Sat Apr 29 13:14:33 UTC 2023 I: starting to build macromoleculebuilder/bullseye/amd64 on jenkins on '2023-04-29 13:14' Sat Apr 29 13:14:33 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_22/10751/console.log Sat Apr 29 13:14:33 UTC 2023 I: Downloading source for bullseye/macromoleculebuilder=3.2+dfsg-2+deb11u1 --2023-04-29 13:14:34-- http://cdn-fastly.deb.debian.org/debian/pool/main/m/macromoleculebuilder/macromoleculebuilder_3.2%2bdfsg-2%2bdeb11u1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2379 (2.3K) [text/prs.lines.tag] Saving to: ‘macromoleculebuilder_3.2+dfsg-2+deb11u1.dsc’ 0K .. 100% 281M=0s 2023-04-29 13:14:34 (281 MB/s) - ‘macromoleculebuilder_3.2+dfsg-2+deb11u1.dsc’ saved [2379/2379] Sat Apr 29 13:14:34 UTC 2023 I: macromoleculebuilder_3.2+dfsg-2+deb11u1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: macromoleculebuilder Binary: libmmblib-dev, libmmblib3.2, mmb, mmb-common Architecture: any all Version: 3.2+dfsg-2+deb11u1 Maintainer: Debichem Team Uploaders: Andrius Merkys , Homepage: https://simtk.org/projects/rnatoolbox Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/debichem-team/macromoleculebuilder Vcs-Git: https://salsa.debian.org/debichem-team/macromoleculebuilder.git Build-Depends: asciidoc-base, cmake, debhelper-compat (= 12), docbook-xml, docbook-xsl, libopenmm-dev, libseqan2-dev, libsimbody-dev, libsimtkmolmodel-dev Package-List: libmmblib-dev deb libdevel optional arch=any libmmblib3.2 deb libs optional arch=any mmb deb science optional arch=any mmb-common deb science optional arch=all Checksums-Sha1: 88b9198cf490b04d9a779feaa40b2234f350fee7 2473540 macromoleculebuilder_3.2+dfsg.orig.tar.xz f5c87d53358997a38807aee0f36bc21596a47f5f 3100 macromoleculebuilder_3.2+dfsg-2+deb11u1.debian.tar.xz Checksums-Sha256: ad75992e77a844a2bb17db59cad0eb3119d3018cb737c9d855b734705d0e0a8a 2473540 macromoleculebuilder_3.2+dfsg.orig.tar.xz 918d6483e9d2ca5d1c136b62be9ba433c79594030cb180d419ad39d513de9ddc 3100 macromoleculebuilder_3.2+dfsg-2+deb11u1.debian.tar.xz Files: 3513a98bf6abc5507654af253a412a7c 2473540 macromoleculebuilder_3.2+dfsg.orig.tar.xz 8e2f70588dcffbcae5ba645f33d70827 3100 macromoleculebuilder_3.2+dfsg-2+deb11u1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEdyKS9veshfrgQdQe5fQ/nCc08ocFAmO7u0QSHG1lcmt5c0Bk ZWJpYW4ub3JnAAoJEOX0P5wnNPKH8PgP/26ZSOs7jRgLS2dad8g6eGRjYlmbaeGx KxFOBl4J+kCXtE4xiX0z4u90W2lE1h+z7BQjkCESMkq3LjqIgJbdHymkNCHqI/02 WnP2YGUhORQq4h9kL+vMZ3uksjiRUCcwGqD7k5H4Bw2wiNd131gHNcsiKUsiVmqs 082bJkm67kKJoW+Bc3emtxtxL72NFOaAqHDTCbQltM6QJ2V2mBnx5g9xVSgCPKUp K3eECqR7/wsYWbOac8ItvoMrwB5Hu5UX2RCHBIjCSB/n7yosRxpg5ov9n1KkqEkV KcKUI6Wn0e2nYZJdOeIPl2KoOxP3rdTIDaj+UiNh/z697I7hgv5yGEEy7cinxasx 7nbo+/DI2EawiwbTy74UuxLIOsGJms03Fe2D45/rgjkO0ObCUQcd+MfKqfG2vdW1 GXaH4z4DypV2lvJyyZ9NtxADPTqmhRnckKWw9/zj147I93abc8Ix48EWIKqnUPfU TO+bVkTJMbE68rX+J3J1m2TA2BwR4/7c/rBAp2VngdS4w//SgqpPJmdNmTBOCmNc lxtq6aeUeAnTWwY1IQeLuiI9SvrsKc7XRsjoZZtHTCA4jMubT9hQL9JORSO/8lXJ ZojoUz/c+SekybIaXfk5zQw/z7u6atQJrxZ3ql4RNhbvwOI0oOhvCJRwTdOqLMXn +GK/OMtkDMGd =86kH -----END PGP SIGNATURE----- Sat Apr 29 13:14:34 UTC 2023 I: Checking whether the package is not for us Sat Apr 29 13:14:34 UTC 2023 I: Starting 1st build on remote node ionos5-amd64.debian.net. Sat Apr 29 13:14:34 UTC 2023 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Sat Apr 29 13:16:46 UTC 2023 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri May 31 07:37:36 -12 2024 I: pbuilder-time-stamp: 1717184256 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [macromoleculebuilder_3.2+dfsg-2+deb11u1.dsc] I: copying [./macromoleculebuilder_3.2+dfsg.orig.tar.xz] I: copying [./macromoleculebuilder_3.2+dfsg-2+deb11u1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.7DTfRfTT/trustedkeys.kbx': General error gpgv: Signature made Sun Jan 8 18:59:16 2023 -12 gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 gpgv: issuer "merkys@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./macromoleculebuilder_3.2+dfsg-2+deb11u1.dsc dpkg-source: info: extracting macromoleculebuilder in macromoleculebuilder-3.2+dfsg dpkg-source: info: unpacking macromoleculebuilder_3.2+dfsg.orig.tar.xz dpkg-source: info: unpacking macromoleculebuilder_3.2+dfsg-2+deb11u1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4106802/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16' DISTRIBUTION='bullseye' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='373716bb6c384ddebbf2255e813882f8' 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='4106802' 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.mSmvXjLf/pbuilderrc_lrEy --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.mSmvXjLf/b1 --logfile b1/build.log macromoleculebuilder_3.2+dfsg-2+deb11u1.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://85.184.249.68:3128' I: uname -a Linux ionos5-amd64 6.1.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 23 2020 date -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd -rwxr-xr-x 1 root root 93936 Sep 23 2020 df -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir -rwxr-xr-x 1 root root 84440 Jan 20 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Jan 24 2023 egrep -rwxr-xr-x 1 root root 39680 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 69032 Jan 20 2022 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98048 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls -rwxr-xr-x 1 root root 149736 Jan 20 2022 lsblk -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 59632 Jan 20 2022 more -rwsr-xr-x 1 root root 55528 Jan 20 2022 mount -rwxr-xr-x 1 root root 18664 Jan 20 2022 mountpoint -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 May 23 03:55 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty -rwsr-xr-x 1 root root 71912 Jan 20 2022 su -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch -rwxr-xr-x 1 root root 39680 Sep 23 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jan 20 2022 umount -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63744 Jan 20 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 5898 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8049 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/4106802/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: asciidoc-base, cmake, debhelper-compat (= 12), docbook-xml, docbook-xsl, libopenmm-dev, libseqan2-dev, libsimbody-dev, libsimtkmolmodel-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 ... 19707 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 asciidoc-base; however: Package asciidoc-base is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 12); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on docbook-xml; however: Package docbook-xml is not installed. pbuilder-satisfydepends-dummy depends on docbook-xsl; however: Package docbook-xsl is not installed. pbuilder-satisfydepends-dummy depends on libopenmm-dev; however: Package libopenmm-dev is not installed. pbuilder-satisfydepends-dummy depends on libseqan2-dev; however: Package libseqan2-dev is not installed. pbuilder-satisfydepends-dummy depends on libsimbody-dev; however: Package libsimbody-dev is not installed. pbuilder-satisfydepends-dummy depends on libsimtkmolmodel-dev; however: Package libsimtkmolmodel-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: asciidoc-base{a} asciidoc-common{a} 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} docbook-xml{a} docbook-xsl{a} dwz{a} file{a} freeglut3{a} freeglut3-dev{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libblas-dev{a} libblas3{a} libbrotli1{a} libbsd0{a} libcurl4{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libegl-dev{a} libegl-mesa0{a} libegl1{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgbm1{a} libgfortran5{a} libgl-dev{a} libgl1{a} libgl1-mesa-dev{a} libgl1-mesa-dri{a} libglapi-mesa{a} libgles-dev{a} libgles1{a} libgles2{a} libglu1-mesa{a} libglu1-mesa-dev{a} libglvnd-dev{a} libglvnd0{a} libglx-dev{a} libglx-mesa0{a} libglx0{a} libice-dev{a} libice6{a} libicu67{a} libjsoncpp24{a} liblapack-dev{a} liblapack3{a} libldap-2.4-2{a} libllvm11{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libmmdb2-0{a} libmpdec3{a} libncurses6{a} libnghttp2-14{a} libopengl-dev{a} libopengl0{a} libopenmm-dev{a} libopenmm7.5{a} libpciaccess0{a} libpipeline1{a} libprocps8{a} libpsl5{a} libpthread-stubs0-dev{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libseqan2-dev{a} libsigsegv2{a} libsimbody-dev{a} libsimbody3.6{a} libsimtkmolmodel-dev{a} libsimtkmolmodel3.0{a} libsm-dev{a} libsm6{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libuv1{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-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcb1-dev{a} libxdamage1{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxfixes-dev{a} libxfixes3{a} libxi-dev{a} libxi6{a} libxml2{a} libxml2-utils{a} libxmu-dev{a} libxmu-headers{a} libxmu6{a} libxshmfence1{a} libxslt1.1{a} libxt-dev{a} libxt6{a} libxxf86vm1{a} libz3-4{a} m4{a} man-db{a} media-types{a} po-debconf{a} procps{a} python3{a} python3-minimal{a} python3.9{a} python3.9-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sgml-data{a} x11-common{a} x11proto-dev{a} x11proto-input-dev{a} x11proto-xext-dev{a} xml-core{a} xorg-sgml-doctools{a} xsltproc{a} xtrans-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx mesa-vulkan-drivers psmisc publicsuffix wget xmlto 0 packages upgraded, 166 newly installed, 0 to remove and 0 not upgraded. Need to get 97.3 MB of archives. After unpacking 405 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8+deb11u1 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 sgml-base all 1.30 [15.1 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2+deb11u1 [102 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 libprocps8 amd64 2:3.3.17-5 [63.9 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 procps amd64 2:3.3.17-5 [502 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 asciidoc-common all 9.0.0~rc2-1 [286 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 libxml2-utils amd64 2.9.10+dfsg-6.7+deb11u4 [109 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 libxslt1.1 amd64 1.1.34-4+deb11u1 [240 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 xsltproc amd64 1.1.34-4+deb11u1 [124 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 asciidoc-base all 9.0.0~rc2-1 [135 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 cmake-data all 3.18.4-2+deb11u1 [1725 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libarchive13 amd64 3.4.3-2+deb11u1 [343 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1+deb11u1 [69.1 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1+deb11u1 [106 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3+deb11u1 [232 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 libcurl4 amd64 7.74.0-1.3+deb11u7 [346 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 libjsoncpp24 amd64 1.9.4-4 [78.9 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 librhash0 amd64 1.4.1-2 [129 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 libuv1 amd64 1.40.0-2 [132 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 cmake amd64 3.18.4-2+deb11u1 [5593 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get: 69 http://deb.debian.org/debian bullseye/main amd64 sgml-data all 2.0.11+nmu1 [179 kB] Get: 70 http://deb.debian.org/debian bullseye/main amd64 docbook-xml all 4.5-9 [84.4 kB] Get: 71 http://deb.debian.org/debian bullseye/main amd64 docbook-xsl all 1.79.2+dfsg-1 [1237 kB] Get: 72 http://deb.debian.org/debian bullseye/main amd64 libglvnd0 amd64 1.3.2-1 [53.6 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get: 75 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1 [108 kB] Get: 76 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 77 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get: 78 http://deb.debian.org/debian bullseye/main amd64 libx11-data all 2:1.7.2-1 [311 kB] Get: 79 http://deb.debian.org/debian bullseye/main amd64 libx11-6 amd64 2:1.7.2-1 [772 kB] Get: 80 http://deb.debian.org/debian bullseye/main amd64 libdrm-common all 2.4.104-1 [14.9 kB] Get: 81 http://deb.debian.org/debian bullseye/main amd64 libdrm2 amd64 2.4.104-1 [41.5 kB] Get: 82 http://deb.debian.org/debian bullseye/main amd64 