Sat Jun  1 10:09:04 UTC 2024  I: starting to build molmodel/unstable/amd64 on jenkins on '2024-06-01 10:08'
Sat Jun  1 10:09:04 UTC 2024  I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_26/8531/console.log
Sat Jun  1 10:09:04 UTC 2024  I: Downloading source for unstable/molmodel=3.1.0-4.1
--2024-06-01 10:09:04--  http://deb.debian.org/debian/pool/main/m/molmodel/molmodel_3.1.0-4.1.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2238 (2.2K) [text/prs.lines.tag]
Saving to: ‘molmodel_3.1.0-4.1.dsc’

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2024-06-01 10:09:04 (216 MB/s) - ‘molmodel_3.1.0-4.1.dsc’ saved [2238/2238]

Sat Jun  1 10:09:05 UTC 2024  I: molmodel_3.1.0-4.1.dsc
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Format: 3.0 (quilt)
Source: molmodel
Binary: libsimtkmolmodel-dev, libsimtkmolmodel3.1t64, libsimtkmolmodel-plugins
Architecture: any
Version: 3.1.0-4.1
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Uploaders:  Andrius Merkys <merkys@debian.org>,
Homepage: https://simtk.org/projects/molmodel
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/debichem-team/molmodel
Vcs-Git: https://salsa.debian.org/debichem-team/molmodel.git
Build-Depends: dpkg-dev (>= 1.22.5), cmake, debhelper-compat (= 13), gemmi-dev, libmmdb2-dev, libopenmm-dev, libopenblas-pthread-dev, libsimbody-dev, tao-pegtl-dev, zlib1g-dev
Package-List:
 libsimtkmolmodel-dev deb libdevel optional arch=any
 libsimtkmolmodel-plugins deb libs optional arch=any
 libsimtkmolmodel3.1t64 deb libs optional arch=any
Checksums-Sha1:
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 efaae5b5d6d58f308d09b977cac013b9be6b0920 4668 molmodel_3.1.0-4.1.debian.tar.xz
Checksums-Sha256:
 d9fef841ce0b5978a20c0fce77e7f74e2a360576388e564fbe84a15cb53fbedd 11118182 molmodel_3.1.0.orig.tar.gz
 9b7b272b68c31804fcc9363601d26d32b0f3d75d82df7dcfda0c8957c6694749 4668 molmodel_3.1.0-4.1.debian.tar.xz
Files:
 082b507dc0ac23db29b0984b28176c41 11118182 molmodel_3.1.0.orig.tar.gz
 5030a4382974e8ede80d8154f14cc268 4668 molmodel_3.1.0-4.1.debian.tar.xz

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Sat Jun  1 10:09:05 UTC 2024  I: Checking whether the package is not for us
Sat Jun  1 10:09:05 UTC 2024  I: Starting 1st build on remote node ionos5-amd64.debian.net.
Sat Jun  1 10:09:05 UTC 2024  I: Preparing to do remote build '1' on ionos5-amd64.debian.net.
Sat Jun  1 10:11:18 UTC 2024  I: Deleting $TMPDIR on ionos5-amd64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Fri May 31 22:09:06 -12 2024
I: pbuilder-time-stamp: 1717236546
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
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tar: ./build: time stamp 2025-07-04 02:07:12 is 34401484.954598601 s in the future
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tar: ./dev/full: time stamp 2025-07-04 02:06:52 is 34401464.953217945 s in the future
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tar: ./dev/tty: time stamp 2025-07-04 02:06:52 is 34401464.953052463 s in the future
tar: ./dev/random: time stamp 2025-07-04 02:06:52 is 34401464.95293581 s in the future
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tar: ./etc/apt/preferences.d/reproducible: time stamp 2025-07-04 02:07:44 is 34401516.946802705 s in the future
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tar: ./usr/lib/locale/tl_PH.utf8: time stamp 2025-07-04 02:07:20 is 34401486.65320086 s in the future
tar: ./usr/lib/locale/ar_LB.utf8/LC_MESSAGES: time stamp 2025-07-04 02:07:20 is 34401486.653165596 s in the future
tar: ./usr/lib/locale/ar_LB.utf8: time stamp 2025-07-04 02:07:20 is 34401486.653124177 s in the future
tar: ./usr/lib/locale/gl_ES: time stamp 2025-07-04 02:07:20 is 34401486.653083764 s in the future
tar: ./usr/lib/locale/ms_MY.utf8/LC_MESSAGES: time stamp 2025-07-04 02:07:20 is 34401486.653046774 s in the future
tar: ./usr/lib/locale/ms_MY.utf8: time stamp 2025-07-04 02:07:20 is 34401486.653005422 s in the future
tar: ./usr/lib/locale/mg_MG.utf8: time stamp 2025-07-04 02:07:20 is 34401486.652964674 s in the future
tar: ./usr/lib/locale/en_IE@euro/LC_MESSAGES: time stamp 2025-07-04 02:07:20 is 34401486.652928367 s in the future
tar: ./usr/lib/locale/en_IE@euro: time stamp 2025-07-04 02:07:20 is 34401486.652889182 s in the future
tar: ./usr/lib/locale/ar_SD/LC_MESSAGES: time stamp 2025-07-04 02:07:20 is 34401486.652847197 s in the future
tar: ./usr/lib/locale/ar_SD: time stamp 2025-07-04 02:07:20 is 34401486.652808363 s in the future
tar: ./usr/lib/locale/ar_JO/LC_MESSAGES: time stamp 2025-07-04 02:07:20 is 34401486.652776072 s in the future
tar: ./usr/lib/locale/ar_JO: time stamp 2025-07-04 02:07:20 is 34401486.652739727 s in the future
tar: ./usr/lib/locale/so_KE: time stamp 2025-07-04 02:07:20 is 34401486.65270249 s in the future
tar: ./usr/lib/locale/cmn_TW: time stamp 2025-07-04 02:07:20 is 34401486.652666525 s in the future
tar: ./usr/lib/locale/ms_MY/LC_MESSAGES: time stamp 2025-07-04 02:07:20 is 34401486.652627677 s in the future
tar: ./usr/lib/locale/ms_MY: time stamp 2025-07-04 02:07:20 is 34401486.652585939 s in the future
tar: ./usr/lib/locale/da_DK: time stamp 2025-07-04 02:07:20 is 34401486.652551329 s in the future
tar: ./usr/lib/locale/pa_IN: time stamp 2025-07-04 02:07:20 is 34401486.65251013 s in the future
tar: ./usr/lib/locale/ar_IN/LC_MESSAGES: time stamp 2025-07-04 02:07:20 is 34401486.65246959 s in the future
tar: ./usr/lib/locale/ar_IN: time stamp 2025-07-04 02:07:20 is 34401486.652433647 s in the future
tar: ./usr/lib/locale/pap_AW: time stamp 2025-07-04 02:07:20 is 34401486.652392155 s in the future
tar: ./usr/lib/locale/ha_NG: time stamp 2025-07-04 02:07:20 is 34401486.652352193 s in the future
tar: ./usr/lib/locale/ru_RU.cp1251: time stamp 2025-07-04 02:07:20 is 34401486.652321642 s in the future
tar: ./usr/lib/locale/gl_ES.utf8: time stamp 2025-07-04 02:07:20 is 34401486.652283219 s in the future
tar: ./usr/lib/locale/fr_LU@euro/LC_MESSAGES: time stamp 2025-07-04 02:07:20 is 34401486.652244635 s in the future
tar: ./usr/lib/locale/fr_LU@euro: time stamp 2025-07-04 02:07:20 is 34401486.652210646 s in the future
tar: ./usr/lib/locale/yi_US.utf8: time stamp 2025-07-04 02:07:20 is 34401486.65217472 s in the future
tar: ./usr/lib/locale/ru_RU.utf8: time stamp 2025-07-04 02:07:20 is 34401486.652138951 s in the future
tar: ./usr/lib/locale/yuw_PG: time stamp 2025-07-04 02:07:20 is 34401486.652103749 s in the future
tar: ./usr/lib/locale/uz_UZ: time stamp 2025-07-04 02:07:20 is 34401486.652066923 s in the future
tar: ./usr/lib/locale/nl_AW/LC_MESSAGES: time stamp 2025-07-04 02:07:20 is 34401486.652030221 s in the future
tar: ./usr/lib/locale/nl_AW: time stamp 2025-07-04 02:07:20 is 34401486.651996666 s in the future
tar: ./usr/lib/locale/ar_SD.utf8/LC_MESSAGES: time stamp 2025-07-04 02:07:20 is 34401486.65196019 s in the future
tar: ./usr/lib/locale/ar_SD.utf8: time stamp 2025-07-04 02:07:20 is 34401486.651926918 s in the future
tar: ./usr/lib/locale/fr_CA: time stamp 2025-07-04 02:07:20 is 34401486.651891915 s in the future
tar: ./usr/lib/locale/kl_GL.utf8: time stamp 2025-07-04 02:07:20 is 34401486.651856125 s in the future
tar: ./usr/lib/locale/cs_CZ: time stamp 2025-07-04 02:07:20 is 34401486.651821153 s in the future
tar: ./usr/lib/locale/eu_FR/LC_MESSAGES: time stamp 2025-07-04 02:07:20 is 34401486.65178535 s in the future
tar: ./usr/lib/locale/eu_FR: time stamp 2025-07-04 02:07:20 is 34401486.651750232 s in the future
