Wed Apr 23 02:17:58 UTC 2025 I: starting to build promod3/unstable/arm64 on jenkins on '2025-04-23 02:17' Wed Apr 23 02:17:58 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_5/91846/console.log Wed Apr 23 02:17:58 UTC 2025 I: Downloading source for unstable/promod3=3.4.2+ds-1 --2025-04-23 02:17:58-- http://deb.debian.org/debian/pool/main/p/promod3/promod3_3.4.2%2bds-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 3240 (3.2K) [text/prs.lines.tag] Saving to: ‘promod3_3.4.2+ds-1.dsc’ 0K ... 100% 429M=0s 2025-04-23 02:17:58 (429 MB/s) - ‘promod3_3.4.2+ds-1.dsc’ saved [3240/3240] Wed Apr 23 02:17:58 UTC 2025 I: promod3_3.4.2+ds-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: promod3 Binary: libpromod3-core-dev, libpromod3-core3.4, libpromod3-loop-dev, libpromod3-loop3.4, libpromod3-modelling-dev, libpromod3-modelling3.4, libpromod3-scoring-dev, libpromod3-scoring3.4, libpromod3-sidechain-dev, libpromod3-sidechain3.4, promod3, promod3-data, python3-promod3 Architecture: any all Version: 3.4.2+ds-1 Maintainer: Debichem Team Uploaders: Andrius Merkys , Homepage: https://openstructure.org/promod3/ Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/debichem-team/promod3 Vcs-Git: https://salsa.debian.org/debichem-team/promod3.git Build-Depends: cmake, debhelper-compat (= 13), dh-python, libboost-filesystem-dev, libboost-iostreams-dev, libboost-program-options-dev, libboost-python-dev, libboost-test-dev, libeigen3-dev, libost-base-dev, libost-conop-dev, libost-geom-dev, libost-img-dev, libost-info-dev, libost-io-dev, libost-mol-alg-dev, libost-mol-dev, libost-mol-mm-dev, libost-seq-alg-dev, libost-seq-dev, libsqlite3-dev, openstructure (>= 2.5.0), python3-dev, python3-ost Package-List: libpromod3-core-dev deb libdevel optional arch=any libpromod3-core3.4 deb libs optional arch=any libpromod3-loop-dev deb libdevel optional arch=any libpromod3-loop3.4 deb libs optional arch=any libpromod3-modelling-dev deb libdevel optional arch=any libpromod3-modelling3.4 deb libs optional arch=any libpromod3-scoring-dev deb libdevel optional arch=any libpromod3-scoring3.4 deb libs optional arch=any libpromod3-sidechain-dev deb libdevel optional arch=any libpromod3-sidechain3.4 deb libs optional arch=any promod3 deb science optional arch=all promod3-data deb science optional arch=all python3-promod3 deb python optional arch=any Checksums-Sha1: fe26d94587be71b7fb6ccc240ad859fac92c81fb 398726492 promod3_3.4.2+ds.orig.tar.xz 957992a7723d0725c56268d9d25b608b36644180 5884 promod3_3.4.2+ds-1.debian.tar.xz Checksums-Sha256: 7a46576b3c73bceaba25b36b10be9b3fc5ef4bdbc1a957d01c7c68eae76dc1b1 398726492 promod3_3.4.2+ds.orig.tar.xz eeee3ec35d048e7fd7cbe8022cf25289d40772ecd89f197a6e30b7182523191f 5884 promod3_3.4.2+ds-1.debian.tar.xz Files: 47857c7c2a40f7ac9798956b6a601c3d 398726492 promod3_3.4.2+ds.orig.tar.xz bbcb4746ab7c2a9e997d04feff944be5 5884 promod3_3.4.2+ds-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEdyKS9veshfrgQdQe5fQ/nCc08ocFAmfrtxASHG1lcmt5c0Bk ZWJpYW4ub3JnAAoJEOX0P5wnNPKHuWMP/iOF/ZMsDErNcI3c3OOYXeiFFQMcAE/W gJ1H40Qk9nUeRf6scL6mn4TREKJ5a6DOT1jyuJvgl4P4q1398OA5zIay6Qv68dS/ f4JLO+eu0I/zzn34bPh1LKDwjLDkSeMqBFzBz+f7VIfBjXgj84Dxxk+5ZcC26QsS iFrqFX1fb6y9+/eDalk8bdZLlsUvU/FCP/gUMZeGlPO77gcnY7ACrqeLC45pTAJ5 tQyejwrs/Ogl6KWtxmNa/QVIDqGWQIJxiFjkVT6zszNRC25q4n3nOxitl4AgtQ0T ccLzaB1WH01xwcg2aDs1bqXsm9ebX8oxgi4N+7ccprEQtC2eOuwt9xBBRHi32jvu SjPJdgJHkmnSzWmb3Av9KG2/74w85qVrrV/pTM4CXT6CSrtxI5IlXpIIYMfy8ypC CUOsuiRRPerkhkK9Bskd+pmDIJG/+ewNXnCqxjVBksjdPPOwhg35EFfCvfWQ0YMB TbVw4SZcvJzwvsLrUcooWetZv4OKj+ak2nfAFWCJqAGGPdSpRPfbVPlYI8gvqBF0 vESGB+4C6dzoivJnrmWzqKtQhAiunzmDLwZwHh/clKCVQHwCYRAYhRfK/LIP6ry5 UW4qNx08eCFWi38qIAhytI18z90lpDAM7a6T/gsskcu15ZM/MA8q7ZbMNOs+eV36 OH3gi8YDkZlR =2u1I -----END PGP SIGNATURE----- Wed Apr 23 02:17:58 UTC 2025 I: Checking whether the package is not for us Wed Apr 23 02:17:58 UTC 2025 I: Starting 1st build on remote node codethink03-arm64.debian.net. Wed Apr 23 02:17:58 