libglapi-mesa amd64 20.3.5-1 [71.7 kB] Get: 83 http://deb.debian.org/debian bullseye/main amd64 libx11-xcb1 amd64 2:1.7.2-1 [203 kB] Get: 84 http://deb.debian.org/debian bullseye/main amd64 libxcb-dri2-0 amd64 1.14-3 [103 kB] Get: 85 http://deb.debian.org/debian bullseye/main amd64 libxcb-dri3-0 amd64 1.14-3 [102 kB] Get: 86 http://deb.debian.org/debian bullseye/main amd64 libxcb-glx0 amd64 1.14-3 [118 kB] Get: 87 http://deb.debian.org/debian bullseye/main amd64 libxcb-present0 amd64 1.14-3 [101 kB] Get: 88 http://deb.debian.org/debian bullseye/main amd64 libxcb-shm0 amd64 1.14-3 [101 kB] Get: 89 http://deb.debian.org/debian bullseye/main amd64 libxcb-sync1 amd64 1.14-3 [105 kB] Get: 90 http://deb.debian.org/debian bullseye/main amd64 libxcb-xfixes0 amd64 1.14-3 [105 kB] Get: 91 http://deb.debian.org/debian bullseye/main amd64 libxdamage1 amd64 1:1.1.5-2 [15.7 kB] Get: 92 http://deb.debian.org/debian bullseye/main amd64 libxext6 amd64 2:1.3.3-1.1 [52.7 kB] Get: 93 http://deb.debian.org/debian bullseye/main amd64 libxfixes3 amd64 1:5.0.3-2 [22.1 kB] Get: 94 http://deb.debian.org/debian bullseye/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get: 95 http://deb.debian.org/debian bullseye/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 96 http://deb.debian.org/debian bullseye/main amd64 libdrm-amdgpu1 amd64 2.4.104-1 [28.5 kB] Get: 97 http://deb.debian.org/debian bullseye/main amd64 libpciaccess0 amd64 0.16-1 [53.6 kB] Get: 98 http://deb.debian.org/debian bullseye/main amd64 libdrm-intel1 amd64 2.4.104-1 [71.8 kB] Get: 99 http://deb.debian.org/debian bullseye/main amd64 libdrm-nouveau2 amd64 2.4.104-1 [26.8 kB] Get: 100 http://deb.debian.org/debian bullseye/main amd64 libdrm-radeon1 amd64 2.4.104-1 [30.2 kB] Get: 101 http://deb.debian.org/debian bullseye/main amd64 libedit2 amd64 3.1-20191231-2+b1 [96.7 kB] Get: 102 http://deb.debian.org/debian bullseye/main amd64 libz3-4 amd64 4.8.10-1 [6949 kB] Get: 103 http://deb.debian.org/debian bullseye/main amd64 libllvm11 amd64 1:11.0.1-2 [17.9 MB] Get: 104 http://deb.debian.org/debian bullseye/main amd64 libsensors-config all 1:3.6.0-7 [32.3 kB] Get: 105 http://deb.debian.org/debian bullseye/main amd64 libsensors5 amd64 1:3.6.0-7 [52.3 kB] Get: 106 http://deb.debian.org/debian bullseye/main amd64 libvulkan1 amd64 1.2.162.0-1 [103 kB] Get: 107 http://deb.debian.org/debian bullseye/main amd64 libgl1-mesa-dri amd64 20.3.5-1 [9633 kB] Get: 108 http://deb.debian.org/debian bullseye/main amd64 libglx-mesa0 amd64 20.3.5-1 [186 kB] Get: 109 http://deb.debian.org/debian bullseye/main amd64 libglx0 amd64 1.3.2-1 [35.7 kB] Get: 110 http://deb.debian.org/debian bullseye/main amd64 libgl1 amd64 1.3.2-1 [89.5 kB] Get: 111 http://deb.debian.org/debian bullseye/main amd64 libxi6 amd64 2:1.7.10-1 [83.4 kB] Get: 112 http://deb.debian.org/debian bullseye/main amd64 freeglut3 amd64 2.8.1-6 [125 kB] Get: 113 http://deb.debian.org/debian bullseye/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 114 http://deb.debian.org/debian bullseye/main amd64 x11proto-dev all 2020.1-1 [594 kB] Get: 115 http://deb.debian.org/debian bullseye/main amd64 libxau-dev amd64 1:1.0.9-1 [22.9 kB] Get: 116 http://deb.debian.org/debian bullseye/main amd64 libxdmcp-dev amd64 1:1.1.2-3 [42.2 kB] Get: 117 http://deb.debian.org/debian bullseye/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 118 http://deb.debian.org/debian bullseye/main amd64 libpthread-stubs0-dev amd64 0.4-1 [5344 B] Get: 119 http://deb.debian.org/debian bullseye/main amd64 libxcb1-dev amd64 1.14-3 [176 kB] Get: 120 http://deb.debian.org/debian bullseye/main amd64 libx11-dev amd64 2:1.7.2-1 [841 kB] Get: 121 http://deb.debian.org/debian bullseye/main amd64 libglx-dev amd64 1.3.2-1 [16.3 kB] Get: 122 http://deb.debian.org/debian bullseye/main amd64 libgl-dev amd64 1.3.2-1 [100 kB] Get: 123 http://deb.debian.org/debian bullseye/main amd64 libwayland-server0 amd64 1.18.0-2~exp1.1 [34.4 kB] Get: 124 http://deb.debian.org/debian bullseye/main amd64 libgbm1 amd64 20.3.5-1 [73.5 kB] Get: 125 http://deb.debian.org/debian bullseye/main amd64 libwayland-client0 amd64 1.18.0-2~exp1.1 [26.9 kB] Get: 126 http://deb.debian.org/debian bullseye/main amd64 libegl-mesa0 amd64 20.3.5-1 [141 kB] Get: 127 http://deb.debian.org/debian bullseye/main amd64 libegl1 amd64 1.3.2-1 [34.8 kB] Get: 128 http://deb.debian.org/debian bullseye/main amd64 libegl-dev amd64 1.3.2-1 [19.6 kB] Get: 129 http://deb.debian.org/debian bullseye/main amd64 libgles1 amd64 1.3.2-1 [12.6 kB] Get: 130 http://deb.debian.org/debian bullseye/main amd64 libgles2 amd64 1.3.2-1 [17.7 kB] Get: 131 http://deb.debian.org/debian bullseye/main amd64 libgles-dev amd64 1.3.2-1 [50.3 kB] Get: 132 http://deb.debian.org/debian bullseye/main amd64 libopengl0 amd64 1.3.2-1 [31.5 kB] Get: 133 http://deb.debian.org/debian bullseye/main amd64 libopengl-dev amd64 1.3.2-1 [5876 B] Get: 134 http://deb.debian.org/debian bullseye/main amd64 libglvnd-dev amd64 1.3.2-1 [13.9 kB] Get: 135 http://deb.debian.org/debian bullseye/main amd64 libgl1-mesa-dev amd64 20.3.5-1 [51.1 kB] Get: 136 http://deb.debian.org/debian bullseye/main amd64 libglu1-mesa amd64 9.0.1-1 [168 kB] Get: 137 http://deb.debian.org/debian bullseye/main amd64 libglu1-mesa-dev amd64 9.0.1-1 [207 kB] Get: 138 http://deb.debian.org/debian bullseye/main amd64 x11proto-xext-dev all 2020.1-1 [3404 B] Get: 139 http://deb.debian.org/debian bullseye/main amd64 libxext-dev amd64 2:1.3.3-1.1 [107 kB] Get: 140 http://deb.debian.org/debian bullseye/main amd64 x11-common all 1:7.7+22 [252 kB] Get: 141 http://deb.debian.org/debian bullseye/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get: 142 http://deb.debian.org/debian bullseye/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get: 143 http://deb.debian.org/debian bullseye/main amd64 libxt6 amd64 1:1.2.0-1 [189 kB] Get: 144 http://deb.debian.org/debian bullseye/main amd64 libice-dev amd64 2:1.0.10-1 [67.1 kB] Get: 145 http://deb.debian.org/debian bullseye/main amd64 libsm-dev amd64 2:1.2.3-1 [38.0 kB] Get: 146 http://deb.debian.org/debian bullseye/main amd64 libxt-dev amd64 1:1.2.0-1 [407 kB] Get: 147 http://deb.debian.org/debian bullseye/main amd64 freeglut3-dev amd64 2.8.1-6 [179 kB] Get: 148 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3 [153 kB] Get: 149 http://deb.debian.org/debian bullseye/main amd64 libblas-dev amd64 3.9.0-3 [161 kB] Get: 150 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get: 151 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3 [2166 kB] Get: 152 http://deb.debian.org/debian bullseye/main amd64 liblapack-dev amd64 3.9.0-3 [4247 kB] Get: 153 http://deb.debian.org/debian bullseye/main amd64 libmmdb2-0 amd64 2.0.5-1 [333 kB] Get: 154 http://deb.debian.org/debian bullseye/main amd64 libopenmm7.5 amd64 7.5.0+dfsg-1 [819 kB] Get: 155 http://deb.debian.org/debian bullseye/main amd64 libopenmm-dev amd64 7.5.0+dfsg-1 [150 kB] Get: 156 http://deb.debian.org/debian bullseye/main amd64 libseqan2-dev all 2.4.0+dfsg-14 [1220 kB] Get: 157 http://deb.debian.org/debian bullseye/main amd64 libxfixes-dev amd64 1:5.0.3-2 [24.1 kB] Get: 158 http://deb.debian.org/debian bullseye/main amd64 x11proto-input-dev all 2020.1-1 [3412 B] Get: 159 http://deb.debian.org/debian bullseye/main amd64 libxi-dev amd64 2:1.7.10-1 [242 kB] Get: 160 http://deb.debian.org/debian bullseye/main amd64 libxmu6 amd64 2:1.1.2-2+b3 [60.8 kB] Get: 161 http://deb.debian.org/debian bullseye/main amd64 libxmu-headers all 2:1.1.2-2 [51.9 kB] Get: 162 http://deb.debian.org/debian bullseye/main amd64 libxmu-dev amd64 2:1.1.2-2+b3 [66.3 kB] Get: 163 http://deb.debian.org/debian bullseye/main amd64 libsimbody3.6 amd64 3.6.1+dfsg-7 [3218 kB] Get: 164 http://deb.debian.org/debian bullseye/main amd64 libsimbody-dev amd64 3.6.1+dfsg-7 [2726 kB] Get: 165 http://deb.debian.org/debian bullseye/main amd64 libsimtkmolmodel3.0 amd64 3.0~svn842-2 [532 kB] Get: 166 http://deb.debian.org/debian bullseye/main amd64 libsimtkmolmodel-dev amd64 3.0~svn842-2 [1858 kB] Fetched 97.3 MB in 1s (77.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19707 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8+deb11u1_amd64.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../1-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_amd64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../3-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libpython3.9-minimal:amd64. Preparing to unpack .../5-libpython3.9-minimal_3.9.2-1_amd64.deb ... Unpacking libpython3.9-minimal:amd64 (3.9.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../6-libexpat1_2.2.10-2+deb11u5_amd64.deb ... Unpacking libexpat1:amd64 (2.2.10-2+deb11u5) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../7-python3.9-minimal_3.9.2-1_amd64.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:amd64 (3.9.2-1) ... Setting up libexpat1:amd64 (2.2.10-2+deb11u5) ... Setting up python3.9-minimal (3.9.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20574 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_amd64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:amd64. Preparing to unpack .../2-libmpdec3_2.5.1-1_amd64.deb ... Unpacking libmpdec3:amd64 (2.5.1-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../3-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../4-libreadline8_8.1-1_amd64.deb ... Unpacking libreadline8:amd64 (8.1-1) ... Selecting previously unselected package libpython3.9-stdlib:amd64. Preparing to unpack .../5-libpython3.9-stdlib_3.9.2-1_amd64.deb ... Unpacking libpython3.9-stdlib:amd64 (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../6-python3.9_3.9.2-1_amd64.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../7-libpython3-stdlib_3.9.2-3_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20995 files and directories currently installed.) Preparing to unpack .../000-python3_3.9.2-3_amd64.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.30_all.deb ... Unpacking sgml-base (1.30) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../002-libncurses6_6.2+20201114-2+deb11u1_amd64.deb ... Unpacking libncurses6:amd64 (6.2+20201114-2+deb11u1) ... Selecting previously unselected package libprocps8:amd64. Preparing to unpack .../003-libprocps8_2%3a3.3.17-5_amd64.deb ... Unpacking libprocps8:amd64 (2:3.3.17-5) ... Selecting previously unselected package procps. Preparing to unpack .../004-procps_2%3a3.3.17-5_amd64.deb ... Unpacking procps (2:3.3.17-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../005-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../006-libmagic-mgc_1%3a5.39-3_amd64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../007-libmagic1_1%3a5.39-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../008-file_1%3a5.39-3_amd64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../009-gettext-base_0.21-4_amd64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package asciidoc-common. Preparing to unpack .../010-asciidoc-common_9.0.0~rc2-1_all.deb ... Unpacking asciidoc-common (9.0.0~rc2-1) ... Selecting previously unselected package libicu67:amd64. Preparing to unpack .../011-libicu67_67.1-7_amd64.deb ... Unpacking libicu67:amd64 (67.1-7) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../012-libxml2_2.9.10+dfsg-6.7+deb11u4_amd64.deb ... Unpacking libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Selecting previously unselected package libxml2-utils. Preparing to unpack .../013-libxml2-utils_2.9.10+dfsg-6.7+deb11u4_amd64.deb ... Unpacking libxml2-utils (2.9.10+dfsg-6.7+deb11u4) ... Selecting previously unselected package libxslt1.1:amd64. Preparing to unpack .../014-libxslt1.1_1.1.34-4+deb11u1_amd64.deb ... Unpacking libxslt1.1:amd64 (1.1.34-4+deb11u1) ... Selecting previously unselected package xsltproc. Preparing to unpack .../015-xsltproc_1.1.34-4+deb11u1_amd64.deb ... Unpacking xsltproc (1.1.34-4+deb11u1) ... Selecting previously unselected package asciidoc-base. Preparing to unpack .../016-asciidoc-base_9.0.0~rc2-1_all.deb ... Unpacking asciidoc-base (9.0.0~rc2-1) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../017-libsigsegv2_2.13-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../018-m4_1.4.18-5_amd64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../019-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../020-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../021-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../022-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package cmake-data. Preparing to unpack .../023-cmake-data_3.18.4-2+deb11u1_all.deb ... Unpacking cmake-data (3.18.4-2+deb11u1) ... Selecting previously unselected package libarchive13:amd64. Preparing to unpack .../024-libarchive13_3.4.3-2+deb11u1_amd64.deb ... Unpacking libarchive13:amd64 (3.4.3-2+deb11u1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../025-libbrotli1_1.0.9-2+b2_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b2) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../026-libsasl2-modules-db_2.1.27+dfsg-2.1+deb11u1_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../027-libsasl2-2_2.1.27+dfsg-2.1+deb11u1_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Selecting previously unselected package libldap-2.4-2:amd64. Preparing to unpack .../028-libldap-2.4-2_2.4.57+dfsg-3+deb11u1_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../029-libnghttp2-14_1.43.