tar: ./usr/lib/locale/am_ET: time stamp 2025-07-04 02:07:20 is 34401486.651714777 s in the future
tar: ./usr/lib/locale/ru_RU: time stamp 2025-07-04 02:07:20 is 34401486.651680258 s in the future
tar: ./usr/lib/locale/en_IE/LC_MESSAGES: time stamp 2025-07-04 02:07:20 is 34401486.651644586 s in the future
tar: ./usr/lib/locale/en_IE: time stamp 2025-07-04 02:07:20 is 34401486.651610103 s in the future
tar: ./usr/lib/locale/hsb_DE: time stamp 2025-07-04 02:07:20 is 34401486.651574988 s in the future
tar: ./usr/lib/locale: time stamp 2025-07-04 02:07:19 is 34401485.651540966 s in the future
tar: ./usr/lib/gold-ld: time stamp 2025-07-04 02:07:00 is 34401466.651507469 s in the future
tar: ./usr/lib/x86_64-linux-gnu/perl/cross-config-5.38.2: time stamp 2025-07-04 02:07:07 is 34401473.651460711 s in the future
tar: ./usr/lib/x86_64-linux-gnu/perl: time stamp 2025-07-04 02:07:07 is 34401473.651421438 s in the future
tar: ./usr/lib/x86_64-linux-gnu: time stamp 2025-07-04 02:07:16 is 34401482.651379645 s in the future
tar: ./usr/lib/apt/planners: time stamp 2025-07-04 02:07:00 is 34401466.651338336 s in the future
tar: ./usr/lib/apt: time stamp 2025-07-04 02:07:00 is 34401466.65130757 s in the future
tar: ./usr/lib/gcc/x86_64-linux-gnu/13: time stamp 2025-07-04 02:07:08 is 34401474.651250655 s in the future
tar: ./usr/lib/gcc/x86_64-linux-gnu: time stamp 2025-07-04 02:07:04 is 34401470.651212853 s in the future
tar: ./usr/lib/gcc: time stamp 2025-07-04 02:07:04 is 34401470.651180724 s in the future
tar: ./usr/lib/compat-ld: time stamp 2025-07-04 02:07:00 is 34401466.651139671 s in the future
tar: ./usr/lib: time stamp 2025-07-04 02:07:11 is 34401477.65110896 s in the future
tar: ./usr/bin: time stamp 2025-07-04 02:07:20 is 34401486.651067722 s in the future
tar: ./usr: time stamp 2025-07-04 02:06:52 is 34401458.651030178 s in the future
tar: ./etc/systemd/system/timers.target.wants: time stamp 2025-07-04 02:07:10 is 34401476.650976965 s in the future
tar: ./etc/systemd/system: time stamp 2025-07-04 02:06:52 is 34401458.650940069 s in the future
tar: ./etc/alternatives: time stamp 2025-07-04 02:07:20 is 34401486.650867164 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_3.1.0-4.1.dsc]
I: copying [./molmodel_3.1.0.orig.tar.gz]
I: copying [./molmodel_3.1.0-4.1.debian.tar.xz]
I: Extracting source
gpgv: Signature made Wed Feb 28 20:18:10 2024 
gpgv:                using RSA key A62D2CFBD50B9B5BF360D54B159EB5C4EFC8774C
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./molmodel_3.1.0-4.1.dsc: no acceptable signature found
dpkg-source: info: extracting molmodel in molmodel-3.1.0
dpkg-source: info: unpacking molmodel_3.1.0.orig.tar.gz
dpkg-source: info: unpacking molmodel_3.1.0-4.1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying drop-CMAKE_CXX_STANDARD.patch
dpkg-source: info: applying plugin_dir.patch
dpkg-source: info: applying f8492b9346dd8a2c32e3aa815294a3248b051d1f.patch
dpkg-source: info: applying 968a0af8bc1a224337a3d1e1bd2fec3aec9e3fa1.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/4117813/tmp/hooks/D02_print_environment starting
I: set
  BUILDDIR='/build/reproducible-path'
  BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
  BUILDUSERNAME='pbuilder1'
  BUILD_ARCH='amd64'
  DEBIAN_FRONTEND='noninteractive'
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 '
  DISTRIBUTION='unstable'
  HOME='/root'
  HOST_ARCH='amd64'
  IFS=' 	
  '
  INVOCATION_ID='4915c0519a934d84a376188ba2dd3098'
  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='4117813'
  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.BaYIv7lN/pbuilderrc_sNQO --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.BaYIv7lN/b1 --logfile b1/build.log molmodel_3.1.0-4.1.dsc'
  SUDO_GID='110'
  SUDO_UID='105'
  SUDO_USER='jenkins'
  TERM='unknown'
  TZ='/usr/share/zoneinfo/Etc/GMT+12'
  USER='root'
  _='/usr/bin/systemd-run'
  http_proxy='http://213.165.73.152:3128'
I: uname -a
  Linux ionos5-amd64 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 Jul  4  2025 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/4117813/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 <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
 This package was created automatically by pbuilder to satisfy the
 build-dependencies of the package being currently built.
Depends: dpkg-dev (>= 1.22.5), cmake, debhelper-compat (= 13), gemmi-dev, libmmdb2-dev, libopenmm-dev, libopenblas-pthread-dev, libsimbody-dev, tao-pegtl-dev, zlib1g-dev
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19719 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
 pbuilder-satisfydepends-dummy depends on cmake; however:
  Package cmake is not installed.
 pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
  Package debhelper-compat is not installed.
 pbuilder-satisfydepends-dummy depends on gemmi-dev; however:
  Package gemmi-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libmmdb2-dev; however:
  Package libmmdb2-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libopenmm-dev; however:
  Package libopenmm-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libopenblas-pthread-dev; however:
  Package libopenblas-pthread-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libsimbody-dev; however:
  Package libsimbody-dev is not installed.
 pbuilder-satisfydepends-dummy depends on tao-pegtl-dev; however:
  Package tao-pegtl-dev is not installed.
 pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
  Package zlib1g-dev is not installed.

Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
  autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} freeglut3-dev{a} gemmi-dev{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libbrotli1{a} libbsd0{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libegl-dev{a} libegl-mesa0{a} libegl1{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgbm1{a} libgfortran5{a} libgl-dev{a} libgl1{a} libgl1-mesa-dev{a} libgl1-mesa-dri{a} libglapi-mesa{a} libgles-dev{a} libgles1{a} libgles2{a} libglu1-mesa{a} libglu1-mesa-dev{a} libglut-dev{a} libglut3.12{a} libglvnd-core-dev{a} libglvnd-dev{a} libglvnd0{a} libglx-dev{a} libglx-mesa0{a} libglx0{a} libgssapi-krb5-2{a} libice-dev{a} libice6{a} libicu72{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-2.5-0{a} libllvm17t64{a} libmagic-mgc{a} libmagic1t64{a} libmmdb2-0{a} libmmdb2-dev{a} libnghttp2-14{a} libopenblas-pthread-dev{a} libopenblas0-pthread{a} libopengl-dev{a} libopengl0{a} libopenmm-dev{a} libopenmm8.1{a} libpciaccess0{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libsimbody-dev{a} libsimbody3.7{a} libsm-dev{a} libsm6{a} libssh2-1t64{a} libtool{a} libuchardet0{a} libuv1t64{a} libvulkan1{a} libwayland-client0{a} libwayland-server0{a} libx11-6{a} libx11-data{a} libx11-dev{a} libx11-xcb1{a} libxau-dev{a} libxau6{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxfixes-dev{a} libxfixes3{a} libxi-dev{a} libxi6{a} libxml2{a} libxmu-dev{a} libxmu-headers{a} libxmu6{a} libxshmfence1{a} libxt-dev{a} libxt6t64{a} libxxf86vm1{a} libz3-4{a} m4{a} man-db{a} po-debconf{a} procps{a} sensible-utils{a} tao-pegtl-dev{a} x11-common{a} x11proto-dev{a} xorg-sgml-doctools{a} xtrans-dev{a} zlib1g-dev{a} 
The following packages are RECOMMENDED but will NOT be installed:
  ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx mesa-vulkan-drivers psmisc publicsuffix wget 
0 packages upgraded, 146 newly installed, 0 to remove and 0 not upgraded.
