Thu May 16 00:41:24 UTC 2024 I: starting to build cnvkit/trixie/amd64 on jenkins on '2024-05-16 00:41' Thu May 16 00:41:24 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_4/20738/console.log Thu May 16 00:41:24 UTC 2024 I: Downloading source for trixie/cnvkit=0.9.10-2 --2024-05-16 00:41:24-- http://deb.debian.org/debian/pool/main/c/cnvkit/cnvkit_0.9.10-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2449 (2.4K) [text/prs.lines.tag] Saving to: ‘cnvkit_0.9.10-2.dsc’ 0K .. 100% 360M=0s 2024-05-16 00:41:24 (360 MB/s) - ‘cnvkit_0.9.10-2.dsc’ saved [2449/2449] Thu May 16 00:41:24 UTC 2024 I: cnvkit_0.9.10-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: cnvkit Binary: cnvkit Architecture: all Version: 0.9.10-2 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 , poppler-utils Package-List: cnvkit deb science optional arch=all Checksums-Sha1: 98f56ef2f4c5258ceef043d0ad0e346993f5931a 23663020 cnvkit_0.9.10.orig.tar.gz 31441a83815f0aa4c84e034fbe6b865f97c472be 17748 cnvkit_0.9.10-2.debian.tar.xz Checksums-Sha256: 56739496f1f59511661107e662d81e5fd8af413571e853b0a1b34d882a19349a 23663020 cnvkit_0.9.10.orig.tar.gz 6664138655aa08f7349c74c257dcdd5bfc9eaf67f3b0608715a96d2dd42817c5 17748 cnvkit_0.9.10-2.debian.tar.xz Files: ac1e8d636fc0fc694d1475a212d0cf98 23663020 cnvkit_0.9.10.orig.tar.gz 5f842d12c34db9964337f7035a88d4c8 17748 cnvkit_0.9.10-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmYTrg8ACgkQPCZ2P2xn 5uL1OA/+JFE3fMRoNRimwh0yT6txfFnHuG0gs8e5hutqvTjjtodh8kqvaAwt1wgH iK0WMDLdot9kB2VDMSQSGRHZFHGBTjJ1Yb7/Ha4PSdFnGJtQgs4dzB40WII+fonN Sr9GIvJxz8409ZeBdT/1jcta53JnSmN+q+j25LJmnmGvGrwPJx9aPJw+7/nB5w/y aDGQylKVomydcMJLIM3mIPwzEd5PDh53Sd1Rwxzm9BkqM6BSPIXjBlLpDtLdOZnD j8vM6zFEwXy9QYe+qZPke3VewxDyj0jsTvKekeYgfLjos4KwBoUR4VsvPmcufQS3 aCKqeu8EgNObp5Ddj61FTsFsgfXxUlj+RKfxFGNPghVDRMGxhjZjeTTbzQCH7ASi CcmA/0bAmGyHx8R+JzUliVjXMchWpJjU20A5K9yHu95bEBlQ9XeQPAafew+cx2gF V9gvp+caaEeIsuxo51hXAW3aSzvGlw85p7JYX2vZlTPhQsFuTyaFducKTi7KOiWg H8cikrIcdaqXvyeBicN349wlc42bh7bdoetVAR/kI3QcWaf78TCOf7AHguuAVo0c 4OP+r19RQetL67yJDRIBymqeZKuXktItNxNkJONby4DG0KgKIZpuxvcEWhpTEzrM SraQ1tpxxIy5kHg3sDlQpKFrwvZc3AVyVuTir/MT9AOaA7woKL0= =Pt4O -----END PGP SIGNATURE----- Thu May 16 00:41:24 UTC 2024 I: Checking whether the package is not for us Thu May 16 00:41:24 UTC 2024 I: Starting 1st build on remote node ionos15-amd64.debian.net. Thu May 16 00:41:24 UTC 2024 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Thu May 16 00:46:44 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Jun 17 19:04:28 -12 2025 I: pbuilder-time-stamp: 1750230268 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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_0.9.10-2.dsc] I: copying [./cnvkit_0.9.10.orig.tar.gz] I: copying [./cnvkit_0.9.10-2.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Apr 8 08:42:55 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./cnvkit_0.9.10-2.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_0.9.10-2.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/1283422/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='944921df8c134af08d16dd609fbaf935' 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='1283422' 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.imKBoxJK/pbuilderrc_yLeV --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.imKBoxJK/b1 --logfile b1/build.log cnvkit_0.9.10-2.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 17 17:46 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1283422/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: 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, 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 ... 19699 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; 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} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{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} libbsd0{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdatrie1{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} libice6{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} libnspr4{a} libnss3{a} libopenjp2-7{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpoppler126t64{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-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} libsm6{a} libssh2-1t64{a} libsub-override-perl{a} libtcl8.6{a} libthai-data{a} libthai0{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} libxt6t64{