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.43.0-1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../030-libpsl5_0.21.0-1.2_amd64.deb ... Unpacking libpsl5:amd64 (0.21.0-1.2) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../031-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../032-libssh2-1_1.9.0-2_amd64.deb ... Unpacking libssh2-1:amd64 (1.9.0-2) ... Selecting previously unselected package libcurl4:amd64. Preparing to unpack .../033-libcurl4_7.74.0-1.3+deb11u7_amd64.deb ... Unpacking libcurl4:amd64 (7.74.0-1.3+deb11u7) ... Selecting previously unselected package libjsoncpp24:amd64. Preparing to unpack .../034-libjsoncpp24_1.9.4-4_amd64.deb ... Unpacking libjsoncpp24:amd64 (1.9.4-4) ... Selecting previously unselected package librhash0:amd64. Preparing to unpack .../035-librhash0_1.4.1-2_amd64.deb ... Unpacking librhash0:amd64 (1.4.1-2) ... Selecting previously unselected package libuv1:amd64. Preparing to unpack .../036-libuv1_1.40.0-2_amd64.deb ... Unpacking libuv1:amd64 (1.40.0-2) ... Selecting previously unselected package cmake. Preparing to unpack .../037-cmake_3.18.4-2+deb11u1_amd64.deb ... Unpacking cmake (3.18.4-2+deb11u1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../038-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../039-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../040-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../041-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../042-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../043-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../044-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../045-libelf1_0.183-1_amd64.deb ... Unpacking libelf1:amd64 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../046-dwz_0.13+20210201-1_amd64.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package gettext. Preparing to unpack .../047-gettext_0.21-4_amd64.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../048-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../049-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../050-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package xml-core. Preparing to unpack .../051-xml-core_0.18+nmu1_all.deb ... Unpacking xml-core (0.18+nmu1) ... Selecting previously unselected package sgml-data. Preparing to unpack .../052-sgml-data_2.0.11+nmu1_all.deb ... Unpacking sgml-data (2.0.11+nmu1) ... Selecting previously unselected package docbook-xml. Preparing to unpack .../053-docbook-xml_4.5-9_all.deb ... Unpacking docbook-xml (4.5-9) ... Selecting previously unselected package docbook-xsl. Preparing to unpack .../054-docbook-xsl_1.79.2+dfsg-1_all.deb ... Unpacking docbook-xsl (1.79.2+dfsg-1) ... Selecting previously unselected package libglvnd0:amd64. Preparing to unpack .../055-libglvnd0_1.3.2-1_amd64.deb ... Unpacking libglvnd0:amd64 (1.3.2-1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../056-libxau6_1%3a1.0.9-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.9-1) ... Selecting previously unselected package libmd0:amd64. Preparing to unpack .../057-libmd0_1.0.3-3_amd64.deb ... Unpacking libmd0:amd64 (1.0.3-3) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../058-libbsd0_0.11.3-1_amd64.deb ... Unpacking libbsd0:amd64 (0.11.3-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../059-libxdmcp6_1%3a1.1.2-3_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../060-libxcb1_1.14-3_amd64.deb ... Unpacking libxcb1:amd64 (1.14-3) ... Selecting previously unselected package libx11-data. Preparing to unpack .../061-libx11-data_2%3a1.7.2-1_all.deb ... Unpacking libx11-data (2:1.7.2-1) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../062-libx11-6_2%3a1.7.2-1_amd64.deb ... Unpacking libx11-6:amd64 (2:1.7.2-1) ... Selecting previously unselected package libdrm-common. Preparing to unpack .../063-libdrm-common_2.4.104-1_all.deb ... Unpacking libdrm-common (2.4.104-1) ... Selecting previously unselected package libdrm2:amd64. Preparing to unpack .../064-libdrm2_2.4.104-1_amd64.deb ... Unpacking libdrm2:amd64 (2.4.104-1) ... Selecting previously unselected package libglapi-mesa:amd64. Preparing to unpack .../065-libglapi-mesa_20.3.5-1_amd64.deb ... Unpacking libglapi-mesa:amd64 (20.3.5-1) ... Selecting previously unselected package libx11-xcb1:amd64. Preparing to unpack .../066-libx11-xcb1_2%3a1.7.2-1_amd64.deb ... Unpacking libx11-xcb1:amd64 (2:1.7.2-1) ... Selecting previously unselected package libxcb-dri2-0:amd64. Preparing to unpack .../067-libxcb-dri2-0_1.14-3_amd64.deb ... Unpacking libxcb-dri2-0:amd64 (1.14-3) ... Selecting previously unselected package libxcb-dri3-0:amd64. Preparing to unpack .../068-libxcb-dri3-0_1.14-3_amd64.deb ... Unpacking libxcb-dri3-0:amd64 (1.14-3) ... Selecting previously unselected package libxcb-glx0:amd64. Preparing to unpack .../069-libxcb-glx0_1.14-3_amd64.deb ... Unpacking libxcb-glx0:amd64 (1.14-3) ... Selecting previously unselected package libxcb-present0:amd64. Preparing to unpack .../070-libxcb-present0_1.14-3_amd64.deb ... Unpacking libxcb-present0:amd64 (1.14-3) ... Selecting previously unselected package libxcb-shm0:amd64. Preparing to unpack .../071-libxcb-shm0_1.14-3_amd64.deb ... Unpacking libxcb-shm0:amd64 (1.14-3) ... Selecting previously unselected package libxcb-sync1:amd64. Preparing to unpack .../072-libxcb-sync1_1.14-3_amd64.deb ... Unpacking libxcb-sync1:amd64 (1.14-3) ... Selecting previously unselected package libxcb-xfixes0:amd64. Preparing to unpack .../073-libxcb-xfixes0_1.14-3_amd64.deb ... Unpacking libxcb-xfixes0:amd64 (1.14-3) ... Selecting previously unselected package libxdamage1:amd64. Preparing to unpack .../074-libxdamage1_1%3a1.1.5-2_amd64.deb ... Unpacking libxdamage1:amd64 (1:1.1.5-2) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../075-libxext6_2%3a1.3.3-1.1_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.3-1.1) ... Selecting previously unselected package libxfixes3:amd64. Preparing to unpack .../076-libxfixes3_1%3a5.0.3-2_amd64.deb ... Unpacking libxfixes3:amd64 (1:5.0.3-2) ... Selecting previously unselected package libxshmfence1:amd64. Preparing to unpack .../077-libxshmfence1_1.3-1_amd64.deb ... Unpacking libxshmfence1:amd64 (1.3-1) ... Selecting previously unselected package libxxf86vm1:amd64. Preparing to unpack .../078-libxxf86vm1_1%3a1.1.4-1+b2_amd64.deb ... Unpacking libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Selecting previously unselected package libdrm-amdgpu1:amd64. Preparing to unpack .../079-libdrm-amdgpu1_2.4.104-1_amd64.deb ... Unpacking libdrm-amdgpu1:amd64 (2.4.104-1) ... Selecting previously unselected package libpciaccess0:amd64. Preparing to unpack .../080-libpciaccess0_0.16-1_amd64.deb ... Unpacking libpciaccess0:amd64 (0.16-1) ... Selecting previously unselected package libdrm-intel1:amd64. Preparing to unpack .../081-libdrm-intel1_2.4.104-1_amd64.deb ... Unpacking libdrm-intel1:amd64 (2.4.104-1) ... Selecting previously unselected package libdrm-nouveau2:amd64. Preparing to unpack .../082-libdrm-nouveau2_2.4.104-1_amd64.deb ... Unpacking libdrm-nouveau2:amd64 (2.4.104-1) ... Selecting previously unselected package libdrm-radeon1:amd64. Preparing to unpack .../083-libdrm-radeon1_2.4.104-1_amd64.deb ... Unpacking libdrm-radeon1:amd64 (2.4.104-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../084-libedit2_3.1-20191231-2+b1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20191231-2+b1) ... Selecting previously unselected package libz3-4:amd64. Preparing to unpack .../085-libz3-4_4.8.10-1_amd64.deb ... Unpacking libz3-4:amd64 (4.8.10-1) ... Selecting previously unselected package libllvm11:amd64. Preparing to unpack .../086-libllvm11_1%3a11.0.1-2_amd64.deb ... Unpacking libllvm11:amd64 (1:11.0.1-2) ... Selecting previously unselected package libsensors-config. Preparing to unpack .../087-libsensors-config_1%3a3.6.0-7_all.deb ... Unpacking libsensors-config (1:3.6.0-7) ... Selecting previously unselected package libsensors5:amd64. Preparing to unpack .../088-libsensors5_1%3a3.6.0-7_amd64.deb ... Unpacking libsensors5:amd64 (1:3.6.0-7) ... Selecting previously unselected package libvulkan1:amd64. Preparing to unpack .../089-libvulkan1_1.2.162.0-1_amd64.deb ... Unpacking libvulkan1:amd64 (1.2.162.0-1) ... Selecting previously unselected package libgl1-mesa-dri:amd64. Preparing to unpack .../090-libgl1-mesa-dri_20.3.5-1_amd64.deb ... Unpacking libgl1-mesa-dri:amd64 (20.3.5-1) ... Selecting previously unselected package libglx-mesa0:amd64. Preparing to unpack .../091-libglx-mesa0_20.3.5-1_amd64.deb ... Unpacking libglx-mesa0:amd64 (20.3.5-1) ... Selecting previously unselected package libglx0:amd64. Preparing to unpack .../092-libglx0_1.3.2-1_amd64.deb ... Unpacking libglx0:amd64 (1.3.2-1) ... Selecting previously unselected package libgl1:amd64. Preparing to unpack .../093-libgl1_1.3.2-1_amd64.deb ... Unpacking libgl1:amd64 (1.3.2-1) ... Selecting previously unselected package libxi6:amd64. Preparing to unpack .../094-libxi6_2%3a1.7.10-1_amd64.deb ... Unpacking libxi6:amd64 (2:1.7.10-1) ... Selecting previously unselected package freeglut3:amd64. Preparing to unpack .../095-freeglut3_2.8.1-6_amd64.deb ... Unpacking freeglut3:amd64 (2.8.1-6) ... Selecting previously unselected package xorg-sgml-doctools. Preparing to unpack .../096-xorg-sgml-doctools_1%3a1.11-1.1_all.deb ... Unpacking xorg-sgml-doctools (1:1.11-1.1) ... Selecting previously unselected package x11proto-dev. Preparing to unpack .../097-x11proto-dev_2020.1-1_all.deb ... Unpacking x11proto-dev (2020.1-1) ... Selecting previously unselected package libxau-dev:amd64. Preparing to unpack .../098-libxau-dev_1%3a1.0.9-1_amd64.deb ... Unpacking libxau-dev:amd64 (1:1.0.9-1) ... Selecting previously unselected package libxdmcp-dev:amd64. Preparing to unpack .../099-libxdmcp-dev_1%3a1.1.2-3_amd64.deb ... Unpacking libxdmcp-dev:amd64 (1:1.1.2-3) ... Selecting previously unselected package xtrans-dev. Preparing to unpack .../100-xtrans-dev_1.4.0-1_all.deb ... Unpacking xtrans-dev (1.4.0-1) ... Selecting previously unselected package libpthread-stubs0-dev:amd64. Preparing to unpack .../101-libpthread-stubs0-dev_0.4-1_amd64.deb ... Unpacking libpthread-stubs0-dev:amd64 (0.4-1) ... Selecting previously unselected package libxcb1-dev:amd64. Preparing to unpack .../102-libxcb1-dev_1.14-3_amd64.deb ... Unpacking libxcb1-dev:amd64 (1.14-3) ... Selecting previously unselected package libx11-dev:amd64. Preparing to unpack .../103-libx11-dev_2%3a1.7.2-1_amd64.deb ... Unpacking libx11-dev:amd64 (2:1.7.2-1) ... Selecting previously unselected package libglx-dev:amd64. Preparing to unpack .../104-libglx-dev_1.3.2-1_amd64.deb ... Unpacking libglx-dev:amd64 (1.3.2-1) ... Selecting previously unselected package libgl-dev:amd64. Preparing to unpack .../105-libgl-dev_1.3.2-1_amd64.deb ... Unpacking libgl-dev:amd64 (1.3.2-1) ... Selecting previously unselected package libwayland-server0:amd64. Preparing to unpack .../106-libwayland-server0_1.18.0-2~exp1.1_amd64.deb ... Unpacking libwayland-server0:amd64 (1.18.0-2~exp1.1) ... Selecting previously unselected package libgbm1:amd64. Preparing to unpack .../107-libgbm1_20.3.5-1_amd64.deb ... Unpacking libgbm1:amd64 (20.3.5-1) ... Selecting previously unselected package libwayland-client0:amd64. Preparing to unpack .../108-libwayland-client0_1.18.0-2~exp1.1_amd64.deb ... Unpacking libwayland-client0:amd64 (1.18.0-2~exp1.1) ... Selecting previously unselected package libegl-mesa0:amd64. Preparing to unpack .../109-libegl-mesa0_20.3.5-1_amd64.deb ... Unpacking libegl-mesa0:amd64 (20.3.5-1) ... Selecting previously unselected package libegl1:amd64. Preparing to unpack .../110-libegl1_1.3.2-1_amd64.deb ... Unpacking libegl1:amd64 (1.3.2-1) ... Selecting previously unselected package libegl-dev:amd64. Preparing to unpack .../111-libegl-dev_1.3.2-1_amd64.deb ... Unpacking libegl-dev:amd64 (1.3.2-1) ... Selecting previously unselected package libgles1:amd64. Preparing to unpack .../112-libgles1_1.3.2-1_amd64.deb ... Unpacking libgles1:amd64 (1.3.2-1) ... Selecting previously unselected package libgles2:amd64. Preparing to unpack .../113-libgles2_1.3.2-1_amd64.deb ... Unpacking libgles2:amd64 (1.3.2-1) ... Selecting previously unselected package libgles-dev:amd64. Preparing to unpack .../114-libgles-dev_1.3.2-1_amd64.deb ... Unpacking libgles-dev:amd64 (1.3.2-1) ... Selecting previously unselected package libopengl0:amd64. Preparing to unpack .../115-libopengl0_1.3.2-1_amd64.deb ... Unpacking libopengl0:amd64 (1.3.2-1) ... Selecting previously unselected package libopengl-dev:amd64. Preparing to unpack .../116-libopengl-dev_1.3.2-1_amd64.deb ... Unpacking libopengl-dev:amd64 (1.3.2-1) ... Selecting previously unselected package libglvnd-dev:amd64. Preparing to unpack .../117-libglvnd-dev_1.3.2-1_amd64.deb ... Unpacking libglvnd-dev:amd64 (1.3.2-1) ... Selecting previously unselected package libgl1-mesa-dev:amd64. Preparing to unpack .../118-libgl1-mesa-dev_20.3.5-1_amd64.deb ... Unpacking libgl1-mesa-dev:amd64 (20.3.5-1) ... Selecting previously unselected package libglu1-mesa:amd64. Preparing to unpack .../119-libglu1-mesa_9.0.1-1_amd64.deb ... Unpacking libglu1-mesa:amd64 (9.0.1-1) ... Selecting previously unselected package libglu1-mesa-dev:amd64. Preparing to unpack .../120-libglu1-mesa-dev_9.0.1-1_amd64.deb ... Unpacking libglu1-mesa-dev:amd64 (9.0.1-1) ... Selecting previously unselected package x11proto-xext-dev. Preparing to unpack .../121-x11proto-xext-dev_2020.1-1_all.deb ... Unpacking x11proto-xext-dev (2020.1-1) ... Selecting previously unselected package libxext-dev:amd64. Preparing to unpack .../122-libxext-dev_2%3a1.3.3-1.1_amd64.deb ... Unpacking libxext-dev:amd64 (2:1.3.3-1.1) ... Selecting previously unselected package x11-common. Preparing to unpack .../123-x11-common_1%3a7.7+22_all.deb ... Unpacking x11-common (1:7.7+22) ... Selecting previously unselected package libice6:amd64. Preparing to unpack .../124-libice6_2%3a1.0.10-1_amd64.deb ... Unpacking libice6:amd64 (2:1.0.10-1) ... Selecting previously unselected package libsm6:amd64. Preparing to unpack .../125-libsm6_2%3a1.2.3-1_amd64.deb ... Unpacking libsm6:amd64 (2:1.2.3-1) ... Selecting previously unselected package libxt6:amd64. Preparing to unpack .../126-libxt6_1%3a1.2.0-1_amd64.deb ... Unpacking libxt6:amd64 (1:1.2.0-1) ... Selecting previously unselected package libice-dev:amd64. Preparing to unpack .../127-libice-dev_2%3a1.0.10-1_amd64.deb ... Unpacking libice-dev:amd64 (2:1.0.10-1) ... Selecting previously unselected package libsm-dev:amd64. Preparing to unpack .../128-libsm-dev_2%3a1.2.3-1_amd64.deb ... Unpacking libsm-dev:amd64 (2:1.2.3-1) ... Selecting previously unselected package libxt-dev:amd64. Preparing to unpack .../129-libxt-dev_1%3a1.2.0-1_amd64.deb ... Unpacking libxt-dev:amd64 (1:1.2.0-1) ... Selecting previously unselected package freeglut3-dev:amd64. Preparing to unpack .../130-freeglut3-dev_2.8.1-6_amd64.deb ... Unpacking freeglut3-dev:amd64 (2.8.1-6) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../131-libblas3_3.9.0-3_amd64.deb ... Unpacking libblas3:amd64 (3.9.0-3) ... Selecting previously unselected package libblas-dev:amd64. Preparing to unpack .../132-libblas-dev_3.9.0-3_amd64.deb ... Unpacking libblas-dev:amd64 (3.9.0-3) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../133-libgfortran5_10.2.1-6_amd64.deb ... Unpacking libgfortran5:amd64 (10.2.1-6) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../134-liblapack3_3.9.0-3_amd64.deb ... Unpacking liblapack3:amd64 (3.9.0-3) ... Selecting previously unselected package liblapack-dev:amd64. Preparing to unpack .../135-liblapack-dev_3.9.0-3_amd64.deb ... Unpacking liblapack-dev:amd64 (3.9.0-3) ... Selecting previously unselected package libmmdb2-0:amd64. Preparing to unpack .../136-libmmdb2-0_2.0.5-1_amd64.deb ... Unpacking libmmdb2-0:amd64 (2.0.5-1) ... Selecting previously unselected package libopenmm7.5. Preparing to unpack .../137-libopenmm7.5_7.5.0+dfsg-1_amd64.deb ... Unpacking libopenmm7.5 (7.5.0+dfsg-1) ... Selecting previously unselected package libopenmm-dev. Preparing to unpack .../138-libopenmm-dev_7.5.0+dfsg-1_amd64.deb ... Unpacking libopenmm-dev (7.5.0+dfsg-1) ... Selecting previously unselected package libseqan2-dev. Preparing to unpack .../139-libseqan2-dev_2.4.0+dfsg-14_all.deb ... Unpacking libseqan2-dev (2.4.0+dfsg-14) ... Selecting previously unselected package libxfixes-dev:amd64. Preparing to unpack .../140-libxfixes-dev_1%3a5.0.3-2_amd64.deb ... Unpacking libxfixes-dev:amd64 (1:5.0.3-2) ... Selecting previously unselected package x11proto-input-dev. Preparing to unpack .../141-x11proto-input-dev_2020.1-1_all.deb ... Unpacking x11proto-input-dev (2020.1-1) ... Selecting previously unselected package libxi-dev:amd64. Preparing to unpack .../142-libxi-dev_2%3a1.7.10-1_amd64.deb ... Unpacking libxi-dev:amd64 (2:1.7.10-1) ... Selecting previously unselected package libxmu6:amd64. Preparing to unpack .../143-libxmu6_2%3a1.1.2-2+b3_amd64.deb ... Unpacking libxmu6:amd64 (2:1.1.2-2+b3) ... Selecting previously unselected package libxmu-headers. Preparing to unpack .../144-libxmu-headers_2%3a1.1.2-2_all.deb ... Unpacking libxmu-headers (2:1.1.2-2) ... Selecting previously unselected package libxmu-dev:amd64. Preparing to unpack .../145-libxmu-dev_2%3a1.1.2-2+b3_amd64.deb ... Unpacking libxmu-dev:amd64 (2:1.1.2-2+b3) ... Selecting previously unselected package libsimbody3.6:amd64. Preparing to unpack .../146-libsimbody3.6_3.6.1+dfsg-7_amd64.deb ... Unpacking libsimbody3.6:amd64 (3.6.1+dfsg-7) ... Selecting previously unselected package libsimbody-dev:amd64. Preparing to unpack .../147-libsimbody-dev_3.6.1+dfsg-7_amd64.deb ... Unpacking libsimbody-dev:amd64 (3.6.1+dfsg-7) ... Selecting previously unselected package libsimtkmolmodel3.0:amd64. Preparing to unpack .../148-libsimtkmolmodel3.0_3.0~svn842-2_amd64.deb ... Unpacking libsimtkmolmodel3.0:amd64 (3.0~svn842-2) ... Selecting previously unselected package libsimtkmolmodel-dev:amd64. Preparing to unpack .../149-libsimtkmolmodel-dev_3.0~svn842-2_amd64.deb ... Unpacking libsimtkmolmodel-dev:amd64 (3.0~svn842-2) ... Setting up media-types (4.0.0) ... Setting up libpipeline1:amd64 (1.5.3-1) ... Setting up libwayland-server0:amd64 (1.18.0-2~exp1.1) ... Setting up libpciaccess0:amd64 (0.16-1) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libpsl5:amd64 (0.21.0-1.2) ... Setting up bsdextrautils (2.36.1-8+deb11u1) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:amd64 (67.1-7) ... Setting up libmmdb2-0:amd64 (2.0.5-1) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglvnd0:amd64 (1.3.2-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b2) ... Setting up x11-common (1:7.7+22) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libsensors-config (1:3.6.0-7) ... Setting up libopenmm7.5 (7.5.0+dfsg-1) ... Setting up libnghttp2-14:amd64 (1.43.0-1) ... Setting up libmagic1:amd64 (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libpthread-stubs0-dev:amd64 (0.4-1) ... Setting up libopenmm-dev (7.5.0+dfsg-1) ... Setting up libopengl0:amd64 (1.3.2-1) ... Setting up libseqan2-dev (2.4.0+dfsg-14) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up asciidoc-common (9.0.0~rc2-1) ... Setting up xtrans-dev (1.4.0-1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libz3-4:amd64 (4.8.10-1) ... Setting up libblas3:amd64 (3.9.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libuv1:amd64 (1.40.0-2) ... Setting up libgles2:amd64 (1.3.2-1) ... Setting up libx11-data (2:1.7.2-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:amd64 (6.2+20201114-2+deb11u1) ... Setting up libgles1:amd64 (1.3.2-1) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up libsensors5:amd64 (1:3.6.0-7) ... Setting up libglapi-mesa:amd64 (20.3.5-1) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up libgfortran5:amd64 (10.2.1-6) ... Setting up libvulkan1:amd64 (1.2.162.0-1) ... Setting up libjsoncpp24:amd64 (1.9.4-4) ... Setting up libmd0:amd64 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up libxshmfence1:amd64 (1.3-1) ... Setting up librhash0:amd64 (1.4.1-2) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libmpdec3:amd64 (2.5.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:amd64 (1.9.0-2) ... Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up sgml-base (1.30) ... Setting up cmake-data (3.18.4-2+deb11u1) ... Setting up libopengl-dev:amd64 (1.3.2-1) ... Setting up libbsd0:amd64 (0.11.3-1) ... Setting up libdrm-common (2.4.104-1) ... Setting up libelf1:amd64 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Setting up libprocps8:amd64 (2:3.3.17-5) ... Setting up libblas-dev:amd64 (3.9.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up libwayland-client0:amd64 (1.18.0-2~exp1.1) ... Setting up x11proto-dev (2020.1-1) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libice6:amd64 (2:1.0.10-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.9.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.14-3) ... Setting up gettext (0.21-4) ... Setting up libxcb-xfixes0:amd64 (1.14-3) ... Setting up libxau-dev:amd64 (1:1.0.9-1) ... Setting up libice-dev:amd64 (2:1.0.10-1) ... Setting up libtool (2.4.6-15) ... Setting up libarchive13:amd64 (3.4.3-2+deb11u1) ... Setting up libxcb-glx0:amd64 (1.14-3) ... Setting up libedit2:amd64 (3.1-20191231-2+b1) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Setting up m4 (1.4.18-5) ... Setting up libxcb-shm0:amd64 (1.14-3) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxcb-present0:amd64 (1.14-3) ... Setting up libxdmcp-dev:amd64 (1:1.1.2-3) ... Setting up libllvm11:amd64 (1:11.0.1-2) ... Setting up libxcb-sync1:amd64 (1.14-3) ... Setting up liblapack-dev:amd64 (3.9.