/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /usr/include/c++/12/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/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:28: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/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++/12/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/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMLog.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMLog.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMLog.cpp.o -c /build/molmodel-3.1.0/src/gbsa/SimTKOpenMMLog.cpp In file included from /build/molmodel-3.1.0/src/gbsa/ObcParameters.h:28, from /build/molmodel-3.1.0/src/gbsa/ObcParameters.cpp:26: /build/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /usr/include/c++/12/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/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:28: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/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++/12/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/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMUtilities.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMUtilities.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMUtilities.cpp.o -c /build/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/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/cpuObcInterface.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/cpuObcInterface.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/cpuObcInterface.cpp.o -c /build/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/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/imd.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/imd.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/imd.cpp.o -c /build/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/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/vmdsock.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/vmdsock.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/vmdsock.cpp.o -c /build/molmodel-3.1.0/src/vmdsock.cpp In file included from /build/molmodel-3.1.0/src/gbsa/SimTKOpenMMLog.h:28, from /build/molmodel-3.1.0/src/gbsa/SimTKOpenMMLog.cpp:25: /build/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /usr/include/c++/12/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/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:28: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/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++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.h:30, from /build/molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:27: /build/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /usr/include/c++/12/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/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:28: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/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++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/molmodel-3.1.0/src/gbsa/SimTKOpenMMLog.h:28, from /build/molmodel-3.1.0/src/gbsa/cpuObcInterface.cpp:27: /build/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /usr/include/c++/12/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/molmodel-3.1.0/src/gbsa/cpuObcInterface.h:34, from /build/molmodel-3.1.0/src/gbsa/cpuObcInterface.cpp:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/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++/12/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/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/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/molmodel-3.1.0/obj-x86_64-linux-gnu' cd /build/molmodel-3.1.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/molmodel-3.1.0 /build/molmodel-3.1.0/OpenMMPlugin /build/molmodel-3.1.0/obj-x86_64-linux-gnu /build/molmodel-3.1.0/obj-x86_64-linux-gnu/OpenMMPlugin /build/molmodel-3.1.0/obj-x86_64-linux-gnu/OpenMMPlugin/CMakeFiles/OpenMMPlugin_shared.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/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/molmodel-3.1.0/obj-x86_64-linux-gnu' [ 96%] Building CXX object OpenMMPlugin/CMakeFiles/OpenMMPlugin_shared.dir/OpenMMPlugin.cpp.o cd /build/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/molmodel-3.1.0/src -I/build/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/molmodel-3.1.0/OpenMMPlugin/OpenMMPlugin.cpp In file included from /build/molmodel-3.1.0/src/gbsa/ObcParameters.h:28, from /build/molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:50, from /build/molmodel-3.1.0/OpenMMPlugin/OpenMMPlugin.cpp:43: /build/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /usr/include/c++/12/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/molmodel-3.1.0/OpenMMPlugin/OpenMMPlugin.cpp:41: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/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++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [100%] Linking CXX shared library libOpenMMPlugin.so cd /build/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/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/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/molmodel-3.1.0/obj-x86_64-linux-gnu' [100%] Built target OpenMMPlugin_shared make[2]: Leaving directory '/build/molmodel-3.1.0/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/molmodel-3.1.0/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/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 -j16 install DESTDIR=/build/molmodel-3.1.0/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/molmodel-3.1.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/molmodel-3.1.0 -B/build/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/molmodel-3.1.0/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/molmodel-3.1.0/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1 -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/doc/api/Molmodel/html -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/doc/MolmodelAPI.html -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/Molmodel.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/SimTKmolmodel.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/AtomSubsystem.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Biotype.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Clonable.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Compound.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/CompoundModeler.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/CompoundSystem.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/DNA.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/DuMMForceFieldSubsystem.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Element.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Exceptions.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/GrinPointer.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Ions.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Ligands.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Linkage.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/MassCenterMotionRemover.