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{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-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-distutils{a} python3-fonttools{a} python3-freetype{a} python3-fs{a} python3-importlib-metadata{a} python3-iniconfig{a} python3-installer{a} python3-joblib{a} python3-kiwisolver{a} python3-lib2to3{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-tz{a} python3-ufolib2{a} python3-wheel{a} python3-yaml{a} python3-zipp{a} python3.11{a} python3.11-minimal{a} python3.12{a} python3.12-minimal{a} r-base-core{a} r-bioc-biocgenerics{a} r-bioc-dnacopy{a} readline-common{a} sensible-utils{a} sgml-base{a} tk8.6-blt2.5{a} tzdata{a} ucf{a} unicode-data{a} unzip{a} w3c-sgml-lib{a} x11-common{a} xdg-utils{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zip{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-dejavu-extra isympy-common javascript-common krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libx11-protocol-perl 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 r-base-dev r-doc-html r-recommended shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 212 newly installed, 0 to remove and 0 not upgraded. Need to get 182 MB of archives. After unpacking 733 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.3-1 [809 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.3-1 [2139 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1 [1034 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libfontenc1 amd64 1:1.1.8-1 [23.0 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 48 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b1 [17.0 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.14-1 [784 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get: 63 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 70 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 python3-distutils all 3.12.3-1 [131 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20240422 [107 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 fonts-lyx all 2.4.0~RC4-1 [189 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.0-3+b1 [531 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1~rc2-1 [22.6 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 94 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.7.1-5 [433 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.7.1-5 [441 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14-20240330-1 [836 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.80.2-1 [1485 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.19+ds-1.1+b1 [448 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.0.10-1+b1 [56.7 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b1 [35.3 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b1 [29.1 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libnspr4 amd64 2:4.35-1.1+b1 [109 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libnss3 amd64 2:3.99-1 [1408 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libopenjp2-7 amd64 2.5.0-2+b3 [190 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.52.2+ds-1 [218 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.52.2+ds-1 [48.1 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.52.2+ds-1 [35.0 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libpaper1 amd64 1.1.29+b1 [12.9 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 1.1.29+b1 [9176 B] Get: 134 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libpoppler126t64 amd64 22.12.0-2.2+b1 [1866 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.3-1 [1951 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libqhull-r8.0 amd64 2020.2-6+b1 [245 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.1-1+b1 [14.2 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.3-1+b1 [33.6 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [110 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libwebpmux3 amd64 1.4.0-0.1 [123 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libxslt1.1 amd64 1.1.35-1+b1 [232 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libyaml-0-2 amd64 0.2.5-1+b1 [52.6 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 poppler-utils amd64 22.12.0-2.2+b1 [196 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.2.0-1 [59.9 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 1.0.0-6 [6696 B] Get: 152 http://deb.debian.org/debian trixie/main amd64 python3-importlib-metadata all 4.12.0-1 [24.9 