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up x11proto-input-dev (2020.1-1) ... Setting up autoconf (2.69-14) ... Setting up libxcb-dri2-0:amd64 (1.14-3) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up x11proto-xext-dev (2020.1-1) ... Setting up libdrm2:amd64 (2.4.104-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up xml-core (0.18+nmu1) ... Setting up procps (2:3.3.17-5) ... Setting up libxslt1.1:amd64 (1.1.34-4+deb11u1) ... Setting up libcurl4:amd64 (7.74.0-1.3+deb11u7) ... Setting up libx11-6:amd64 (2:1.7.2-1) ... Setting up libxml2-utils (2.9.10+dfsg-6.7+deb11u4) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up libdrm-amdgpu1:amd64 (2.4.104-1) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libxcb-dri3-0:amd64 (1.14-3) ... Setting up libx11-xcb1:amd64 (2:1.7.2-1) ... Setting up libdrm-nouveau2:amd64 (2.4.104-1) ... Setting up libxdamage1:amd64 (1:1.1.5-2) ... Setting up libxcb1-dev:amd64 (1.14-3) ... Setting up libgbm1:amd64 (20.3.5-1) ... Setting up libsm-dev:amd64 (2:1.2.3-1) ... Setting up libdrm-radeon1:amd64 (2.4.104-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libdrm-intel1:amd64 (2.4.104-1) ... Setting up libgl1-mesa-dri:amd64 (20.3.5-1) ... Setting up xsltproc (1.1.34-4+deb11u1) ... Setting up libx11-dev:amd64 (2:1.7.2-1) ... Setting up libxext6:amd64 (2:1.3.3-1.1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up dh-autoreconf (20) ... Setting up libegl-mesa0:amd64 (20.3.5-1) ... Setting up libxfixes3:amd64 (1:5.0.3-2) ... Setting up libxt6:amd64 (1:1.2.0-1) ... Setting up libxext-dev:amd64 (2:1.3.3-1.1) ... Setting up libegl1:amd64 (1.3.2-1) ... Setting up cmake (3.18.4-2+deb11u1) ... Setting up python3.9 (3.9.2-1) ... Setting up libxmu-headers (2:1.1.2-2) ... Setting up libxmu6:amd64 (2:1.1.2-2+b3) ... Setting up libglx-mesa0:amd64 (20.3.5-1) ... Setting up libxi6:amd64 (2:1.7.10-1) ... Setting up libglx0:amd64 (1.3.2-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up libxfixes-dev:amd64 (1:5.0.3-2) ... Setting up asciidoc-base (9.0.0~rc2-1) ... Setting up libgl1:amd64 (1.3.2-1) ... Setting up libxt-dev:amd64 (1:1.2.0-1) ... Setting up libglx-dev:amd64 (1.3.2-1) ... Setting up libglu1-mesa:amd64 (9.0.1-1) ... Setting up libxi-dev:amd64 (2:1.7.10-1) ... Setting up libgl-dev:amd64 (1.3.2-1) ... Setting up freeglut3:amd64 (2.8.1-6) ... Setting up libegl-dev:amd64 (1.3.2-1) ... Setting up libxmu-dev:amd64 (2:1.1.2-2+b3) ... Setting up libglu1-mesa-dev:amd64 (9.0.1-1) ... Setting up libsimbody3.6:amd64 (3.6.1+dfsg-7) ... Setting up libgles-dev:amd64 (1.3.2-1) ... Setting up libsimtkmolmodel3.0:amd64 (3.0~svn842-2) ... Setting up libsimtkmolmodel-dev:amd64 (3.0~svn842-2) ... Setting up libglvnd-dev:amd64 (1.3.2-1) ... Setting up libgl1-mesa-dev:amd64 (20.3.5-1) ... Setting up freeglut3-dev:amd64 (2.8.1-6) ... Setting up libsimbody-dev:amd64 (3.6.1+dfsg-7) ... Processing triggers for libc-bin (2.31-13+deb11u6) ... Processing triggers for sgml-base (1.30) ... Setting up sgml-data (2.0.11+nmu1) ... Setting up docbook-xsl (1.79.2+dfsg-1) ... Processing triggers for sgml-base (1.30) ... Setting up docbook-xml (4.5-9) ... Processing triggers for sgml-base (1.30) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/macromoleculebuilder-3.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../macromoleculebuilder_3.2+dfsg-2+deb11u1_source.changes dpkg-buildpackage: info: source package macromoleculebuilder dpkg-buildpackage: info: source version 3.2+dfsg-2+deb11u1 dpkg-buildpackage: info: source distribution bullseye dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/macromoleculebuilder-3.2+dfsg' rm -rf parameterization/build dh_auto_configure -- \ -DOpenMM_INCLUDE_DIR=/usr/include \ -DCMAKE_CXX_FLAGS="-D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0" cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DOpenMM_INCLUDE_DIR=/usr/include "-DCMAKE_CXX_FLAGS=-D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0" .. -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/macromoleculebuilder-3.2+dfsg' dh_auto_build cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/macromoleculebuilder-3.2+dfsg -B/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/MMBlib.dir/build.make CMakeFiles/MMBlib.dir/depend make[3]: Entering directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' cd /build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/macromoleculebuilder-3.2+dfsg /build/macromoleculebuilder-3.2+dfsg /build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu /build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu /build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/MMBlib.dir/DependInfo.cmake --color= Dependee "/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/MMBlib.dir/DependInfo.cmake" is newer than depender "/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/MMBlib.dir/depend.internal". Dependee "/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/MMBlib.dir/depend.internal". Scanning dependencies of target MMBlib make[3]: Leaving directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/MMBlib.dir/build.make CMakeFiles/MMBlib.dir/build make[3]: Entering directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' [ 3%] Building CXX object CMakeFiles/MMBlib.dir/src/Utils.cpp.o [ 6%] Building CXX object CMakeFiles/MMBlib.dir/src/UnitCellParameters.cpp.o [ 10%] Building CXX object CMakeFiles/MMBlib.dir/src/BiopolymerClass.cpp.o [ 13%] Building CXX object CMakeFiles/MMBlib.dir/src/DisplacementContainer.cpp.o [ 17%] Building CXX object CMakeFiles/MMBlib.dir/src/AtomSpringContainer.cpp.o [ 20%] Building CXX object CMakeFiles/MMBlib.dir/src/MoleculeContainer.cpp.o [ 27%] Building CXX object CMakeFiles/MMBlib.dir/src/MobilizerContainer.cpp.o [ 27%] Building CXX object CMakeFiles/MMBlib.dir/src/DensityContainer.cpp.o [ 31%] Building CXX object CMakeFiles/MMBlib.dir/src/BasePairContainer.cpp.o [ 34%] Building CXX object CMakeFiles/MMBlib.dir/src/ContactContainer.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/Utils.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/Utils.cpp /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/BiopolymerClass.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/UnitCellParameters.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/UnitCellParameters.cpp /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/AtomSpringContainer.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/AtomSpringContainer.cpp [ 37%] Building CXX object CMakeFiles/MMBlib.dir/src/ConstraintContainer.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/MobilizerContainer.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/MobilizerContainer.cpp /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/MoleculeContainer.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/MoleculeContainer.cpp [ 41%] Building CXX object CMakeFiles/MMBlib.dir/src/Repel.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/DisplacementContainer.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/DisplacementContainer.cpp /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/DensityContainer.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/DensityContainer.cpp /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/BasePairContainer.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/BasePairContainer.cpp /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/ContactContainer.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/ContactContainer.cpp [ 44%] Building CXX object CMakeFiles/MMBlib.dir/src/MonoAtoms.cpp.o [ 48%] Building CXX object CMakeFiles/MMBlib.dir/src/ParameterReader.cpp.o [ 51%] Building CXX object CMakeFiles/MMBlib.dir/src/BaseInteractionParameterReader.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/ConstraintContainer.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/ConstraintContainer.cpp /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/Repel.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/Repel.cpp /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/MonoAtoms.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/MonoAtoms.cpp /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/ParameterReader.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/ParameterReader.cpp /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/BaseInteractionParameterReader.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/BaseInteractionParameterReader.cpp [ 55%] Building CXX object CMakeFiles/MMBlib.dir/src/TetherForce.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/TetherForce.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/TetherForce.cpp /build/macromoleculebuilder-3.2+dfsg/src/UnitCellParameters.cpp: In member function 'const double UnitCellParameters::angleInRange(double)': /build/macromoleculebuilder-3.2+dfsg/src/UnitCellParameters.cpp:165:2: warning: control reaches end of non-void function [-Wreturn-type] 165 | } | ^ /build/macromoleculebuilder-3.2+dfsg/src/UnitCellParameters.cpp: In member function 'const bool UnitCellParameters::exitIfNotValid() const': /build/macromoleculebuilder-3.2+dfsg/src/UnitCellParameters.cpp:270:1: warning: control reaches end of non-void function [-Wreturn-type] 270 | } | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/include/AtomSpringContainer.h:14, from /build/macromoleculebuilder-3.2+dfsg/src/AtomSpringContainer.cpp:12: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/include/AtomSpringContainer.h:14, from /build/macromoleculebuilder-3.2+dfsg/include/ParameterReader.h:20, from /build/macromoleculebuilder-3.2+dfsg/include/PeriodicScrubber.h:16, from /build/macromoleculebuilder-3.2+dfsg/include/Repel.h:21, from /build/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:12: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/src/Utils.cpp:11: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/src/MobilizerContainer.cpp:11: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/include/ConstraintContainer.h:14, from /build/macromoleculebuilder-3.2+dfsg/include/MoleculeContainer.h:9, from /build/macromoleculebuilder-3.2+dfsg/src/MoleculeContainer.cpp:3: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/include/BaseInteractionParameterReader.h:22, from /build/macromoleculebuilder-3.2+dfsg/src/BaseInteractionParameterReader.cpp:16: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/src/MonoAtoms.cpp:11: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/include/AtomSpringContainer.h:14, from /build/macromoleculebuilder-3.2+dfsg/include/ParameterReader.h:20, from /build/macromoleculebuilder-3.2+dfsg/include/TetherForce.h:20, from /build/macromoleculebuilder-3.2+dfsg/src/TetherForce.cpp:11: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/include/Mutation.h:4, from /build/macromoleculebuilder-3.2+dfsg/include/BiopolymerClass.h:18, from /build/macromoleculebuilder-3.2+dfsg/include/BasePairContainer.h:14, from /build/macromoleculebuilder-3.2+dfsg/src/BasePairContainer.cpp:11: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ [ 58%] Building CXX object CMakeFiles/MMBlib.dir/src/BiopolymerClassTwoTransformForces.cpp.o In file included from /build/macromoleculebuilder-3.2+dfsg/include/Mutation.h:4, from /build/macromoleculebuilder-3.2+dfsg/include/BiopolymerClass.h:18, from /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:13: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/BiopolymerClassTwoTransformForces.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp In file included from /build/macromoleculebuilder-3.2+dfsg/include/Mutation.h:4, from /build/macromoleculebuilder-3.2+dfsg/include/BiopolymerClass.h:18, from /build/macromoleculebuilder-3.2+dfsg/include/DensityContainer.h:14, from /build/macromoleculebuilder-3.2+dfsg/src/DensityContainer.cpp:11: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/include/Mutation.h:4, from /build/macromoleculebuilder-3.2+dfsg/include/BiopolymerClass.h:18, from /build/macromoleculebuilder-3.2+dfsg/include/DisplacementContainer.h:14, from /build/macromoleculebuilder-3.2+dfsg/src/DisplacementContainer.cpp:12: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/include/ConstraintContainer.h:14, from /build/macromoleculebuilder-3.2+dfsg/src/ConstraintContainer.cpp:10: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/include/AtomSpringContainer.h:14, from /build/macromoleculebuilder-3.2+dfsg/include/ParameterReader.h:20, from /build/macromoleculebuilder-3.2+dfsg/src/ParameterReader.cpp:17: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ /build/macromoleculebuilder-3.2+dfsg/src/Repel.cpp: In member function 'void ConstrainedDynamics::constraintsAndRestraints(ParameterReader&, BiopolymerClassContainer&, SimTK::GeneralForceSubsystem&, SimTK::SimbodyMatterSubsystem&, SimTK::State&, SimTK::CompoundSystem&)': /build/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:127:49: note: '#pragma message: USE_OPENMM is defined' 127 | #pragma message ("USE_OPENMM is defined") | ^ /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp: In member function 'bool BiopolymerClass::setRenumberPdbResidues(bool)': /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1067:5: warning: no return statement in function returning non-void [-Wreturn-type] 1067 | } | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/src/ContactContainer.cpp:11: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp: In member function 'bool BiopolymerClassContainer::setRenumberPdbResidues(bool)': /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:4725:1: warning: no return statement in function returning non-void [-Wreturn-type] 4725 | } | ^ /build/macromoleculebuilder-3.2+dfsg/src/MoleculeContainer.cpp: In member function 'SimTK::Compound