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Wed Apr 23 02:18:38 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon May 25 20:41:15 -12 2026 I: pbuilder-time-stamp: 1779784875 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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 [promod3_3.4.2+ds-1.dsc] I: copying [./promod3_3.4.2+ds.orig.tar.xz] I: copying [./promod3_3.4.2+ds-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./promod3_3.4.2+ds-1.dsc: unsupported subcommand dpkg-source: info: extracting promod3 in promod3-3.4.2+ds dpkg-source: info: unpacking promod3_3.4.2+ds.orig.tar.xz dpkg-source: info: unpacking promod3_3.4.2+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying find-OST.patch dpkg-source: info: applying add-python3-shebangs.patch dpkg-source: info: applying promod-executable.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2184673/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='8f2dbd05b6bc48ee8d163e279a0bd549' 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='2184673' 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.V09yVrzS/pbuilderrc_KXZI --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.V09yVrzS/b1 --logfile b1/build.log promod3_3.4.2+ds-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.1.0-33-cloud-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2184673/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: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: cmake, debhelper-compat (= 13), dh-python, libboost-filesystem-dev, libboost-iostreams-dev, libboost-program-options-dev, libboost-python-dev, libboost-test-dev, libeigen3-dev, libost-base-dev, libost-conop-dev, libost-geom-dev, libost-img-dev, libost-info-dev, libost-io-dev, libost-mol-alg-dev, libost-mol-dev, libost-mol-mm-dev, libost-seq-alg-dev, libost-seq-dev, libsqlite3-dev, openstructure (>= 2.5.0), python3-dev, python3-ost dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19953 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on libboost-filesystem-dev; however: Package libboost-filesystem-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however: Package libboost-program-options-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-python-dev; however: Package libboost-python-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-test-dev; however: Package libboost-test-dev is not installed. pbuilder-satisfydepends-dummy depends on libeigen3-dev; however: Package libeigen3-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-base-dev; however: Package libost-base-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-conop-dev; however: Package libost-conop-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-geom-dev; however: Package libost-geom-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-img-dev; however: Package libost-img-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-info-dev; however: Package libost-info-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-io-dev; however: Package libost-io-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-mol-alg-dev; however: Package libost-mol-alg-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-mol-dev; however: Package libost-mol-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-mol-mm-dev; however: Package libost-mol-mm-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-seq-alg-dev; however: Package libost-seq-alg-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-seq-dev; however: Package libost-seq-dev is not installed. pbuilder-satisfydepends-dummy depends on libsqlite3-dev; however: Package libsqlite3-dev is not installed. pbuilder-satisfydepends-dummy depends on openstructure (>= 2.5.0); however: Package openstructure is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-ost; however: Package python3-ost