Need to get 113 MB of archives. After unpacking 533 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB]
Get: 2 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-4 [880 kB]
Get: 3 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB]
Get: 4 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB]
Get: 5 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB]
Get: 6 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB]
Get: 7 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB]
Get: 8 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB]
Get: 9 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB]
Get: 10 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.1-4 [95.7 kB]
Get: 11 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB]
Get: 12 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB]
Get: 13 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB]
Get: 14 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB]
Get: 15 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 16 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get: 17 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB]
Get: 18 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB]
Get: 19 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-2 [670 kB]
Get: 20 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.2-2 [346 kB]
Get: 21 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB]
Get: 22 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB]
Get: 23 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB]
Get: 24 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB]
Get: 25 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B]
Get: 26 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB]
Get: 27 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB]
Get: 28 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB]
Get: 29 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB]
Get: 30 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB]
Get: 31 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB]
Get: 32 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB]
Get: 33 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB]
Get: 34 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-5 [215 kB]
Get: 35 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.8.0-1 [441 kB]
Get: 36 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB]
Get: 37 http://deb.debian.org/debian unstable/main amd64 libjsoncpp25 amd64 1.9.5-6+b2 [81.9 kB]
Get: 38 http://deb.debian.org/debian unstable/main amd64 librhash0 amd64 1.4.3-3+b1 [132 kB]
Get: 39 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-4 [148 kB]
Get: 40 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.29.3-1 [2167 kB]
Get: 41 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.29.3-1+b1 [10.7 MB]
Get: 42 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB]
Get: 43 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB]
Get: 44 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 45 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 46 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 47 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 48 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB]
Get: 49 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 50 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB]
Get: 51 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 52 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 53 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB]
Get: 54 http://deb.debian.org/debian unstable/main amd64 libglvnd0 amd64 1.7.0-1+b1 [56.3 kB]
Get: 55 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB]
Get: 56 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-1 [131 kB]
Get: 57 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB]
Get: 58 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2 [144 kB]
Get: 59 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.7-1 [328 kB]
Get: 60 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB]
Get: 61 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.120-2 [7688 B]
Get: 62 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB]
Get: 63 http://deb.debian.org/debian unstable/main amd64 libglapi-mesa amd64 24.1.0-2 [36.6 kB]
Get: 64 http://deb.debian.org/debian unstable/main amd64 libx11-xcb1 amd64 2:1.8.7-1+b1 [232 kB]
Get: 65 http://deb.debian.org/debian unstable/main amd64 libxcb-dri2-0 amd64 1.17.0-2 [106 kB]
Get: 66 http://deb.debian.org/debian unstable/main amd64 libxcb-dri3-0 amd64 1.17.0-2 [107 kB]
Get: 67 http://deb.debian.org/debian unstable/main amd64 libxcb-glx0 amd64 1.17.0-2 [122 kB]
Get: 68 http://deb.debian.org/debian unstable/main amd64 libxcb-present0 amd64 1.17.0-2 [105 kB]
Get: 69 http://deb.debian.org/debian unstable/main amd64 libxcb-randr0 amd64 1.17.0-2 [116 kB]
Get: 70 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2 [105 kB]
Get: 71 http://deb.debian.org/debian unstable/main amd64 libxcb-sync1 amd64 1.17.0-2 [108 kB]
Get: 72 http://deb.debian.org/debian unstable/main amd64 libxcb-xfixes0 amd64 1.17.0-2 [109 kB]
Get: 73 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB]
Get: 74 http://deb.debian.org/debian unstable/main amd64 libxfixes3 amd64 1:6.0.0-2+b1 [20.3 kB]
Get: 75 http://deb.debian.org/debian unstable/main amd64 libxshmfence1 amd64 1.3-1+b1 [8852 B]
Get: 76 http://deb.debian.org/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB]
Get: 77 http://deb.debian.org/debian unstable/main amd64 libvulkan1 amd64 1.3.283.0-1 [125 kB]
Get: 78 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB]
Get: 79 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB]
Get: 80 http://deb.debian.org/debian unstable/main amd64 libdrm-intel1 amd64 2.4.120-2 [62.7 kB]
Get: 81 http://deb.debian.org/debian unstable/main amd64 libdrm-radeon1 amd64 2.4.120-2 [22.2 kB]
Get: 82 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20240517-1 [93.3 kB]
Get: 83 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB]
Get: 84 http://deb.debian.org/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-12 [23.7 MB]
Get: 85 http://deb.debian.org/debian unstable/main amd64 libsensors-config all 1:3.6.0-9 [14.6 kB]
Get: 86 http://deb.debian.org/debian unstable/main amd64 libsensors5 amd64 1:3.6.0-9 [34.6 kB]
Get: 87 http://deb.debian.org/debian unstable/main amd64 libgl1-mesa-dri amd64 24.1.0-2 [8638 kB]
Get: 88 http://deb.debian.org/debian unstable/main amd64 libglx-mesa0 amd64 24.1.0-2 [151 kB]
Get: 89 http://deb.debian.org/debian unstable/main amd64 libglx0 amd64 1.7.0-1+b1 [35.0 kB]
Get: 90 http://deb.debian.org/debian unstable/main amd64 libgl1 amd64 1.7.0-1+b1 [89.8 kB]
Get: 91 http://deb.debian.org/debian unstable/main amd64 libxi6 amd64 2:1.8.1-1 [79.0 kB]
Get: 92 http://deb.debian.org/debian unstable/main amd64 libglut3.12 amd64 3.4.0-1+b1 [139 kB]
Get: 93 http://deb.debian.org/debian unstable/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB]
Get: 94 http://deb.debian.org/debian unstable/main amd64 x11proto-dev all 2024.1-1 [603 kB]
Get: 95 http://deb.debian.org/debian unstable/main amd64 libxau-dev amd64 1:1.0.9-1+b1 [21.3 kB]
Get: 96 http://deb.debian.org/debian unstable/main amd64 libxdmcp-dev amd64 1:1.1.2-3+b1 [40.8 kB]
Get: 97 http://deb.debian.org/debian unstable/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB]
Get: 98 http://deb.debian.org/debian unstable/main amd64 libxcb1-dev amd64 1.17.0-2 [181 kB]
Get: 99 http://deb.debian.org/debian unstable/main amd64 libx11-dev amd64 2:1.8.7-1+b1 [875 kB]
Get: 100 http://deb.debian.org/debian unstable/main amd64 libglx-dev amd64 1.7.0-1+b1 [15.8 kB]
Get: 101 http://deb.debian.org/debian unstable/main amd64 libgl-dev amd64 1.7.0-1+b1 [101 kB]
Get: 102 http://deb.debian.org/debian unstable/main amd64 libglvnd-core-dev amd64 1.7.0-1+b1 [13.4 kB]
Get: 103 http://deb.debian.org/debian unstable/main amd64 libwayland-server0 amd64 1.22.0-2.1+b1 [33.0 kB]
Get: 104 http://deb.debian.org/debian unstable/main amd64 libgbm1 amd64 24.1.0-2 [40.9 kB]
Get: 105 http://deb.debian.org/debian unstable/main amd64 libwayland-client0 amd64 1.22.0-2.1+b1 [25.7 kB]
Get: 106 http://deb.debian.org/debian unstable/main amd64 libegl-mesa0 amd64 24.1.0-2 [127 kB]
Get: 107 http://deb.debian.org/debian unstable/main amd64 libegl1 amd64 1.7.0-1+b1 [34.3 kB]
Get: 108 http://deb.debian.org/debian unstable/main amd64 libegl-dev amd64 1.7.0-1+b1 [19.5 kB]
Get: 109 http://deb.debian.org/debian unstable/main amd64 libgles1 amd64 1.7.0-1+b1 [12.2 kB]
Get: 110 http://deb.debian.org/debian unstable/main amd64 libgles2 amd64 1.7.0-1+b1 [17.3 kB]
Get: 111 http://deb.debian.org/debian unstable/main amd64 libgles-dev amd64 1.7.0-1+b1 [50.8 kB]