CompoundObjectMapContainer::fetchCompound(SimTK::String)': /build/macromoleculebuilder-3.2+dfsg/src/MoleculeContainer.cpp:73:1: warning: control reaches end of non-void function [-Wreturn-type] 73 | } | ^ /build/macromoleculebuilder-3.2+dfsg/src/MoleculeContainer.cpp: In member function 'SimTK::Biotype CompoundObjectMapContainer::fetchBiotype(SimTK::String)': /build/macromoleculebuilder-3.2+dfsg/src/MoleculeContainer.cpp:92:1: warning: control reaches end of non-void function [-Wreturn-type] 92 | } | ^ /build/macromoleculebuilder-3.2+dfsg/src/MoleculeContainer.cpp: In member function 'const SimTK::Element CompoundObjectMapContainer::fetchElement(SimTK::String)': /build/macromoleculebuilder-3.2+dfsg/src/MoleculeContainer.cpp:220:1: warning: control reaches end of non-void function [-Wreturn-type] 220 | } | ^ /build/macromoleculebuilder-3.2+dfsg/src/MoleculeContainer.cpp: In member function 'SimTK::Compound::SingleAtom CompoundObjectMapContainer::fetchSingleAtom(SimTK::String, SimTK::Compound::AtomName&, SimTK::String, SimTK::Angle)': /build/macromoleculebuilder-3.2+dfsg/src/MoleculeContainer.cpp:244:1: warning: control reaches end of non-void function [-Wreturn-type] 244 | } | ^ /build/macromoleculebuilder-3.2+dfsg/src/MoleculeContainer.cpp: In member function 'bool MoleculeClassContainer::hasChainID(SimTK::String)': /build/macromoleculebuilder-3.2+dfsg/src/MoleculeContainer.cpp:722:1: warning: control reaches end of non-void function [-Wreturn-type] 722 | } | ^ /build/macromoleculebuilder-3.2+dfsg/src/Utils.cpp: In function 'int ValidateNonNegativeInt(int)': /build/macromoleculebuilder-3.2+dfsg/src/Utils.cpp:526:1: warning: control reaches end of non-void function [-Wreturn-type] 526 | } | ^ /build/macromoleculebuilder-3.2+dfsg/src/DisplacementContainer.cpp: In member function 'Displacement& DisplacementContainer::updDisplacement(SimTK::String)': /build/macromoleculebuilder-3.2+dfsg/src/DisplacementContainer.cpp:41:1: warning: control reaches end of non-void function [-Wreturn-type] 41 | }; | ^ /build/macromoleculebuilder-3.2+dfsg/src/MonoAtoms.cpp: In member function 'const int MonoAtoms::getResidueIndex(ResidueID)': /build/macromoleculebuilder-3.2+dfsg/src/MonoAtoms.cpp:153:1: warning: control reaches end of non-void function [-Wreturn-type] 153 | } | ^ /build/macromoleculebuilder-3.2+dfsg/src/MonoAtoms.cpp: In member function 'MonoAtoms MonoAtomsContainer::getMonoAtoms(SimTK::String)': /build/macromoleculebuilder-3.2+dfsg/src/MonoAtoms.cpp:277:1: warning: control reaches end of non-void function [-Wreturn-type] 277 | } | ^ [ 62%] Building CXX object CMakeFiles/MMBlib.dir/src/WaterDroplet.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/WaterDroplet.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/WaterDroplet.cpp [ 65%] Building CXX object CMakeFiles/MMBlib.dir/src/DensityMap.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/DensityMap.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp [ 68%] Building CXX object CMakeFiles/MMBlib.dir/src/DensityForce.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/DensityForce.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/DensityForce.cpp [ 72%] Building CXX object CMakeFiles/MMBlib.dir/src/ElectrostaticPotentialGridForce.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/ElectrostaticPotentialGridForce.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/ElectrostaticPotentialGridForce.cpp [ 75%] Building CXX object CMakeFiles/MMBlib.dir/src/ErrorManager.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/ErrorManager.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/ErrorManager.cpp [ 79%] Building CXX object CMakeFiles/MMBlib.dir/src/PeriodicPdbAndEnergyWriter.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/PeriodicPdbAndEnergyWriter.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp [ 82%] Building CXX object CMakeFiles/MMBlib.dir/src/NTC_PARAMETER_READER.cpp.o /build/macromoleculebuilder-3.2+dfsg/src/BasePairContainer.cpp: In member function 'bool BasePairContainer::hasWatsonCrickCisPair(SimTK::String, ResidueID)': /build/macromoleculebuilder-3.2+dfsg/src/BasePairContainer.cpp:184:1: warning: control reaches end of non-void function [-Wreturn-type] 184 | } | ^ /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/NTC_PARAMETER_READER.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/NTC_PARAMETER_READER.cpp /build/macromoleculebuilder-3.2+dfsg/src/BasePairContainer.cpp: In member function 'const BaseInteraction BasePairContainer::getWatsonCrickCisPair(SimTK::String, ResidueID)': /build/macromoleculebuilder-3.2+dfsg/src/BasePairContainer.cpp:206:1: warning: control reaches end of non-void function [-Wreturn-type] 206 | } // of method | ^ /build/macromoleculebuilder-3.2+dfsg/src/BasePairContainer.cpp: In member function 'const ResidueID BasePairContainer::getWatsonCrickCisPairingResidue(SimTK::String, ResidueID)': /build/macromoleculebuilder-3.2+dfsg/src/BasePairContainer.cpp:223:1: warning: control reaches end of non-void function [-Wreturn-type] 223 | } | ^ /build/macromoleculebuilder-3.2+dfsg/src/BasePairContainer.cpp: In member function 'const SimTK::String BasePairContainer::getWatsonCrickCisPairingChain(SimTK::String, ResidueID)': /build/macromoleculebuilder-3.2+dfsg/src/BasePairContainer.cpp:237:1: warning: control reaches end of non-void function [-Wreturn-type] 237 | } | ^ /build/macromoleculebuilder-3.2+dfsg/src/BasePairContainer.cpp: In member function 'const ResidueID BasePairContainer::getLastWatsonCrickCisPairingResidueOfRun(SimTK::String, ResidueID, BiopolymerClassContainer&)': /build/macromoleculebuilder-3.2+dfsg/src/BasePairContainer.cpp:289:1: warning: control reaches end of non-void function [-Wreturn-type] 289 | } // of getLastWatsonCrickCisPairingResidueOfRun | ^ [ 86%] Building CXX object CMakeFiles/MMBlib.dir/src/NtCClassContainer.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/NtCClassContainer.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/NtCClassContainer.cpp /build/macromoleculebuilder-3.2+dfsg/src/ErrorManager.cpp: In member function 'ErrorManager& ErrorManager::operator=(const ErrorManager&)': /build/macromoleculebuilder-3.2+dfsg/src/ErrorManager.cpp:25:1: warning: no return statement in function returning non-void [-Wreturn-type] 24 | _buffer << em._buffer.rdbuf(); +++ |+ return *this; 25 | } | ^ [ 89%] Building CXX object CMakeFiles/MMBlib.dir/src/NtCForces.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/NtCForces.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/NtCForces.cpp /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp: In member function 'int BiopolymerClass::validateBiopolymerType() const': /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:356:1: warning: control reaches end of non-void function [-Wreturn-type] 356 | } | ^ /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp: In member function 'SimTK::String BiopolymerClass::getBiopolymerTypeAsString()': /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1062:1: warning: control reaches end of non-void function [-Wreturn-type] 1062 | } | ^ /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp: In member function 'int BiopolymerClass::validateAtomPathName(SimTK::Compound::AtomPathName)': /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1133:1: warning: control reaches end of non-void function [-Wreturn-type] 1133 | } | ^ /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp: In member function 'const SimTK::ResidueInfo::Index BiopolymerClass::getResidueIndex(ResidueID)': /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1529:1: warning: control reaches end of non-void function [-Wreturn-type] 1529 | } | ^ /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp: In member function 'SimTK::String BiopolymerClass::getRepresentativeAtomName()': /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1552:1: warning: control reaches end of non-void function [-Wreturn-type] 1552 | } | ^ /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp: In member function 'double BiopolymerClass::getRepresentativeAtomMassThreshold()': /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1569:1: warning: control reaches end of non-void function [-Wreturn-type] 1569 | } | ^ /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp: In member function 'int BiopolymerClassContainer::initializeBiopolymer(SimTK::String, SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, double, std::vector, double, double, std::vector)': /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:2749:1: warning: control reaches end of non-void function [-Wreturn-type] 2749 | } | ^ /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp: In member function 'int BiopolymerClassContainer::getBiopolymerClassIndex(SimTK::String)': /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:2850:1: warning: control reaches end of non-void function [-Wreturn-type] 2850 | } | ^ /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp: In member function 'BiopolymerClass& BiopolymerClassContainer::updBiopolymerClass(int)': /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:2867:1: warning: control reaches end of non-void function [-Wreturn-type] 2867 | } | ^ /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp: In member function 'int BiopolymerClassContainer::validateChainID(SimTK::String)': /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:3038:1: warning: control reaches end of non-void function [-Wreturn-type] 3038 | } | ^ /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp: In member function 'ResidueID BiopolymerClassContainer::residueID(std::map, const char*, SimTK::String)': /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:4174:1: warning: control reaches end of non-void function [-Wreturn-type] 4174 | } | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/include/AtomSpringContainer.h:14, from /build/macromoleculebuilder-3.2+dfsg/include/ParameterReader.h:20, from /build/macromoleculebuilder-3.2+dfsg/include/BiopolymerClassTwoTransformForces.h:18, from /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:10: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/include/WaterDroplet.h:16, from /build/macromoleculebuilder-3.2+dfsg/src/WaterDroplet.cpp:11: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/include/AtomSpringContainer.h:14, from /build/macromoleculebuilder-3.2+dfsg/include/ParameterReader.h:20, from /build/macromoleculebuilder-3.2+dfsg/include/ElectrostaticPotentialGridForce.h:20, from /build/macromoleculebuilder-3.2+dfsg/src/ElectrostaticPotentialGridForce.cpp:11: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/include/Mutation.h:4, from /build/macromoleculebuilder-3.2+dfsg/include/BiopolymerClass.h:18, from /build/macromoleculebuilder-3.2+dfsg/include/NtC_Class_Container.h:14, from /build/macromoleculebuilder-3.2+dfsg/src/NTC_PARAMETER_READER.cpp:16: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp:11: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/include/AtomSpringContainer.h:14, from /build/macromoleculebuilder-3.2+dfsg/include/ParameterReader.h:20, from /build/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbAndEnergyWriter.h:13, from /build/macromoleculebuilder-3.