is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libboost-atomic1.83-dev{a} libboost-atomic1.83.0{a} libboost-filesystem-dev{a} libboost-filesystem1.83-dev{a} libboost-filesystem1.83.0{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost-python-dev{a} libboost-python1.83-dev{a} libboost-python1.83.0{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-system1.83-dev{a} libboost-system1.83.0{a} libboost-test-dev{a} libboost-test1.83-dev{a} libboost-test1.83.0{a} libboost1.83-dev{a} libbrotli1{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libeigen3-dev{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgnutls30t64{a} libgssapi-krb5-2{a} libicu-dev{a} libicu76{a} libidn2-0{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl5t64{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsqlite3-dev{a} libssh2-1t64{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python3{a} python3-dev{a} python3-minimal{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 112 newly installed, 0 to remove and 0 not upgraded. Need to get 81.5 MB of archives. After unpacking 484 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: libost-base-dev which is a virtual package and is not provided by any available package Depends: libost-conop-dev which is a virtual package and is not provided by any available package Depends: libost-geom-dev which is a virtual package and is not provided by any available package Depends: libost-img-dev which is a virtual package and is not provided by any available package Depends: libost-info-dev which is a virtual package and is not provided by any available package Depends: libost-io-dev which is a virtual package and is not provided by any available package Depends: libost-mol-alg-dev which is a virtual package and is not provided by any available package Depends: libost-mol-dev which is a virtual package and is not provided by any available package Depends: libost-mol-mm-dev which is a virtual package and is not provided by any available package Depends: libost-seq-alg-dev which is a virtual package and is not provided by any available package Depends: libost-seq-dev which is a virtual package and is not provided by any available package Depends: openstructure (>= 2.5.0) which is a virtual package and is not provided by any available package Depends: python3-ost which is a virtual package and is not provided by any available package Unable to resolve dependencies! Giving up... The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libboost-atomic1.83-dev{a} libboost-atomic1.83.0{a} libboost-filesystem-dev{a} libboost-filesystem1.83-dev{a} libboost-filesystem1.83.0{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost-python-dev{a} libboost-python1.83-dev{a} libboost-python1.83.0{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-system1.83-dev{a} libboost-system1.83.0{a} libboost-test-dev{a} libboost-test1.83-dev{a} libboost-test1.83.0{a} libboost1.83-dev{a} libbrotli1{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libeigen3-dev{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgnutls30t64{a} libgssapi-krb5-2{a} libicu-dev{a} libicu76{a} libidn2-0{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl5t64{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsqlite3-dev{a} libssh2-1t64{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python3{a} python3-dev{a} python3-minimal{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 112 newly installed, 0 to remove and 0 not upgraded. Need to get 81.5 MB of archives. After unpacking 484 MB will be used. Abort. E: pbuilder-satisfydepends failed. 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/2184673 and its subdirectories Wed Apr 23 02:18:40 UTC 2025 W: No second build log, what happened? Wed Apr 23 02:18:40 UTC 2025 W: Downloading the build dependencies failed Wed Apr 23 02:18:40 UTC 2025 W: Maybe there was a network problem, or the build dependencies are currently uninstallable; consider filing a bug in the last case. Wed Apr 23 02:18:40 UTC 2025 W: Network problems are automatically rescheduled after some hours.