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.0-1 [45.5 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 python3-pyproject-hooks all 1.0.0-2 [10.6 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 python3-toml all 0.10.2-1 [16.2 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 python3-wheel all 0.43.0-1 [52.5 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 python3-build all 1.2.1-1 [34.1 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 pybuild-plugin-pyproject all 6.20240422 [11.1 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 python-matplotlib-data all 3.6.3-2 [2744 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.3-1 [659 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 python3-all amd64 3.11.8-1 [1056 B] Get: 163 http://deb.debian.org/debian trixie/main amd64 python3-appdirs all 1.4.4-4 [12.5 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 python3-attr all 23.2.0-2 [65.5 kB] Get: 165 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-8 [5466 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 python3-tk amd64 3.12.3-1 [109 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 python3-pil.imagetk amd64 10.3.0-2 [79.5 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 python3-pil amd64 10.3.0-2 [564 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 python3-cairo amd64 1.26.0-1 [142 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 python3-freetype all 2.4.0-1 [80.3 kB] Get: 172 http://deb.debian.org/debian trixie/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 173 http://deb.debian.org/debian trixie/main amd64 python3-reportlab all 4.2.0-2 [1149 kB] Get: 174 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 python3-biopython amd64 1.83+dfsg1-2 [1634 kB] Get: 177 http://deb.debian.org/debian trixie/main amd64 python3-brotli amd64 1.1.0-2+b3 [312 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 python3-contourpy amd64 1.0.7-3 [285 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get: 180 http://deb.debian.org/debian trixie/main amd64 python3-six all 1.16.0-6 [16.3 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 python3-dateutil all 2.9.0-2 [79.4 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 python3-scipy amd64 1.11.4-6 [19.5 MB] Get: 184 http://deb.debian.org/debian trixie/main amd64 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 python3-sympy all 1.12-7 [3869 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 python3-tz all 2024.1-2 [30.9 kB] Get: 188 http://deb.debian.org/debian trixie/main amd64 python3-fs all 2.4.16-4 [95.4 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 python3-lxml amd64 5.1.0-1 [2092 kB] Get: 190 http://deb.debian.org/debian trixie/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b3 [25.5 kB] Get: 191 http://deb.debian.org/debian trixie/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get: 192 http://deb.debian.org/debian trixie/main amd64 python3-fonttools amd64 4.46.0-1 [1623 kB] Get: 193 http://deb.debian.org/debian trixie/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 194 http://deb.debian.org/debian trixie/main amd64 python3-joblib all 1.3.2-2 [218 kB] Get: 195 http://deb.debian.org/debian trixie/main amd64 python3-kiwisolver amd64 1.4.5-1 [80.7 kB] Get: 196 http://deb.debian.org/debian trixie/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 197 http://deb.debian.org/debian trixie/main amd64 python3-matplotlib amd64 3.6.3-2 [8167 kB] Get: 198 http://deb.debian.org/debian trixie/main amd64 python3-networkx all 2.8.8-2 [1425 kB] Get: 199 http://deb.debian.org/debian trixie/main amd64 python3-pandas-lib amd64 2.1.4+dfsg-8 [7882 kB] Get: 200 http://deb.debian.org/debian trixie/main amd64 python3-pandas all 2.1.4+dfsg-8 [3015 kB] Get: 201 http://deb.debian.org/debian trixie/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 202 http://deb.debian.org/debian trixie/main amd64 python3-yaml amd64 6.0.1-2 [177 kB] Get: 203 http://deb.debian.org/debian trixie/main amd64 python3-pomegranate amd64 0.14.8-6 [4048 kB] Get: 204 http://deb.debian.org/debian trixie/main amd64 python3-pyfaidx all 0.8.1.1-2 [29.0 kB] Get: 205 http://deb.debian.org/debian trixie/main amd64 python3-pysam amd64 0.22.0+ds-1+b2 [4646 kB] Get: 206 http://deb.debian.org/debian trixie/main amd64 python3-pytest all 7.4.4-3 [239 kB] Get: 207 http://deb.debian.org/debian trixie/main amd64 zip amd64 3.0-13 [230 kB] Get: 208 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get: 209 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 210 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.4.0-2 [28.2 MB] Get: 211 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocgenerics all 0.48.1-2 [597 kB] Get: 212 http://deb.debian.org/debian trixie/main amd64 r-bioc-dnacopy amd64 1.76.0-1 [380 kB] Fetched 182 MB in 8s (24.