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:15: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/include/AtomSpringContainer.h:14, from /build/macromoleculebuilder-3.2+dfsg/include/ParameterReader.h:20, from /build/macromoleculebuilder-3.2+dfsg/include/DensityForce.h:20, from /build/macromoleculebuilder-3.2+dfsg/src/DensityForce.cpp:11: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/include/Mutation.h:4, from /build/macromoleculebuilder-3.2+dfsg/include/BiopolymerClass.h:18, from /build/macromoleculebuilder-3.2+dfsg/src/NtCClassContainer.cpp:12: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/include/AtomSpringContainer.h:14, from /build/macromoleculebuilder-3.2+dfsg/include/ParameterReader.h:20, from /build/macromoleculebuilder-3.2+dfsg/include/NtCForces.h:19, from /build/macromoleculebuilder-3.2+dfsg/src/NtCForces.cpp:10: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ /build/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp: In member function 'GridPoint& DensityMap::updGridPoint(GridIndices)': /build/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp:127:5: warning: control reaches end of non-void function [-Wreturn-type] 127 | } | ^ /build/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp: In member function 'SimTK::Vec3 DensityMap::calcInterpolatedFirstQuadrantGradient(GridPoint&, SimTK::Vec3) const': /build/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp:1448:1: warning: control reaches end of non-void function [-Wreturn-type] 1448 | } | ^ /build/macromoleculebuilder-3.2+dfsg/src/WaterDroplet.cpp: In member function 'WaterDroplet WaterDropletContainer::getWaterDroplet(std::string)': /build/macromoleculebuilder-3.2+dfsg/src/WaterDroplet.cpp:108:1: warning: control reaches end of non-void function [-Wreturn-type] 108 | } | ^ /build/macromoleculebuilder-3.2+dfsg/src/WaterDroplet.cpp: In member function 'WaterDroplet& WaterDropletContainer::updWaterDroplet(std::string)': /build/macromoleculebuilder-3.2+dfsg/src/WaterDroplet.cpp:120:1: warning: control reaches end of non-void function [-Wreturn-type] 120 | } | ^ [ 93%] Linking CXX shared library libMMBlib.so /usr/bin/cmake -E cmake_link_script CMakeFiles/MMBlib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -Wl,-z,relro -shared -Wl,-soname,libMMBlib.so.3.2 -o libMMBlib.so.3.2 CMakeFiles/MMBlib.dir/src/Utils.cpp.o CMakeFiles/MMBlib.dir/src/BiopolymerClass.cpp.o CMakeFiles/MMBlib.dir/src/UnitCellParameters.cpp.o CMakeFiles/MMBlib.dir/src/AtomSpringContainer.cpp.o CMakeFiles/MMBlib.dir/src/DisplacementContainer.cpp.o CMakeFiles/MMBlib.dir/src/MobilizerContainer.cpp.o CMakeFiles/MMBlib.dir/src/MoleculeContainer.cpp.o CMakeFiles/MMBlib.dir/src/DensityContainer.cpp.o CMakeFiles/MMBlib.dir/src/BasePairContainer.cpp.o CMakeFiles/MMBlib.dir/src/ContactContainer.cpp.o CMakeFiles/MMBlib.dir/src/ConstraintContainer.cpp.o CMakeFiles/MMBlib.dir/src/Repel.cpp.o CMakeFiles/MMBlib.dir/src/MonoAtoms.cpp.o CMakeFiles/MMBlib.dir/src/ParameterReader.cpp.o CMakeFiles/MMBlib.dir/src/BaseInteractionParameterReader.cpp.o CMakeFiles/MMBlib.dir/src/TetherForce.cpp.o CMakeFiles/MMBlib.dir/src/BiopolymerClassTwoTransformForces.cpp.o CMakeFiles/MMBlib.dir/src/WaterDroplet.cpp.o CMakeFiles/MMBlib.dir/src/DensityMap.cpp.o CMakeFiles/MMBlib.dir/src/DensityForce.cpp.o CMakeFiles/MMBlib.dir/src/ElectrostaticPotentialGridForce.cpp.o CMakeFiles/MMBlib.dir/src/ErrorManager.cpp.o CMakeFiles/MMBlib.dir/src/PeriodicPdbAndEnergyWriter.cpp.o CMakeFiles/MMBlib.dir/src/NTC_PARAMETER_READER.cpp.o CMakeFiles/MMBlib.dir/src/NtCClassContainer.cpp.o CMakeFiles/MMBlib.dir/src/NtCForces.cpp.o -L/usr/lib/x86_64-linux-gnu64 -L/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu -Wl,-rpath,/usr/lib/x86_64-linux-gnu64:/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu: -lSimTKmolmodel /usr/lib/x86_64-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/x86_64-linux-gnu/libSimTKmath.so.3.6 /usr/lib/x86_64-linux-gnu/libSimTKcommon.so.3.6 -lOpenMM -llapack -lblas -ldl -lrt -lblas -llapack -lblas -llapack -lpthread -ldl -lrt -lm /usr/bin/cmake -E cmake_symlink_library libMMBlib.so.3.2 libMMBlib.so.3.2 libMMBlib.so make[3]: Leaving directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' [ 93%] Built target MMBlib make -f CMakeFiles/MMB.dir/build.make CMakeFiles/MMB.dir/depend make[3]: Entering directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' cd /build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/macromoleculebuilder-3.2+dfsg /build/macromoleculebuilder-3.2+dfsg /build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu /build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu /build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/MMB.dir/DependInfo.cmake --color= Dependee "/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/MMB.dir/DependInfo.cmake" is newer than depender "/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/MMB.dir/depend.internal". Dependee "/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/MMB.dir/depend.internal". Scanning dependencies of target MMB make[3]: Leaving directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/MMB.dir/build.make CMakeFiles/MMB.dir/build make[3]: Entering directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' [ 96%] Building CXX object CMakeFiles/MMB.dir/src/RNABuilder.cpp.o /usr/bin/c++ -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -o CMakeFiles/MMB.dir/src/RNABuilder.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/RNABuilder.cpp In file included from /build/macromoleculebuilder-3.2+dfsg/include/AtomSpringContainer.h:14, from /build/macromoleculebuilder-3.2+dfsg/include/ParameterReader.h:20, from /build/macromoleculebuilder-3.2+dfsg/src/RNABuilder.cpp:15: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ [100%] Linking CXX executable MMB /usr/bin/cmake -E cmake_link_script CMakeFiles/MMB.dir/link.txt --verbose=1 /usr/bin/c++ -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -Wl,-z,relro -rdynamic CMakeFiles/MMB.dir/src/RNABuilder.cpp.o -o MMB -L/usr/lib/x86_64-linux-gnu64 -L/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu -Wl,-rpath,/usr/lib/x86_64-linux-gnu64:/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu: libMMBlib.so.3.2 -lSimTKmolmodel /usr/lib/x86_64-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/x86_64-linux-gnu/libSimTKmath.so.3.6 /usr/lib/x86_64-linux-gnu/libSimTKcommon.so.3.6 -lOpenMM -llapack -lblas -ldl -lrt -lblas -llapack -lblas -llapack -lpthread -lm -ldl -lrt make[3]: Leaving directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' [100%] Built target MMB make[2]: Leaving directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/macromoleculebuilder-3.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/macromoleculebuilder-3.2+dfsg -B/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/MMBlib.dir/build.make CMakeFiles/MMBlib.dir/depend make[3]: Entering directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' cd /build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/macromoleculebuilder-3.2+dfsg /build/macromoleculebuilder-3.2+dfsg /build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu /build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu /build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/MMBlib.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/MMBlib.dir/build.make CMakeFiles/MMBlib.dir/build make[3]: Entering directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/MMBlib.dir/build'. make[3]: Leaving directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' [ 93%] Built target MMBlib make -f CMakeFiles/MMB.dir/build.make CMakeFiles/MMB.dir/depend make[3]: Entering directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' cd /build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/macromoleculebuilder-3.2+dfsg /build/macromoleculebuilder-3.2+dfsg /build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu /build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu /build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/MMB.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/MMB.dir/build.make CMakeFiles/MMB.dir/build make[3]: Entering directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/MMB.dir/build'. make[3]: Leaving directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' [100%] Built target MMB make[2]: Leaving directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/lib/libMMBlib.so.3.2 -- Set runtime path of "/build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/lib/libMMBlib.so.3.2" to "" -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/lib/libMMBlib.so -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/bin/MMB -- Set runtime path of "/build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/bin/MMB" to "" -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/share/MMB/parameters.csv -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/scripts -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/scripts/renumber.pl -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/scripts/renumber-loop.pl -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/scripts/parse-restraints.pl -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/scripts/format-for-pdb.awk -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/scripts/extract_FASTA.bak.awk -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/scripts/extract_FASTA.awk -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/scripts/b-factor-per-residue.pl -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/scripts/add-precision.awk -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/scripts/add-chain-IDs.pl -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/tRNA.pdb -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/protein-template.pdb -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/parameters.csv -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/commands.template_docking.dat -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/commands.template-docking.dat -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/commands.tRNA-fitting.dat -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/commands.singlebasepair.dat -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/commands.protein-morphing.dat -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/commands.protein-homology-modeling.dat -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/commands.long-chain-ID.dat -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/commands.hairpin-short.dat -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/commands.disulphide-bonded-cysteines.dat -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/commands.benzene.dat -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/commands.antibody-antigen.flexible-interfaces.dat -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/commands.TetR_threading_TUT.dat -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/commands.TetRB.scanning.dat -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/commands.TAR.dat -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/commands.RNA-homology-modeling.dat -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/commands.RBP-fitting.dat -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/commands.NMR.dat -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/commands.GlnBP-thermal-exploration.dat -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/commands.GNRA-NtC.dat -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/commands.DNA-helix.dat -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/commands.A_N.32.N.dat -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/commands.A_N.32.G.dat -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/antibody-antigen.pdb -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/TetRB.scanning.pdb -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/TetR.pdb -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/6TNA.short.pdb -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/5MRC.GNRA.pdb -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/2AVY.A.pdb -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/1mlc.DEF.pdb -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/1mlb.AB.pdb -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/1dpx.C.pdb -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/1WDN.short.pdb -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/1UAO.short.pdb -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/1UAO.atoms-renamed.pdb -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/1UAO-disre-simple.txt -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/1GID.shifted.pdb -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/1GGG.short.pdb -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/1FC2.pdb -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/1FC2.C-to-A.pdb -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/1BA2.aligned.pdb -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/1ARJ.short.pdb -- Installing: /build/macromoleculebuilder-3.2+dfsg/debian/tmp/usr/examples/.commands.GNRA-NtC.dat.swp make[1]: Leaving directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' debian/rules override_dh_install make[1]: Entering directory '/build/macromoleculebuilder-3.2+dfsg' dh_install dh_install -plibmmblib3.2 debian/tmp/usr/lib/libMMBlib.so.