Get: 112 http://deb.debian.org/debian unstable/main amd64 libopengl0 amd64 1.7.0-1+b1 [31.1 kB]
Get: 113 http://deb.debian.org/debian unstable/main amd64 libopengl-dev amd64 1.7.0-1+b1 [5380 B]
Get: 114 http://deb.debian.org/debian unstable/main amd64 libglvnd-dev amd64 1.7.0-1+b1 [5144 B]
Get: 115 http://deb.debian.org/debian unstable/main amd64 libgl1-mesa-dev amd64 24.1.0-2 [17.2 kB]
Get: 116 http://deb.debian.org/debian unstable/main amd64 libglu1-mesa amd64 9.0.2-1.1+b1 [180 kB]
Get: 117 http://deb.debian.org/debian unstable/main amd64 libglu1-mesa-dev amd64 9.0.2-1.1+b1 [219 kB]
Get: 118 http://deb.debian.org/debian unstable/main amd64 libxext-dev amd64 2:1.3.4-1+b1 [107 kB]
Get: 119 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23 [252 kB]
Get: 120 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.0.10-1+b1 [56.7 kB]
Get: 121 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.3-1+b1 [33.6 kB]
Get: 122 http://deb.debian.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB]
Get: 123 http://deb.debian.org/debian unstable/main amd64 libice-dev amd64 2:1.0.10-1+b1 [64.8 kB]
Get: 124 http://deb.debian.org/debian unstable/main amd64 libsm-dev amd64 2:1.2.3-1+b1 [36.1 kB]
Get: 125 http://deb.debian.org/debian unstable/main amd64 libxt-dev amd64 1:1.2.1-1.2 [406 kB]
Get: 126 http://deb.debian.org/debian unstable/main amd64 libglut-dev amd64 3.4.0-1+b1 [163 kB]
Get: 127 http://deb.debian.org/debian unstable/main amd64 freeglut3-dev amd64 3.4.0-1+b1 [53.4 kB]
Get: 128 http://deb.debian.org/debian unstable/main amd64 gemmi-dev amd64 0.6.5+ds-1 [1138 kB]
Get: 129 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.1.0-1 [836 kB]
Get: 130 http://deb.debian.org/debian unstable/main amd64 libopenblas0-pthread amd64 0.3.27+ds-2 [6813 kB]
Get: 131 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB]
Get: 132 http://deb.debian.org/debian unstable/main amd64 libopenblas-pthread-dev amd64 0.3.27+ds-2 [4780 kB]
Get: 133 http://deb.debian.org/debian unstable/main amd64 liblapack-dev amd64 3.12.0-3 [4880 kB]
Get: 134 http://deb.debian.org/debian unstable/main amd64 libmmdb2-0 amd64 2.0.22-1+b1 [341 kB]
Get: 135 http://deb.debian.org/debian unstable/main amd64 libmmdb2-dev amd64 2.0.22-1+b1 [92.9 kB]
Get: 136 http://deb.debian.org/debian unstable/main amd64 libopenmm8.1 amd64 8.1.1+dfsg-1 [1034 kB]
Get: 137 http://deb.debian.org/debian unstable/main amd64 libopenmm-dev amd64 8.1.1+dfsg-1 [344 kB]
Get: 138 http://deb.debian.org/debian unstable/main amd64 libxfixes-dev amd64 1:6.0.0-2+b1 [22.3 kB]
Get: 139 http://deb.debian.org/debian unstable/main amd64 libxi-dev amd64 2:1.8.1-1 [241 kB]
Get: 140 http://deb.debian.org/debian unstable/main amd64 libxmu6 amd64 2:1.1.3-3+b2 [58.7 kB]
Get: 141 http://deb.debian.org/debian unstable/main amd64 libxmu-headers all 2:1.1.3-3 [68.5 kB]
Get: 142 http://deb.debian.org/debian unstable/main amd64 libxmu-dev amd64 2:1.1.3-3+b2 [65.1 kB]
Get: 143 http://deb.debian.org/debian unstable/main amd64 libsimbody3.7 amd64 3.7+dfsg-3 [3230 kB]
Get: 144 http://deb.debian.org/debian unstable/main amd64 libsimbody-dev amd64 3.7+dfsg-3 [2727 kB]
Get: 145 http://deb.debian.org/debian unstable/main amd64 tao-pegtl-dev all 3.2.7-1 [69.4 kB]
Get: 146 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB]
Fetched 113 MB in 4s (30.3 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libproc2-0:amd64.
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(Reading database ... 19719 files and directories currently installed.)
Preparing to unpack .../000-libproc2-0_2%3a4.0.4-4_amd64.deb ...
Unpacking libproc2-0:amd64 (2:4.0.4-4) ...
Selecting previously unselected package procps.
Preparing to unpack .../001-procps_2%3a4.0.4-4_amd64.deb ...
Unpacking procps (2:4.0.4-4) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../002-sensible-utils_0.0.22_all.deb ...
Unpacking sensible-utils (0.0.22) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../003-libmagic-mgc_1%3a5.45-3_amd64.deb ...
Unpacking libmagic-mgc (1:5.45-3) ...
Selecting previously unselected package libmagic1t64:amd64.
Preparing to unpack .../004-libmagic1t64_1%3a5.45-3_amd64.deb ...
Unpacking libmagic1t64:amd64 (1:5.45-3) ...
Selecting previously unselected package file.
Preparing to unpack .../005-file_1%3a5.45-3_amd64.deb ...
Unpacking file (1:5.45-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../006-gettext-base_0.21-14+b1_amd64.deb ...
Unpacking gettext-base (0.21-14+b1) ...
Selecting previously unselected package libuchardet0:amd64.
Preparing to unpack .../007-libuchardet0_0.0.8-1+b1_amd64.deb ...
Unpacking libuchardet0:amd64 (0.0.8-1+b1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../008-groff-base_1.23.0-4_amd64.deb ...
Unpacking groff-base (1.23.0-4) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../009-bsdextrautils_2.40.1-4_amd64.deb ...
Unpacking bsdextrautils (2.40.1-4) ...
Selecting previously unselected package libpipeline1:amd64.
Preparing to unpack .../010-libpipeline1_1.5.7-2_amd64.deb ...
Unpacking libpipeline1:amd64 (1.5.7-2) ...
Selecting previously unselected package man-db.
Preparing to unpack .../011-man-db_2.12.1-1_amd64.deb ...
Unpacking man-db (2.12.1-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../012-m4_1.4.19-4_amd64.deb ...
Unpacking m4 (1.4.19-4) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../013-autoconf_2.71-3_all.deb ...
Unpacking autoconf (2.71-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../014-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../015-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../016-autopoint_0.21-14_all.deb ...
Unpacking autopoint (0.21-14) ...
Selecting previously unselected package libicu72:amd64.
Preparing to unpack .../017-libicu72_72.1-4+b1_amd64.deb ...
Unpacking libicu72:amd64 (72.1-4+b1) ...
Selecting previously unselected package libxml2:amd64.
Preparing to unpack .../018-libxml2_2.12.7+dfsg-2_amd64.deb ...
Unpacking libxml2:amd64 (2.12.7+dfsg-2) ...
Selecting previously unselected package libarchive13t64:amd64.
Preparing to unpack .../019-libarchive13t64_3.7.2-2_amd64.deb ...
Unpacking libarchive13t64:amd64 (3.7.2-2) ...
Selecting previously unselected package libbrotli1:amd64.
Preparing to unpack .../020-libbrotli1_1.1.0-2+b3_amd64.deb ...
Unpacking libbrotli1:amd64 (1.1.0-2+b3) ...
Selecting previously unselected package libkrb5support0:amd64.
Preparing to unpack .../021-libkrb5support0_1.20.1-6+b1_amd64.deb ...
Unpacking libkrb5support0:amd64 (1.20.1-6+b1) ...
Selecting previously unselected package libcom-err2:amd64.
Preparing to unpack .../022-libcom-err2_1.47.1-1_amd64.deb ...
Unpacking libcom-err2:amd64 (1.47.1-1) ...
Selecting previously unselected package libk5crypto3:amd64.
Preparing to unpack .../023-libk5crypto3_1.20.1-6+b1_amd64.deb ...
Unpacking libk5crypto3:amd64 (1.20.1-6+b1) ...
Selecting previously unselected package libkeyutils1:amd64.
Preparing to unpack .../024-libkeyutils1_1.6.3-3_amd64.deb ...
Unpacking libkeyutils1:amd64 (1.6.3-3) ...
Selecting previously unselected package libkrb5-3:amd64.
Preparing to unpack .../025-libkrb5-3_1.20.1-6+b1_amd64.deb ...
Unpacking libkrb5-3:amd64 (1.20.1-6+b1) ...
Selecting previously unselected package libgssapi-krb5-2:amd64.
Preparing to unpack .../026-libgssapi-krb5-2_1.20.1-6+b1_amd64.deb ...
Unpacking libgssapi-krb5-2:amd64 (1.20.1-6+b1) ...
Selecting previously unselected package libsasl2-modules-db:amd64.
Preparing to unpack .../027-libsasl2-modules-db_2.1.28+dfsg1-6_amd64.deb ...
Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ...
Selecting previously unselected package libsasl2-2:amd64.
Preparing to unpack .../028-libsasl2-2_2.1.28+dfsg1-6_amd64.deb ...
Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-6) ...
Selecting previously unselected package libldap-2.5-0:amd64.
Preparing to unpack .../029-libldap-2.5-0_2.5.17+dfsg-1_amd64.deb ...
Unpacking libldap-2.5-0:amd64 (2.5.17+dfsg-1) ...
Selecting previously unselected package libnghttp2-14:amd64.
Preparing to unpack .../030-libnghttp2-14_1.61.0-1+b1_amd64.deb ...
Unpacking libnghttp2-14:amd64 (1.61.0-1+b1) ...
Selecting previously unselected package libpsl5t64:amd64.
Preparing to unpack .../031-libpsl5t64_0.21.2-1.1_amd64.deb ...
Unpacking libpsl5t64:amd64 (0.21.2-1.1) ...
Selecting previously unselected package librtmp1:amd64.
Preparing to unpack .../032-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_amd64.deb ...
Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ...
Selecting previously unselected package libssh2-1t64:amd64.
Preparing to unpack .../033-libssh2-1t64_1.11.0-5_amd64.deb ...
Unpacking libssh2-1t64:amd64 (1.11.0-5) ...
