Sun Sep 8 03:19:33 UTC 2024 I: starting to build cnvkit/experimental/armhf on jenkins on '2024-09-08 03:19' Sun Sep 8 03:19:33 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_4/8851/console.log Sun Sep 8 03:19:33 UTC 2024 I: Downloading source for experimental/cnvkit=0.9.10-3~0exp0 --2024-09-08 03:19:33-- http://cdn-fastly.deb.debian.org/debian/pool/main/c/cnvkit/cnvkit_0.9.10-3%7e0exp0.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2485 (2.4K) [text/prs.lines.tag] Saving to: ‘cnvkit_0.9.10-3~0exp0.dsc’ 0K .. 100% 340M=0s 2024-09-08 03:19:33 (340 MB/s) - ‘cnvkit_0.9.10-3~0exp0.dsc’ saved [2485/2485] Sun Sep 8 03:19:33 UTC 2024 I: cnvkit_0.9.10-3~0exp0.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: cnvkit Binary: cnvkit Architecture: all Version: 0.9.10-3~0exp0 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Steffen Moeller , Olivier Sallou Homepage: https://cnvkit.readthedocs.org Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/cnvkit Vcs-Git: https://salsa.debian.org/med-team/cnvkit.git Testsuite: autopkgtest, autopkgtest-pkg-pybuild Testsuite-Triggers: poppler-utils Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all, python3-setuptools, pybuild-plugin-pyproject, python3-pytest , python3-pyfaidx , python3-biopython , python3-pandas , python3-numpy , python3-pysam , python3-scipy , python3-matplotlib , python3-pomegranate , r-bioc-dnacopy (>= 1.78.0) , poppler-utils Package-List: cnvkit deb science optional arch=all Checksums-Sha1: 98f56ef2f4c5258ceef043d0ad0e346993f5931a 23663020 cnvkit_0.9.10.orig.tar.gz f7484c46900519e20a2c8cc3ab1b556cb3019c13 17732 cnvkit_0.9.10-3~0exp0.debian.tar.xz Checksums-Sha256: 56739496f1f59511661107e662d81e5fd8af413571e853b0a1b34d882a19349a 23663020 cnvkit_0.9.10.orig.tar.gz 696ffcc1cc38377e62932d50df600747ab8bbfb7a986ab9f4090d758ca9ff7c0 17732 cnvkit_0.9.10-3~0exp0.debian.tar.xz Files: ac1e8d636fc0fc694d1475a212d0cf98 23663020 cnvkit_0.9.10.orig.tar.gz d6423a6acc31aea516cf9f337be69c58 17732 cnvkit_0.9.10-3~0exp0.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmaeeYMACgkQPCZ2P2xn 5uIsABAApF6vdPs8ZTgv6rRnDeFByt1Bt6jMaETnIFx2HuqO10tqhFamBiN9mKS/ 9lK+82hAWBowR/lYaMPZ+W6Ob3C8PzlstbK95+t9kD2rkEECdytLWonyb7BawV/u hIwxZKOxeEAww8/q6vOEom6VCModBQgB5Q57ASUE5TUgfLsKK6m0grKrulP7UOlr WA3xMxgeVPOVabocLqU+7vOT9dMV7tmq3rXLbLgBNkiadMcIljZRFh+a0+9CPvMt M6+2Zy+nJ8TpC5dA8VFles68cdgZpZ8GjDCpc27NKEFMpe4QjL1EEf86QRxCLWJ4 tDFpIYB7xOdi+L/3lp05E48zWruofJa4ovk8hYdxmnpbSHFh1PQp1fy6Pofp8E02 QIt4CM0wYQ/Q4pfOteMzKPVT1wy1ubcxPfnMmiVKWDX9d8BNmtBUjx2/mtBeatO4 q3Mc+sw9xOlAcjGVWyRnDkVkejcIoCdnYvcMzOeRznRSseLhN5WZXItB4SdZde22 /XiW2BR1cdZwmtDzbbqhQvM5tISwkMb0y80RSbJj6XBqlUo5QKDfhM87RT8NkMRL qFLzIzYLXGJkqlD2Kcu01r8ZYjZnPEK7eoyv/cviOHv3nIKKb9d5fgmYjmMY19ZY +E5SAMqVU5ljM/9PLcSgO4KUd4wUmP/JnlqOu3Wl+FJ5Yy/wUes= =aJK8 -----END PGP SIGNATURE----- Sun Sep 8 03:19:33 UTC 2024 I: Checking whether the package is not for us Sun Sep 8 03:19:33 UTC 2024 I: Starting 1st build on remote node virt64z-armhf-rb.debian.net. Sun Sep 8 03:19:33 UTC 2024 I: Preparing to do remote build '1' on virt64z-armhf-rb.debian.net. Sun Sep 8 03:20:13 UTC 2024 I: Deleting $TMPDIR on virt64z-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Sep 7 15:19:44 -12 2024 I: pbuilder-time-stamp: 1725765584 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-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 [cnvkit_0.9.10-3~0exp0.dsc] I: copying [./cnvkit_0.9.10.orig.tar.gz] I: copying [./cnvkit_0.9.10-3~0exp0.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Jul 22 15:23:47 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./cnvkit_0.9.10-3~0exp0.dsc: no acceptable signature found dpkg-source: info: extracting cnvkit in cnvkit-0.9.10 dpkg-source: info: unpacking cnvkit_0.9.10.orig.tar.gz dpkg-source: info: unpacking cnvkit_0.9.10-3~0exp0.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying python3compat.patch dpkg-source: info: applying spelling dpkg-source: info: applying controldir dpkg-source: info: applying ignore-warnings-in-tests.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/24248/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='experimental' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='62ed86ce74dd47c78cbe556593717916' 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='24248' 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.qSpGzudF/pbuilderrc_mvSi --distribution experimental --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.qSpGzudF/b1 --logfile b1/build.log cnvkit_0.9.10-3~0exp0.dsc' SUDO_GID='110' SUDO_UID='103' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt64z 6.1.0-25-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/24248/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: armhf 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: debhelper-compat (= 13), dh-sequence-python3, python3-all, python3-setuptools, pybuild-plugin-pyproject, python3-pytest, python3-pyfaidx, python3-biopython, python3-pandas, python3-numpy, python3-pysam, python3-scipy, python3-matplotlib, python3-pomegranate, r-bioc-dnacopy (>= 1.78.0), poppler-utils dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19491 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 debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on pybuild-plugin-pyproject; however: Package pybuild-plugin-pyproject is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-pyfaidx; however: Package python3-pyfaidx is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam; however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-pomegranate; however: Package python3-pomegranate is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-dnacopy (>= 1.78.0); however: Package r-bioc-dnacopy is not installed. pbuilder-satisfydepends-dummy depends on poppler-utils; however: Package poppler-utils 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} blt{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-lyx{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnsl2{a} libnspr4{a} libnss3{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpoppler140{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libssh2-1t64{a} libtcl8.6{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxslt1.1{a} libxss1{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} poppler-utils{a} procps{a} pybuild-plugin-pyproject{a} python-matplotlib-data{a} python3{a} python3-all{a} python3-appdirs{a} python3-attr{a} python3-autocommand{a} python3-biopython{a} python3-brotli{a} python3-build{a} python3-cairo{a} python3-chardet{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-fonttools{a} python3-freetype{a} python3-fs{a} python3-importlib-metadata{a} python3-inflect{a} python3-iniconfig{a} python3-installer{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-joblib{a} python3-kiwisolver{a} python3-lxml{a} python3-lz4{a} python3-matplotlib{a} python3-minimal{a} python3-more-itertools{a} python3-mpmath{a} python3-networkx{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-pluggy{a} python3-pomegranate{a} python3-pyfaidx{a} python3-pyparsing{a} python3-pyproject-hooks{a} python3-pysam{a} python3-pytest{a} python3-reportlab{a} python3-rlpycairo{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3-sympy{a} python3-tk{a} python3-toml{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-ufolib2{a} python3-wheel{a} python3-yaml{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} python3.12-tk{a} python3.13-tk{a} readline-common{a} sensible-utils{a} sgml-base{a} tk8.6-blt2.5{a} tzdata{a} unicode-data{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-dejavu-extra isympy-common javascript-common krb5-locales libarchive-cpio-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx ncbi-blast+ poppler-data psmisc publicsuffix python-biopython-doc python3-bottleneck python3-bs4 python3-cssselect python3-gdal python3-html5lib python3-jinja2 python3-numexpr python3-odf python3-olefile python3-openpyxl python3-psutil python3-pydot python3-pygments python3-pygraphviz python3-simplejson python3-tables shared-mime-info wget xdg-user-dirs 0 packages upgraded, 194 newly installed, 0 to remove and 0 not upgraded. Need to get 134 MB of archives. After unpacking 559 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: r-bioc-dnacopy (>= 1.78.0) 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} blt{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-lyx{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnsl2{a} libnspr4{a} libnss3{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpoppler140{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libssh2-1t64{a} libtcl8.6{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxslt1.1{a} libxss1{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} poppler-utils{a} procps{a} pybuild-plugin-pyproject{a} python-matplotlib-data{a} python3{a} python3-all{a} python3-appdirs{a} python3-attr{a} python3-autocommand{a} python3-biopython{a} python3-brotli{a} python3-build{a} python3-cairo{a} python3-chardet{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-fonttools{a} python3-freetype{a} python3-fs{a} python3-importlib-metadata{a} python3-inflect{a} python3-iniconfig{a} python3-installer{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-joblib{a} python3-kiwisolver{a} python3-lxml{a} python3-lz4{a} python3-matplotlib{a} python3-minimal{a} python3-more-itertools{a} python3-mpmath{a} python3-networkx{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-pluggy{a} python3-pomegranate{a} python3-pyfaidx{a} python3-pyparsing{a} python3-pyproject-hooks{a} python3-pysam{a} python3-pytest{a} python3-reportlab{a} python3-rlpycairo{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3-sympy{a} python3-tk{a} python3-toml{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-ufolib2{a} python3-wheel{a} python3-yaml{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} python3.12-tk{a} python3.13-tk{a} readline-common{a} sensible-utils{a} sgml-base{a} tk8.6-blt2.5{a} tzdata{a} unicode-data{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-dejavu-extra isympy-common javascript-common krb5-locales libarchive-cpio-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx ncbi-blast+ poppler-data psmisc publicsuffix python-biopython-doc python3-bottleneck python3-bs4 python3-cssselect python3-gdal python3-html5lib python3-jinja2 python3-numexpr python3-odf python3-olefile python3-openpyxl python3-psutil python3-pydot python3-pygments python3-pygraphviz python3-simplejson python3-tables shared-mime-info wget xdg-user-dirs 0 packages upgraded, 194 newly installed, 0 to remove and 0 not upgraded. Need to get 134 MB of archives. After unpacking 559 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/24248 and its subdirectories Sun Sep 8 03:20:16 UTC 2024 W: No second build log, what happened? Sun Sep 8 03:20:16 UTC 2024 W: Downloading the build dependencies failed Sun Sep 8 03:20:16 UTC 2024 W: Maybe there was a network problem, or the build dependencies are currently uninstallable; consider filing a bug in the last case. Sun Sep 8 03:20:16 UTC 2024 W: Network problems are automatically rescheduled after some hours.