* usr/lib/x86_64-linux-gnu dh_install -plibmmblib-dev debian/tmp/usr/lib/libMMBlib.so usr/lib/x86_64-linux-gnu make[1]: Leaving directory '/build/macromoleculebuilder-3.2+dfsg' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/macromoleculebuilder-3.2+dfsg' a2x -d manpage -f manpage -D debian/tmp debian/MMB.1.asciidoc dh_installman make[1]: Leaving directory '/build/macromoleculebuilder-3.2+dfsg' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_missing: warning: usr/examples/.commands.GNRA-NtC.dat.swp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/1ARJ.short.pdb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/1BA2.aligned.pdb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/1FC2.C-to-A.pdb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/1FC2.pdb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/1GGG.short.pdb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/1GID.shifted.pdb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/1UAO-disre-simple.txt exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/1UAO.atoms-renamed.pdb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/1UAO.short.pdb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/1WDN.short.pdb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/1dpx.C.pdb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/1mlb.AB.pdb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/1mlc.DEF.pdb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/2AVY.A.pdb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/5MRC.GNRA.pdb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/6TNA.short.pdb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/TetR.pdb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/TetRB.scanning.pdb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/antibody-antigen.pdb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/commands.A_N.32.G.dat exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/commands.A_N.32.N.dat exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/commands.DNA-helix.dat exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/commands.GNRA-NtC.dat exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/commands.GlnBP-thermal-exploration.dat exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/commands.NMR.dat exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/commands.RBP-fitting.dat exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/commands.RNA-homology-modeling.dat exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/commands.TAR.dat exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/commands.TetRB.scanning.dat exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/commands.TetR_threading_TUT.dat exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/commands.antibody-antigen.flexible-interfaces.dat exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/commands.benzene.dat exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/commands.disulphide-bonded-cysteines.dat exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/commands.hairpin-short.dat exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/commands.long-chain-ID.dat exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/commands.protein-homology-modeling.dat exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/commands.protein-morphing.dat exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/commands.singlebasepair.dat exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/commands.tRNA-fitting.dat exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/commands.template-docking.dat exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/commands.template_docking.dat exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/parameters.csv exists in debian/tmp but is not installed to anywhere (related file: "debian/tmp/usr/share/MMB/parameters.csv") dh_missing: warning: usr/examples/protein-template.pdb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/examples/tRNA.pdb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/scripts/add-chain-IDs.pl exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/scripts/add-precision.awk exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/scripts/b-factor-per-residue.pl exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/scripts/extract_FASTA.awk exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/scripts/extract_FASTA.bak.awk exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/scripts/format-for-pdb.awk exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/scripts/parse-restraints.pl exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/scripts/renumber-loop.pl exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/scripts/renumber.pl exists in debian/tmp but is not installed to anywhere While detecting missing files, dh_missing noted some files with a similar name to those that were missing. This warning /might/ be resolved by replacing references to the missing files with the similarly named ones that dh_missing found - assuming the content is identical. As an example, you might want to replace: * debian/tmp/usr/share/MMB/parameters.csv with: * usr/examples/parameters.csv in a file in debian/ or as argument to one of the dh_* tools called from debian/rules. (Note it is possible the paths are not used verbatim but instead directories containing or globs matching them are used instead) Alternatively, add the missing file to debian/not-installed if it cannot and should not be used. The following debhelper tools have reported what they installed (with files per package) * dh_install: libmmblib-dev (1), libmmblib3.2 (1), mmb (1), mmb-common (1) * dh_installdocs: libmmblib-dev (0), libmmblib3.2 (0), mmb (0), mmb-common (0) * dh_installman: libmmblib-dev (0), libmmblib3.2 (0), mmb (1), mmb-common (0) If the missing files are installed by another tool, please file a bug against it. When filing the report, if the tool is not part of debhelper itself, please reference the "Logging helpers and dh_missing" section from the "PROGRAMMING" guide for debhelper (10.6.3+). (in the debhelper package: /usr/share/doc/debhelper/PROGRAMMING.gz) Be sure to test with dpkg-buildpackage -A/-B as the results may vary when only a subset is built If the omission is intentional or no other helper can take care of this consider adding the paths to debian/not-installed. dh_dwz dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libmmblib-dev' in '../libmmblib-dev_3.2+dfsg-2+deb11u1_amd64.deb'. dpkg-deb: building package 'mmb-dbgsym' in '../mmb-dbgsym_3.2+dfsg-2+deb11u1_amd64.deb'. dpkg-deb: building package 'libmmblib3.2-dbgsym' in '../libmmblib3.2-dbgsym_3.2+dfsg-2+deb11u1_amd64.deb'. dpkg-deb: building package 'mmb' in '../mmb_3.2+dfsg-2+deb11u1_amd64.deb'. dpkg-deb: building package 'mmb-common' in '../mmb-common_3.2+dfsg-2+deb11u1_all.deb'. dpkg-deb: building package 'libmmblib3.2' in '../libmmblib3.2_3.2+dfsg-2+deb11u1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../macromoleculebuilder_3.2+dfsg-2+deb11u1_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/4106802 and its subdirectories I: Current time: Fri May 31 07:39:46 -12 2024 I: pbuilder-time-stamp: 1717184386 Sat Apr 29 13:16:47 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Sat Apr 29 13:16:47 UTC 2023 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Sat Apr 29 13:25:42 UTC 2023 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Sat Apr 29 13:25:42 UTC 2023 I: macromoleculebuilder_3.2+dfsg-2+deb11u1_amd64.changes: Format: 1.8 Date: Wed, 04 Jan 2023 07:13:05 -0500 Source: macromoleculebuilder Binary: libmmblib-dev libmmblib3.2 libmmblib3.2-dbgsym mmb mmb-common mmb-dbgsym Architecture: amd64 all Version: 3.2+dfsg-2+deb11u1 Distribution: bullseye Urgency: medium Maintainer: Debichem Team Changed-By: Andrius Merkys Description: libmmblib-dev - development files of MacroMoleculeBuilder libmmblib3.2 - shared library of MacroMoleculeBuilder mmb - model the structure and dynamics of macromolecules mmb-common - model the structure and dynamics of macromolecules (common files) Closes: 1027828 Changes: macromoleculebuilder (3.2+dfsg-2+deb11u1) bullseye; urgency=medium . * Build depends on docbook-xsl (Closes: #1027828) Checksums-Sha1: b7506a2ab4395c0a2195dbaa0b14a2557a9e11f1 2676 libmmblib-dev_3.2+dfsg-2+deb11u1_amd64.deb eb9a13f089c62ba56432ddf435f2393ba827d9b0 8148044 libmmblib3.2-dbgsym_3.2+dfsg-2+deb11u1_amd64.deb e38fea06743b26f14aea17a5ea335c5a20a06717 939332 libmmblib3.2_3.2+dfsg-2+deb11u1_amd64.deb b25c70237dffc4af6ac8a7f171aacbb6a9583db4 10706 macromoleculebuilder_3.2+dfsg-2+deb11u1_amd64.buildinfo 030e825d9af5b3d4118326c95cd60d84019c4b21 255884 mmb-common_3.2+dfsg-2+deb11u1_all.deb 60de040d9cf3ba5866471e423954edf142f8dc85 1065852 mmb-dbgsym_3.2+dfsg-2+deb11u1_amd64.deb d91988a62ae6e4e309165afcea2af68375107d2a 54868 mmb_3.2+dfsg-2+deb11u1_amd64.deb Checksums-Sha256: fc32df20b0a0a6e720c3f56b45b48742493a4fc0e93210888d215631c9abf2b6 2676 libmmblib-dev_3.2+dfsg-2+deb11u1_amd64.deb 3969672aa5420d80741a8581598ccd0e006942bf31a0ea6098ed393fcfc563f8 8148044 libmmblib3.2-dbgsym_3.2+dfsg-2+deb11u1_amd64.deb 7e6e34e845a6c8fabbc1371a9fc8013f1e1372c4b96ef5f0bcdc4768ceec61cd 939332 libmmblib3.2_3.2+dfsg-2+deb11u1_amd64.deb 1f8c1639f91879feab968bd87b34039f9bc066b5afa83a3c92fefdb5ea8fbcbd 10706 macromoleculebuilder_3.2+dfsg-2+deb11u1_amd64.buildinfo 810ca0fb0126d003ab7f520019e9c7ff7eed3a2f58d5b30f33f8ba396b0d8942 255884 mmb-common_3.2+dfsg-2+deb11u1_all.deb 9b69c53e6cd4d037a10485ee20b694e4b2827f213ce83a3411044e043b02c815 1065852 mmb-dbgsym_3.2+dfsg-2+deb11u1_amd64.deb dcdb2281267007776ba0c250b03c20935feae4f6eba40805b2c0585634681701 54868 mmb_3.2+dfsg-2+deb11u1_amd64.deb Files: de790c4a415f81408b831460574dfbe4 2676 libdevel optional libmmblib-dev_3.2+dfsg-2+deb11u1_amd64.deb f407917d30cd0b7958b57de2c559619e 8148044 debug optional libmmblib3.2-dbgsym_3.2+dfsg-2+deb11u1_amd64.deb e0f76f9e0b846d9477dcf2b4ba416035 939332 libs optional libmmblib3.2_3.2+dfsg-2+deb11u1_amd64.deb de09f4e7fc184deef6b19881db7b0fae 10706 science optional macromoleculebuilder_3.2+dfsg-2+deb11u1_amd64.buildinfo 03610b1cec27911b12c87d28da2f1a7b 255884 science optional mmb-common_3.2+dfsg-2+deb11u1_all.deb c9b337df7654aae2f3775b9b29af0a96 1065852 debug optional mmb-dbgsym_3.2+dfsg-2+deb11u1_amd64.deb 10b43e13cf6cd4ccecb5563e6196333d 54868 science optional mmb_3.2+dfsg-2+deb11u1_amd64.deb Sat Apr 29 13:25:43 UTC 2023 I: diffoscope 240 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.mSmvXjLf/macromoleculebuilder_3.2+dfsg-2+deb11u1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.mSmvXjLf/macromoleculebuilder_3.2+dfsg-2+deb11u1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.mSmvXjLf/macromoleculebuilder_3.2+dfsg-2+deb11u1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.mSmvXjLf/b1/macromoleculebuilder_3.2+dfsg-2+deb11u1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.mSmvXjLf/b2/macromoleculebuilder_3.2+dfsg-2+deb11u1_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: 0.421s) 0.421s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.161s) 0.161s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.001s) 0.001s 1 call specialize Sat Apr 29 13:25:45 UTC 2023 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists. Sat Apr 29 13:25:45 UTC 2023 I: macromoleculebuilder from bullseye built successfully and reproducibly on amd64. Sat Apr 29 13:25:47 UTC 2023 I: Submitting .buildinfo files to external archives: Sat Apr 29 13:25:47 UTC 2023 I: Submitting 12K b1/macromoleculebuilder_3.2+dfsg-2+deb11u1_amd64.buildinfo.asc Sat Apr 29 13:25:48 UTC 2023 I: Submitting 12K b2/macromoleculebuilder_3.2+dfsg-2+deb11u1_amd64.buildinfo.asc Sat Apr 29 13:25:49 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Apr 29 13:25:49 UTC 2023 I: Done submitting .buildinfo files. Sat Apr 29 13:25:49 UTC 2023 I: Removing signed macromoleculebuilder_3.2+dfsg-2+deb11u1_amd64.buildinfo.asc files: removed './b1/macromoleculebuilder_3.2+dfsg-2+deb11u1_amd64.buildinfo.asc' removed './b2/macromoleculebuilder_3.2+dfsg-2+deb11u1_amd64.buildinfo.asc'