Selecting previously unselected package libcurl4t64:amd64.
Preparing to unpack .../034-libcurl4t64_8.8.0-1_amd64.deb ...
Unpacking libcurl4t64:amd64 (8.8.0-1) ...
Selecting previously unselected package libexpat1:amd64.
Preparing to unpack .../035-libexpat1_2.6.2-1_amd64.deb ...
Unpacking libexpat1:amd64 (2.6.2-1) ...
Selecting previously unselected package libjsoncpp25:amd64.
Preparing to unpack .../036-libjsoncpp25_1.9.5-6+b2_amd64.deb ...
Unpacking libjsoncpp25:amd64 (1.9.5-6+b2) ...
Selecting previously unselected package librhash0:amd64.
Preparing to unpack .../037-librhash0_1.4.3-3+b1_amd64.deb ...
Unpacking librhash0:amd64 (1.4.3-3+b1) ...
Selecting previously unselected package libuv1t64:amd64.
Preparing to unpack .../038-libuv1t64_1.48.0-4_amd64.deb ...
Unpacking libuv1t64:amd64 (1.48.0-4) ...
Selecting previously unselected package cmake-data.
Preparing to unpack .../039-cmake-data_3.29.3-1_all.deb ...
Unpacking cmake-data (3.29.3-1) ...
Selecting previously unselected package cmake.
Preparing to unpack .../040-cmake_3.29.3-1+b1_amd64.deb ...
Unpacking cmake (3.29.3-1+b1) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../041-libdebhelper-perl_13.15.3_all.deb ...
Unpacking libdebhelper-perl (13.15.3) ...
Selecting previously unselected package libtool.
Preparing to unpack .../042-libtool_2.4.7-7_all.deb ...
Unpacking libtool (2.4.7-7) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../043-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../044-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../045-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../046-dh-strip-nondeterminism_1.14.0-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.14.0-1) ...
Selecting previously unselected package libelf1t64:amd64.
Preparing to unpack .../047-libelf1t64_0.191-1+b1_amd64.deb ...
Unpacking libelf1t64:amd64 (0.191-1+b1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../048-dwz_0.15-1+b1_amd64.deb ...
Unpacking dwz (0.15-1+b1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../049-gettext_0.21-14+b1_amd64.deb ...
Unpacking gettext (0.21-14+b1) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../050-intltool-debian_0.35.0+20060710.6_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.6) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../051-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../052-debhelper_13.15.3_all.deb ...
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dpkg-buildpackage: info: source package molmodel
dpkg-buildpackage: info: source version 3.1.0-4.1
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dpkg-buildpackage: info: source changed by Benjamin Drung <bdrung@debian.org>
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[ 34%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Pdb.cpp.o
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/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/CompoundSystem.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/CompoundSystem.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/CompoundSystem.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/CompoundSystem.cpp
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/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/DuMMForceFieldSubsystemRep.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/DuMMForceFieldSubsystemRep.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/DuMMForceFieldSubsystemRep.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp
[ 37%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/PDBReader.cpp.o
/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/Element.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/Element.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/Element.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/Element.cpp
/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/MolecularMechanicsSystem.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/MolecularMechanicsSystem.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/MolecularMechanicsSystem.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/MolecularMechanicsSystem.cpp
[ 40%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/PeriodicVmdReporter.cpp.o
/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/Pdb.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/Pdb.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/Pdb.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/Pdb.cpp
[ 43%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Representation.cpp.o
/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/PDBReader.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/PDBReader.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/PDBReader.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/PDBReader.cpp
[ 46%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/RiboseMobilizer.cpp.o
/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/PeriodicVmdReporter.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/PeriodicVmdReporter.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/PeriodicVmdReporter.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/PeriodicVmdReporter.cpp
/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/Representation.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/Representation.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/Representation.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/Representation.cpp
/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/RiboseMobilizer.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/RiboseMobilizer.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/RiboseMobilizer.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/RiboseMobilizer.cpp
[ 50%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/VanderWallSphere.cpp.o
[ 56%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/VmdConnection.cpp.o
/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/VanderWallSphere.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/VanderWallSphere.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/VanderWallSphere.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/VanderWallSphere.cpp
[ 56%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/VelocityRescalingThermostat.cpp.o
[ 59%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuObc.cpp.o
[ 65%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuImplicitSolvent.cpp.o
[ 65%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/ImplicitSolventParameters.cpp.o
/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/VelocityRescalingThermostat.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/VelocityRescalingThermostat.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/VelocityRescalingThermostat.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/VelocityRescalingThermostat.cpp
[ 68%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/TinkerAmber99.cpp.o
/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/TinkerAmber99.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/TinkerAmber99.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/TinkerAmber99.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/TinkerAmber99.cpp
[ 71%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/ObcParameters.cpp.o
/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/VmdConnection.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/VmdConnection.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/VmdConnection.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/VmdConnection.cpp
[ 75%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMCommon.cpp.o
[ 78%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMLog.cpp.o
/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuImplicitSolvent.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuImplicitSolvent.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuImplicitSolvent.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.cpp
[ 81%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMUtilities.cpp.o
/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuObc.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuObc.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuObc.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/gbsa/CpuObc.cpp
/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/ImplicitSolventParameters.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/ImplicitSolventParameters.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/ImplicitSolventParameters.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/gbsa/ImplicitSolventParameters.cpp
[ 84%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/cpuObcInterface.cpp.o
/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/ObcParameters.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/ObcParameters.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/ObcParameters.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/gbsa/ObcParameters.cpp
/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMCommon.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMCommon.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMCommon.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.cpp
/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMLog.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMLog.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMLog.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMLog.cpp
[ 87%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/imd.cpp.o
/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMUtilities.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMUtilities.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMUtilities.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp
/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/cpuObcInterface.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/cpuObcInterface.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/cpuObcInterface.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/gbsa/cpuObcInterface.cpp
/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/imd.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/imd.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/imd.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/imd.cpp
[ 90%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/vmdsock.cpp.o
/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/vmdsock.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/vmdsock.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/vmdsock.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/vmdsock.cpp
In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.h:30,
                 from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:27:
/build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > {
      |                                               ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49,
                 from /usr/include/c++/13/bits/locale_classes.h:40,
                 from /usr/include/c++/13/bits/ios_base.h:41,
                 from /usr/include/c++/13/ios:44,
                 from /usr/include/c++/13/istream:40,
                 from /usr/include/c++/13/sstream:40,
                 from /usr/include/c++/13/complex:45,
                 from /usr/include/simbody/SimTKcommon/internal/common.h:257,
                 from /usr/include/simbody/SimTKcommon/basics.h:38,
                 from /usr/include/simbody/SimTKcommon.h:32,
                 from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:28:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
/build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:172:44: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  172 | class StringComparisonForMap : public std::binary_function< const std::string&, const std::string&, bool > {
      |                                            ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/ImplicitSolventParameters.cpp:25:
/build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > {
      |                                               ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49,
                 from /usr/include/c++/13/bits/locale_classes.h:40,
                 from /usr/include/c++/13/bits/ios_base.h:41,
                 from /usr/include/c++/13/ios:44,
                 from /usr/include/c++/13/istream:40,
                 from /usr/include/c++/13/sstream:40,
                 from /usr/include/c++/13/complex:45,
                 from /usr/include/simbody/SimTKcommon/internal/common.h:257,
                 from /usr/include/simbody/SimTKcommon/basics.h:38,
                 from /usr/include/simbody/SimTKcommon.h:32,
                 from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:28:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
/build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:172:44: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  172 | class StringComparisonForMap : public std::binary_function< const std::string&, const std::string&, bool > {