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/MolecularMechanicsSystem.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/NA.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/NoseHooverThermostat.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/PDBReader.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Pdb.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/PeriodicPdbWriter.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/PeriodicVmdReporter.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Protein.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/RNA.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/RiboseMobilizer.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Superpose.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/VanDerWaalsForce.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/VanderWallSphere.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/VelocityRescalingThermostat.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/VmdConnection.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/VoxelHash.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Water.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/bondGeometry.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/common.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/units.h -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/doc/MolmodelUsersGuide.pdf -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/molmodel/MolmodelConfig.cmake -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/molmodel/MolmodelConfigVersion.cmake -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/molmodel/MolmodelTargets.cmake -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/molmodel/MolmodelTargets-none.cmake -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/molmodel.pc -- Installing: /build/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/molmodel/plugins/libOpenMMPlugin.so -- Set runtime path of "/build/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/molmodel/plugins/libOpenMMPlugin.so" to "" make[1]: Leaving directory '/build/molmodel-3.1.0/obj-x86_64-linux-gnu' dh_install dh_installdocs dh_installchangelogs 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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libsimtkmolmodel3.1' in '../libsimtkmolmodel3.1_3.1.0-2_amd64.deb'. dpkg-deb: building package 'libsimtkmolmodel3.1-dbgsym' in '../libsimtkmolmodel3.1-dbgsym_3.1.0-2_amd64.deb'. dpkg-deb: building package 'libsimtkmolmodel-plugins-dbgsym' in '../libsimtkmolmodel-plugins-dbgsym_3.1.0-2_amd64.deb'. dpkg-deb: building package 'libsimtkmolmodel-dev' in '../libsimtkmolmodel-dev_3.1.0-2_amd64.deb'. dpkg-deb: building package 'libsimtkmolmodel-plugins' in '../libsimtkmolmodel-plugins_3.1.0-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../molmodel_3.1.0-2_amd64.buildinfo dpkg-genchanges --build=binary -O../molmodel_3.1.0-2_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/1711909 and its subdirectories I: Current time: Thu Jul 4 02:01:19 -12 2024 I: pbuilder-time-stamp: 1720101679 Fri Jun 2 07:38:18 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Fri Jun 2 07:38:18 UTC 2023 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Fri Jun 2 07:47:32 UTC 2023 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Fri Jun 2 07:47:33 UTC 2023 I: molmodel_3.1.0-2_amd64.changes: Format: 1.8 Date: Sun, 04 Dec 2022 03:39:42 -0500 Source: molmodel Binary: libsimtkmolmodel-dev libsimtkmolmodel-plugins libsimtkmolmodel-plugins-dbgsym libsimtkmolmodel3.1 libsimtkmolmodel3.1-dbgsym Architecture: amd64 Version: 3.1.0-2 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Andrius Merkys 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 libsimtkmolmodel3.1 - C++ API for creating molecular models for SimTK Changes: molmodel (3.1.0-2) unstable; urgency=medium . * libopenmm-dev is a strict dependency. Checksums-Sha1: a7d704e5b79f50f294773c916afb62370adb1a11 1863144 libsimtkmolmodel-dev_3.1.0-2_amd64.deb 6d72429ae8fc4e1f41ddd60d0e2a67fb8b361cfb 576316 libsimtkmolmodel-plugins-dbgsym_3.1.0-2_amd64.deb c7d6d41e1c029e84c3a6bc00e4f5a18759adf5a4 18884 libsimtkmolmodel-plugins_3.1.0-2_amd64.deb 7374146fc6c86e4eb8527cbc44d2a764a043af5e 13859660 libsimtkmolmodel3.1-dbgsym_3.1.0-2_amd64.deb 218af0d17c7cb6551c7ace262d30cf2e0803c965 675536 libsimtkmolmodel3.1_3.1.0-2_amd64.deb ab20be1080a6baf62590e45181faef04eb3b42e8 9578 molmodel_3.1.0-2_amd64.buildinfo Checksums-Sha256: 031c0bf607443caed60268d847b404df57da90dfe93bf11d93d79f9e80c8ce10 1863144 libsimtkmolmodel-dev_3.1.0-2_amd64.deb 65e6dc5802916bf6b1181adb2830ba5b7d09c76d0193cbbf6af9ccba3d8f3677 576316 libsimtkmolmodel-plugins-dbgsym_3.1.0-2_amd64.deb 951cd40425de00fbdd6d79bab0b92ce1121104f926fef48c4fe4ed3f81b4d5db 18884 libsimtkmolmodel-plugins_3.1.0-2_amd64.deb 74a7515efd1b679a738fd86b26c98d5bce8677489ab5f916d578e79ff505618e 13859660 libsimtkmolmodel3.1-dbgsym_3.1.0-2_amd64.deb e22fc636448e7c0202e04102b402e82dbffa8519eec442f5c9f5cc4c04efd6a7 675536 libsimtkmolmodel3.1_3.1.0-2_amd64.deb b3e0f70a2f5b7f10f2ace462df4031b9f2d943f82fb4ebd3689a766b38b67bcb 9578 molmodel_3.1.0-2_amd64.buildinfo Files: 9210cb5c9b6e33e4e458a7eb4d7c72c8 1863144 libdevel optional libsimtkmolmodel-dev_3.1.0-2_amd64.deb 751a4243d1579eebd33d6345e0ddeb67 576316 debug optional libsimtkmolmodel-plugins-dbgsym_3.1.0-2_amd64.deb 56c2f9193de237a41c9a4bc8e47d785e 18884 libs optional libsimtkmolmodel-plugins_3.1.0-2_amd64.deb beffb3e5e8f6562b9b696ba18f18f287 13859660 debug optional libsimtkmolmodel3.1-dbgsym_3.1.0-2_amd64.deb af2284b772bbe16e25661f69e02e1153 675536 libs optional libsimtkmolmodel3.1_3.1.0-2_amd64.deb 567e43d175241f572ed76e471d08abef 9578 libs optional molmodel_3.1.0-2_amd64.buildinfo Fri Jun 2 07:47:33 UTC 2023 I: diffoscope 242 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.XpsqAnvW/molmodel_3.1.0-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.XpsqAnvW/molmodel_3.1.0-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.XpsqAnvW/molmodel_3.1.0-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.XpsqAnvW/b1/molmodel_3.1.0-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.XpsqAnvW/b2/molmodel_3.1.0-2_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: 0.485s) 0.485s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.192s) 0.192s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Fri Jun 2 07:47:35 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists. Fri Jun 2 07:47:35 UTC 2023 I: molmodel from bookworm built successfully and reproducibly on amd64. Fri Jun 2 07:47:36 UTC 2023 I: Submitting .buildinfo files to external archives: Fri Jun 2 07:47:36 UTC 2023 I: Submitting 12K b1/molmodel_3.1.0-2_amd64.buildinfo.asc Fri Jun 2 07:47:36 UTC 2023 I: Submitting 12K b2/molmodel_3.1.0-2_amd64.buildinfo.asc Fri Jun 2 07:47:38 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Jun 2 07:47:38 UTC 2023 I: Done submitting .buildinfo files. Fri Jun 2 07:47:38 UTC 2023 I: Removing signed molmodel_3.1.0-2_amd64.buildinfo.asc files: removed './b1/molmodel_3.1.0-2_amd64.buildinfo.asc' removed './b2/molmodel_3.1.0-2_amd64.buildinfo.asc'