      |                                            ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/CpuObc.cpp:26:
/build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > {
      |                                               ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49,
                 from /usr/include/c++/13/bits/locale_classes.h:40,
                 from /usr/include/c++/13/bits/ios_base.h:41,
                 from /usr/include/c++/13/ios:44,
                 from /usr/include/c++/13/istream:40,
                 from /usr/include/c++/13/sstream:40,
                 from /usr/include/c++/13/complex:45,
                 from /usr/include/simbody/SimTKcommon/internal/common.h:257,
                 from /usr/include/simbody/SimTKcommon/basics.h:38,
                 from /usr/include/simbody/SimTKcommon.h:32,
                 from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:28:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
/build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:172:44: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  172 | class StringComparisonForMap : public std::binary_function< const std::string&, const std::string&, bool > {
      |                                            ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMLog.h:28,
                 from /build/reproducible-path/molmodel-3.1.0/src/gbsa/cpuObcInterface.cpp:27:
/build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > {
      |                                               ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49,
                 from /usr/include/c++/13/bits/locale_classes.h:40,
                 from /usr/include/c++/13/bits/ios_base.h:41,
                 from /usr/include/c++/13/ios:44,
                 from /usr/include/c++/13/istream:40,
                 from /usr/include/c++/13/sstream:40,
                 from /usr/include/c++/13/complex:45,
                 from /usr/include/simbody/SimTKcommon/internal/common.h:257,
                 from /usr/include/simbody/SimTKcommon/basics.h:38,
                 from /usr/include/simbody/SimTKcommon.h:32,
                 from /build/reproducible-path/molmodel-3.1.0/src/gbsa/cpuObcInterface.h:34,
                 from /build/reproducible-path/molmodel-3.1.0/src/gbsa/cpuObcInterface.cpp:25:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
/build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:172:44: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  172 | class StringComparisonForMap : public std::binary_function< const std::string&, const std::string&, bool > {
      |                                            ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMLog.h:28,
                 from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMLog.cpp:25:
/build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > {
      |                                               ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49,
                 from /usr/include/c++/13/bits/locale_classes.h:40,
                 from /usr/include/c++/13/bits/ios_base.h:41,
                 from /usr/include/c++/13/ios:44,
                 from /usr/include/c++/13/istream:40,
                 from /usr/include/c++/13/sstream:40,
                 from /usr/include/c++/13/complex:45,
                 from /usr/include/simbody/SimTKcommon/internal/common.h:257,
                 from /usr/include/simbody/SimTKcommon/basics.h:38,
                 from /usr/include/simbody/SimTKcommon.h:32,
                 from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:28:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
/build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:172:44: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  172 | class StringComparisonForMap : public std::binary_function< const std::string&, const std::string&, bool > {
      |                                            ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.cpp:25:
/build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > {
      |                                               ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49,
                 from /usr/include/c++/13/bits/locale_classes.h:40,
                 from /usr/include/c++/13/bits/ios_base.h:41,
                 from /usr/include/c++/13/ios:44,
                 from /usr/include/c++/13/istream:40,
                 from /usr/include/c++/13/sstream:40,
                 from /usr/include/c++/13/complex:45,
                 from /usr/include/simbody/SimTKcommon/internal/common.h:257,
                 from /usr/include/simbody/SimTKcommon/basics.h:38,
                 from /usr/include/simbody/SimTKcommon.h:32,
                 from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:28:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
/build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:172:44: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  172 | class StringComparisonForMap : public std::binary_function< const std::string&, const std::string&, bool > {
      |                                            ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/ObcParameters.h:28,
                 from /build/reproducible-path/molmodel-3.1.0/src/gbsa/ObcParameters.cpp:26:
/build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > {
      |                                               ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49,
                 from /usr/include/c++/13/bits/locale_classes.h:40,
                 from /usr/include/c++/13/bits/ios_base.h:41,
                 from /usr/include/c++/13/ios:44,
                 from /usr/include/c++/13/istream:40,
                 from /usr/include/c++/13/sstream:40,
                 from /usr/include/c++/13/complex:45,
                 from /usr/include/simbody/SimTKcommon/internal/common.h:257,
                 from /usr/include/simbody/SimTKcommon/basics.h:38,
                 from /usr/include/simbody/SimTKcommon.h:32,
                 from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:28:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
/build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:172:44: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  172 | class StringComparisonForMap : public std::binary_function< const std::string&, const std::string&, bool > {
      |                                            ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.cpp:25:
/build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > {
      |                                               ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49,
                 from /usr/include/c++/13/bits/locale_classes.h:40,
                 from /usr/include/c++/13/bits/ios_base.h:41,
                 from /usr/include/c++/13/ios:44,
                 from /usr/include/c++/13/istream:40,
                 from /usr/include/c++/13/sstream:40,
                 from /usr/include/c++/13/complex:45,
                 from /usr/include/simbody/SimTKcommon/internal/common.h:257,
                 from /usr/include/simbody/SimTKcommon/basics.h:38,
                 from /usr/include/simbody/SimTKcommon.h:32,
                 from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:28:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
/build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:172:44: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  172 | class StringComparisonForMap : public std::binary_function< const std::string&, const std::string&, bool > {
      |                                            ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/ObcParameters.h:28,
                 from /build/reproducible-path/molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:50,
                 from /build/reproducible-path/molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:40:
/build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > {
      |                                               ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49,
                 from /usr/include/c++/13/bits/locale_classes.h:40,
                 from /usr/include/c++/13/bits/ios_base.h:41,
                 from /usr/include/c++/13/ios:44,
                 from /usr/include/c++/13/istream:40,
                 from /usr/include/c++/13/sstream:40,
                 from /usr/include/c++/13/complex:45,
                 from /usr/include/simbody/SimTKcommon/internal/common.h:257,
                 from /usr/include/simbody/SimTKcommon/basics.h:38,
                 from /usr/include/simbody/SimTKcommon.h:32,
                 from /build/reproducible-path/molmodel-3.1.0/./include/molmodel/internal/common.h:40,
                 from /build/reproducible-path/molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:38:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
/build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:172:44: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  172 | class StringComparisonForMap : public std::binary_function< const std::string&, const std::string&, bool > {
      |                                            ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/ObcParameters.h:28,
                 from /build/reproducible-path/molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:50,
                 from /build/reproducible-path/molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:43:
/build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > {
      |                                               ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49,
                 from /usr/include/c++/13/bits/locale_classes.h:40,
                 from /usr/include/c++/13/bits/ios_base.h:41,
                 from /usr/include/c++/13/ios:44,
                 from /usr/include/c++/13/istream:40,
                 from /usr/include/c++/13/sstream:40,
                 from /usr/include/c++/13/complex:45,
                 from /usr/include/simbody/SimTKcommon/internal/common.h:257,
                 from /usr/include/simbody/SimTKcommon/basics.h:38,
                 from /usr/include/simbody/SimTKcommon.h:32,
                 from /build/reproducible-path/molmodel-3.1.0/./include/molmodel/internal/common.h:40,
                 from /build/reproducible-path/molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:40:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
/build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:172:44: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  172 | class StringComparisonForMap : public std::binary_function< const std::string&, const std::string&, bool > {
      |                                            ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/molmodel-3.1.0/src/AtomSubsystem.cpp:1:
/build/reproducible-path/molmodel-3.1.0/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  180 |         : public std::iterator<std::forward_iterator_tag, std::pair<AtomSubsystem::AtomIndex, AtomSubsystem::AtomIndex> >
      |                       ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/bits/specfun.h:43,
                 from /usr/include/c++/13/cmath:3699,
                 from /usr/include/simbody/SimTKcommon/internal/common.h:255,
                 from /usr/include/simbody/SimTKcommon/basics.h:38,
                 from /usr/include/simbody/SimTKcommon.h:32,
                 from /usr/include/simbody/SimTKsimbody.h:43,
                 from /build/reproducible-path/molmodel-3.1.0/./include/molmodel/internal/AtomSubsystem.h:4:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from /build/reproducible-path/molmodel-3.1.0/src/CompoundAtom.h:36,
                 from /build/reproducible-path/molmodel-3.1.0/src/CompoundRep.h:42,
                 from /build/reproducible-path/molmodel-3.1.0/src/CompoundSystem.cpp:3:
/build/reproducible-path/molmodel-3.1.0/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  180 |         : public std::iterator<std::forward_iterator_tag, std::pair<AtomSubsystem::AtomIndex, AtomSubsystem::AtomIndex> >
      |                       ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/bits/specfun.h:43,
                 from /usr/include/c++/13/cmath:3699,
                 from /usr/include/simbody/SimTKcommon/internal/common.h:255,
                 from /usr/include/simbody/SimTKcommon/basics.h:38,
                 from /usr/include/simbody/SimTKcommon.h:32,
                 from /usr/include/simbody/SimTKsimbody.h:43,
                 from /build/reproducible-path/molmodel-3.1.0/./include/molmodel/internal/CompoundSystem.h:4,
                 from /build/reproducible-path/molmodel-3.1.0/src/CompoundSystem.cpp:1:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from /build/reproducible-path/molmodel-3.1.0/src/CompoundAtom.h:36,
                 from /build/reproducible-path/molmodel-3.1.0/src/CompoundRep.h:42,
                 from /build/reproducible-path/molmodel-3.1.0/src/Compound.cpp:45:
/build/reproducible-path/molmodel-3.1.0/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  180 |         : public std::iterator<std::forward_iterator_tag, std::pair<AtomSubsystem::AtomIndex, AtomSubsystem::AtomIndex> >
      |                       ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/bits/specfun.h:43,
                 from /usr/include/c++/13/cmath:3699,
                 from /usr/include/simbody/SimTKcommon/internal/common.h:255,
                 from /usr/include/simbody/SimTKcommon/basics.h:38,
                 from /usr/include/simbody/SimTKcommon.h:32,
                 from /usr/include/simbody/SimTKsimbody.h:43,
                 from /build/reproducible-path/molmodel-3.1.0/src/Compound.cpp:32:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
[ 93%] Linking CXX shared library libSimTKmolmodel.so
/usr/bin/cmake -E cmake_link_script CMakeFiles/SimTKmolmodel.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -shared -Wl,-soname,libSimTKmolmodel.so.3.1 -o libSimTKmolmodel.so.3.1 CMakeFiles/SimTKmolmodel.dir/src/About.cpp.o CMakeFiles/SimTKmolmodel.dir/src/AtomSubsystem.cpp.o CMakeFiles/SimTKmolmodel.dir/src/Biotype.cpp.o CMakeFiles/SimTKmolmodel.dir/src/BondGeometry.cpp.o CMakeFiles/SimTKmolmodel.dir/src/Compound.cpp.o CMakeFiles/SimTKmolmodel.dir/src/CompoundSystem.cpp.o CMakeFiles/SimTKmolmodel.dir/src/DuMMForceFieldSubsystem.cpp.o CMakeFiles/SimTKmolmodel.dir/src/DuMMForceFieldSubsystemRep.cpp.o CMakeFiles/SimTKmolmodel.dir/src/Element.cpp.o CMakeFiles/SimTKmolmodel.dir/src/MolecularMechanicsSystem.cpp.o CMakeFiles/SimTKmolmodel.dir/src/PDBReader.cpp.o CMakeFiles/SimTKmolmodel.dir/src/Pdb.cpp.o CMakeFiles/SimTKmolmodel.dir/src/PeriodicVmdReporter.cpp.o CMakeFiles/SimTKmolmodel.dir/src/Representation.cpp.o CMakeFiles/SimTKmolmodel.dir/src/RiboseMobilizer.cpp.o CMakeFiles/SimTKmolmodel.dir/src/TinkerAmber99.cpp.o CMakeFiles/SimTKmolmodel.dir/src/VanderWallSphere.cpp.o CMakeFiles/SimTKmolmodel.dir/src/VelocityRescalingThermostat.cpp.o CMakeFiles/SimTKmolmodel.dir/src/VmdConnection.cpp.o CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuImplicitSolvent.cpp.o CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuObc.cpp.o CMakeFiles/SimTKmolmodel.dir/src/gbsa/ImplicitSolventParameters.cpp.o CMakeFiles/SimTKmolmodel.dir/src/gbsa/ObcParameters.cpp.o CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMCommon.cpp.o CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMLog.cpp.o CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMUtilities.cpp.o CMakeFiles/SimTKmolmodel.dir/src/gbsa/cpuObcInterface.cpp.o CMakeFiles/SimTKmolmodel.dir/src/imd.cpp.o CMakeFiles/SimTKmolmodel.dir/src/vmdsock.cpp.o  /usr/lib/x86_64-linux-gnu/libSimTKsimbody.so.3.7 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libSimTKmath.so.3.7 /usr/lib/x86_64-linux-gnu/libSimTKcommon.so.3.7 /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lpthread -lrt -ldl -lm
/usr/bin/cmake -E cmake_symlink_library libSimTKmolmodel.so.3.1 libSimTKmolmodel.so.3.1 libSimTKmolmodel.so
make[3]: Leaving directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu'
[ 93%] Built target SimTKmolmodel
make  -f OpenMMPlugin/CMakeFiles/OpenMMPlugin_shared.dir/build.make OpenMMPlugin/CMakeFiles/OpenMMPlugin_shared.dir/depend
make[3]: Entering directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu'
cd /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/molmodel-3.1.0 /build/reproducible-path/molmodel-3.1.0/OpenMMPlugin /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu/OpenMMPlugin /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu/OpenMMPlugin/CMakeFiles/OpenMMPlugin_shared.dir/DependInfo.cmake "--color="
make[3]: Leaving directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu'
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make[3]: Entering directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu'
[ 96%] Building CXX object OpenMMPlugin/CMakeFiles/OpenMMPlugin_shared.dir/OpenMMPlugin.cpp.o
cd /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu/OpenMMPlugin && /usr/bin/c++ -DOpenMMPlugin_shared_EXPORTS -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT OpenMMPlugin/CMakeFiles/OpenMMPlugin_shared.dir/OpenMMPlugin.cpp.o -MF CMakeFiles/OpenMMPlugin_shared.dir/OpenMMPlugin.cpp.o.d -o CMakeFiles/OpenMMPlugin_shared.dir/OpenMMPlugin.cpp.o -c /build/reproducible-path/molmodel-3.1.0/OpenMMPlugin/OpenMMPlugin.cpp
In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/ObcParameters.h:28,
                 from /build/reproducible-path/molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:50,
                 from /build/reproducible-path/molmodel-3.1.0/OpenMMPlugin/OpenMMPlugin.cpp:43:
/build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > {
      |                                               ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49,
                 from /usr/include/c++/13/bits/locale_classes.h:40,
                 from /usr/include/c++/13/bits/ios_base.h:41,
                 from /usr/include/c++/13/ios:44,
                 from /usr/include/c++/13/istream:40,
                 from /usr/include/c++/13/sstream:40,
                 from /usr/include/c++/13/complex:45,
                 from /usr/include/simbody/SimTKcommon/internal/common.h:257,
                 from /usr/include/simbody/SimTKcommon/basics.h:38,
                 from /usr/include/simbody/SimTKcommon.h:32,
                 from /build/reproducible-path/molmodel-3.1.0/OpenMMPlugin/OpenMMPlugin.cpp:41:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
/build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:172:44: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  172 | class StringComparisonForMap : public std::binary_function< const std::string&, const std::string&, bool > {
      |                                            ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
[100%] Linking CXX shared library libOpenMMPlugin.so
cd /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu/OpenMMPlugin && /usr/bin/cmake -E cmake_link_script CMakeFiles/OpenMMPlugin_shared.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -shared -Wl,-soname,libOpenMMPlugin.so -o libOpenMMPlugin.so CMakeFiles/OpenMMPlugin_shared.dir/OpenMMPlugin.cpp.o  -Wl,-rpath,/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu: ../libSimTKmolmodel.so.3.1 /usr/lib/x86_64-linux-gnu/libSimTKsimbody.so.3.7 /usr/lib/x86_64-linux-gnu/libOpenMM.so /usr/lib/x86_64-linux-gnu/libSimTKmath.so.3.7 /usr/lib/x86_64-linux-gnu/libSimTKcommon.so.3.7 /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lpthread -lrt -ldl -lm
make[3]: Leaving directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu'
[100%] Built target OpenMMPlugin_shared
make[2]: Leaving directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu'
/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu/CMakeFiles 0
make[1]: Leaving directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu'
   dh_auto_test
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   dh_prep
   dh_auto_install
	cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/molmodel-3.1.0/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu'
/usr/bin/cmake -S/build/reproducible-path/molmodel-3.1.0 -B/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
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make[2]: Nothing to be done for 'preinstall'.
make[2]: Leaving directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/doc/api/Molmodel/html
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/doc/MolmodelAPI.html
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/Molmodel.h
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/SimTKmolmodel.h
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/AtomSubsystem.h
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Biotype.h
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Clonable.h
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Compound.h
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/CompoundModeler.h
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/CompoundSystem.h
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/DNA.h
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/DuMMForceFieldSubsystem.h
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Element.h
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Exceptions.h
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/GrinPointer.h
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-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Linkage.h
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/MassCenterMotionRemover.h
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-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/PDBReader.h
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-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/PeriodicPdbWriter.h
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/PeriodicVmdReporter.h
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Protein.h
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/RNA.h
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/RiboseMobilizer.h
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Superpose.h
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/VanDerWaalsForce.h
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/VanderWallSphere.h
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/VelocityRescalingThermostat.h
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/VmdConnection.h
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/VoxelHash.h
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/Water.h
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/bondGeometry.h
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/common.h
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/include/molmodel/molmodel/internal/units.h
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/doc/MolmodelUsersGuide.pdf
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/molmodel/MolmodelConfig.cmake
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/molmodel/MolmodelConfigVersion.cmake
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/molmodel/MolmodelTargets.cmake
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/molmodel/MolmodelTargets-none.cmake
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/molmodel.pc
-- Installing: /build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/molmodel/plugins/libOpenMMPlugin.so
-- Set non-toolchain portion of runtime path of "/build/reproducible-path/molmodel-3.1.0/debian/tmp/usr/lib/x86_64-linux-gnu/molmodel/plugins/libOpenMMPlugin.so" to ""
make[1]: Leaving directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu'
   dh_install
   dh_installdocs
   dh_installchangelogs
   dh_lintian
   dh_perl
   dh_link
   dh_strip_nondeterminism
   dh_compress
   dh_fixperms
   dh_missing
   dh_dwz -a
   dh_strip -a
   dh_makeshlibs -a
   dh_shlibdeps -a
dpkg-shlibdeps: warning: symbol _ZN5gemmi12MaybeGzippedD1Ev used by debian/libsimtkmolmodel3.1t64/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries
dpkg-shlibdeps: warning: symbol _ZN5gemmi8GzStream4getsEPci used by debian/libsimtkmolmodel3.1t64/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries
dpkg-shlibdeps: warning: symbol _ZN5gemmi25make_structure_from_blockERKNS_3cif5BlockE used by debian/libsimtkmolmodel3.1t64/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries
dpkg-shlibdeps: warning: symbol _ZN5gemmi12MaybeGzipped24get_uncompressing_streamEv used by debian/libsimtkmolmodel3.1t64/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries
dpkg-shlibdeps: warning: symbol _ZN5gemmi12MaybeGzippedC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE used by debian/libsimtkmolmodel3.1t64/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries
dpkg-shlibdeps: warning: symbol _ZN5gemmi16assign_subchainsERNS_9StructureEbb used by debian/libsimtkmolmodel3.1t64/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries
dpkg-shlibdeps: warning: symbol _ZN5gemmi19remove_entity_typesERNS_9StructureE used by debian/libsimtkmolmodel3.1t64/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries
dpkg-shlibdeps: warning: symbol _ZN5gemmi12MaybeGzipped22uncompress_into_bufferEm used by debian/libsimtkmolmodel3.1t64/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries
dpkg-shlibdeps: warning: symbol _ZN5gemmi8GzStream4getcEv used by debian/libsimtkmolmodel3.1t64/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries
dpkg-shlibdeps: warning: symbol _ZN5gemmi15change_ccd_codeERNS_9StructureERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_ used by debian/libsimtkmolmodel3.1t64/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries
   dh_installdeb
   dh_gencontrol
   dh_md5sums
   dh_builddeb
dpkg-deb: building package 'libsimtkmolmodel-dev' in '../libsimtkmolmodel-dev_3.1.0-4.1_amd64.deb'.
dpkg-deb: building package 'libsimtkmolmodel3.1t64' in '../libsimtkmolmodel3.1t64_3.1.0-4.1_amd64.deb'.
dpkg-deb: building package 'libsimtkmolmodel3.1t64-dbgsym' in '../libsimtkmolmodel3.1t64-dbgsym_3.1.0-4.1_amd64.deb'.
dpkg-deb: building package 'libsimtkmolmodel-plugins' in '../libsimtkmolmodel-plugins_3.1.0-4.1_amd64.deb'.
dpkg-deb: building package 'libsimtkmolmodel-plugins-dbgsym' in '../libsimtkmolmodel-plugins-dbgsym_3.1.0-4.1_amd64.deb'.
 dpkg-genbuildinfo --build=binary -O../molmodel_3.1.0-4.1_amd64.buildinfo
 dpkg-genchanges --build=binary -O../molmodel_3.1.0-4.1_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env 
I: removing directory /srv/workspace/pbuilder/4117813 and its subdirectories
I: Current time: Fri Jul  4 04:34:17 -12 2025
I: pbuilder-time-stamp: 1751646857
Sat Jun  1 10:11:18 UTC 2024  I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net.
Sat Jun  1 10:11:18 UTC 2024  I: Preparing to do remote build '2' on ionos1-amd64.debian.net.
Sat Jun  1 10:21:50 UTC 2024  I: Deleting $TMPDIR on ionos1-amd64.debian.net.
Sat Jun  1 10:21:50 UTC 2024  I: molmodel_3.1.0-4.1_amd64.changes:
Format: 1.8
Date: Wed, 28 Feb 2024 20:17:19 +0000
Source: molmodel
Binary: libsimtkmolmodel-dev libsimtkmolmodel-plugins libsimtkmolmodel-plugins-dbgsym libsimtkmolmodel3.1t64 libsimtkmolmodel3.1t64-dbgsym
Architecture: amd64
Version: 3.1.0-4.1
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Changed-By: Benjamin Drung <bdrung@debian.org>
Description:
 libsimtkmolmodel-dev - C++ API for creating molecular models for SimTK (development file
 libsimtkmolmodel-plugins - Plugins for C++ API for creating molecular models for SimTK
 libsimtkmolmodel3.1t64 - C++ API for creating molecular models for SimTK
Closes: 1062945
Changes:
 molmodel (3.1.0-4.1) unstable; urgency=medium
 .
   * Non-maintainer upload.
   * Rename libraries for 64-bit time_t transition.  Closes: #1062945
Checksums-Sha1:
 691cd8bf09c6cfab80895c92b04cb00bc7f87e00 1863396 libsimtkmolmodel-dev_3.1.0-4.1_amd64.deb
 a7ea511372eb6863c563f280a542c6b92cd2493f 572392 libsimtkmolmodel-plugins-dbgsym_3.1.0-4.1_amd64.deb
 3eac73224eddefaa16f575222356afe81ad0118c 19760 libsimtkmolmodel-plugins_3.1.0-4.1_amd64.deb
 736cf3bd913a4ec84beee4b900b8ff7a269f8f85 13302664 libsimtkmolmodel3.1t64-dbgsym_3.1.0-4.1_amd64.deb
 6cd87b1a8edba04facd19f96430b60574d8fc1d2 669072 libsimtkmolmodel3.1t64_3.1.0-4.1_amd64.deb
 a0b4c70c0670370752a47a83c13bcd36d8cc5e02 9764 molmodel_3.1.0-4.1_amd64.buildinfo
Checksums-Sha256:
 caa22b333029a9e5b6b731e637cf4a2ba2b5a98f93b1f0441a8b19087c9c1903 1863396 libsimtkmolmodel-dev_3.1.0-4.1_amd64.deb
 ba75027ba989ad893c172a91a3af70fd56b1ecd1e6e85c2656ee7b529f364990 572392 libsimtkmolmodel-plugins-dbgsym_3.1.0-4.1_amd64.deb
 ce20f6f0bbf5e27fcd1a8086e30f1d1756e22d97372df3016f31470df172ef72 19760 libsimtkmolmodel-plugins_3.1.0-4.1_amd64.deb
 37ece5a6073759f6ff00278d2f622450674d734cd80b7e35557fc822d8b180f2 13302664 libsimtkmolmodel3.1t64-dbgsym_3.1.0-4.1_amd64.deb
 e052d7e64e389b4d511aa2fd2e65b75ffbbace2acfafaabd23853fee4e0c3e8f 669072 libsimtkmolmodel3.1t64_3.1.0-4.1_amd64.deb
 421824dea63de8ea1ee8c5a011b524cbd346d442aadd74febc1dc68570400785 9764 molmodel_3.1.0-4.1_amd64.buildinfo
Files:
 8fb77ce8508bf743c1a92433c418159b 1863396 libdevel optional libsimtkmolmodel-dev_3.1.0-4.1_amd64.deb
 5d439c8b47551c101abfa9d9ab8d5319 572392 debug optional libsimtkmolmodel-plugins-dbgsym_3.1.0-4.1_amd64.deb
 e0551aec948dabd2274635af226361ef 19760 libs optional libsimtkmolmodel-plugins_3.1.0-4.1_amd64.deb
 7bffe64a3972d551de9dc25f578d4237 13302664 debug optional libsimtkmolmodel3.1t64-dbgsym_3.1.0-4.1_amd64.deb
 499b2842a96967008a034e53bae4f5ed 669072 libs optional libsimtkmolmodel3.1t64_3.1.0-4.1_amd64.deb
 4300311178f4dc9beb4281a0c17bd87d 9764 libs optional molmodel_3.1.0-4.1_amd64.buildinfo
Sat Jun  1 10:21:52 UTC 2024  I: diffoscope 268 will be used to compare the two builds:
Running as unit: rb-diffoscope-amd64_26-8531.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.BaYIv7lN/molmodel_3.1.0-4.1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.BaYIv7lN/molmodel_3.1.0-4.1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.BaYIv7lN/molmodel_3.1.0-4.1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.BaYIv7lN/b1/molmodel_3.1.0-4.1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.BaYIv7lN/b2/molmodel_3.1.0-4.1_amd64.changes

## command (total time: 0.000s)
       0.000s      1 call     cmp (internal)

## has_same_content_as (total time: 0.000s)
       0.000s      1 call     abc.DotChangesFile

## main (total time: 0.527s)
       0.527s      2 calls    outputs
       0.000s      1 call     cleanup

## recognizes (total time: 0.188s)
       0.188s     12 calls    diffoscope.comparators.binary.FilesystemFile

## specialize (total time: 0.000s)
       0.000s      1 call     specialize
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 858ms
CPU time consumed: 859ms
Sat Jun  1 10:21:53 UTC 2024  I: diffoscope 268 found no differences in the changes files, and a .buildinfo file also exists.
Sat Jun  1 10:21:53 UTC 2024  I: molmodel from unstable built successfully and reproducibly on amd64.
Sat Jun  1 10:21:54 UTC 2024  I: Submitting .buildinfo files to external archives:
Sat Jun  1 10:21:54 UTC 2024  I: Submitting 12K	b1/molmodel_3.1.0-4.1_amd64.buildinfo.asc
Sat Jun  1 10:21:55 UTC 2024  I: Submitting 12K	b2/molmodel_3.1.0-4.1_amd64.buildinfo.asc
Sat Jun  1 10:21:56 UTC 2024  I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sat Jun  1 10:21:56 UTC 2024  I: Done submitting .buildinfo files.
Sat Jun  1 10:21:56 UTC 2024  I: Removing signed molmodel_3.1.0-4.1_amd64.buildinfo.asc files:
removed './b1/molmodel_3.1.0-4.1_amd64.buildinfo.asc'
removed './b2/molmodel_3.1.0-4.1_amd64.buildinfo.asc'