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. 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Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Jun 18 07:05:41 UTC 2025. Universal Time is now: Wed Jun 18 07:05:41 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... Setting up zip (3.0-13) ... Setting up libfontenc1:amd64 (1:1.1.8-1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:amd64 (2.80.2-1) ... No schema files found: doing nothing. Setting up libblas3:amd64 (3.12.0-3) ... 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 libjpeg62-turbo:amd64 (1:2.1.5-3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libnspr4:amd64 (2:4.35-1.1+b1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.13-3+b1) ... 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Setting up libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up python-matplotlib-data (3.6.3-2) ... Setting up openssl (3.2.1-3) ... Setting up libwebpmux3:amd64 (1.4.0-0.1) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.12-minimal (3.12.3-1) ... Setting up libice6:amd64 (2:1.0.10-1+b1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up liblapack3:amd64 (3.12.0-3) ... 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 (1.15-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... Setting up libnss3:amd64 (2:3.99-1) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libthai0:amd64 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up ucf (3.0043+nmu1) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:amd64 (1.1.35-1+b1) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2+b1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up libsm6:amd64 (2:1.2.3-1+b1) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b1) ... Setting up libpaper1:amd64 (1.1.29+b1) ... Creating config file /etc/papersize with new version Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libpython3.12-stdlib:amd64 (3.12.3-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up libcurl4t64:amd64 (8.7.1-5) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up python3.12 (3.12.3-1) ... Setting up libpango-1.0-0:amd64 (1.52.2+ds-1) ... Setting up libcurl3t64-gnutls:amd64 (8.7.1-5) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libpaper-utils (1.1.29+b1) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.18.0-3+b1) ... Setting up libpoppler126t64:amd64 (22.12.0-2.2+b1) ... Setting up libraqm0:amd64 (0.10.1-1+b1) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2) ... Setting up libhts3t64:amd64 (1.19+ds-1.1+b1) ... Setting up libxss1:amd64 (1:1.2.3-1+b1) ... Setting up poppler-utils (22.12.0-2.2+b1) ... Setting up libpangoft2-1.0-0:amd64 (1.52.2+ds-1) ... Setting up libpangocairo-1.0-0:amd64 (1.52.2+ds-1) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up libxft2:amd64 (2.3.6-1+b1) ... Setting up libtk8.6:amd64 (8.6.14-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-freetype (2.4.0-1) ... Setting up python3-wheel (0.43.0-1) ... Setting up python3-tz (2024.1-2) ... Setting up python3-six (1.16.0-6) ... Setting up python3-pil:amd64 (10.3.0-2) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.0-1) ... Setting up python3-pyproject-hooks (1.0.0-2) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-brotli (1.1.0-2+b3) ... Setting up python3-cycler (0.12.1-1) ... Setting up r-base-core (4.4.0-2) ... Creating config file /etc/R/Renviron with new version Setting up python3-kiwisolver (1.4.5-1) ... Setting up python3-toml (0.10.2-1) ... Setting up python3-installer (0.7.0+dfsg1-3) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-lxml:amd64 (5.1.0-1) ... Setting up python3-dateutil (2.9.0-2) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-build (1.2.1-1) ... Setting up python3-lib2to3 (3.12.3-1) ... Setting up python3-appdirs (1.4.4-4) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... python3.12: can't get files for byte-compilation Setting up python3-more-itertools (10.2.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-sympy (1.12-7) ... Setting up python3-attr (23.2.0-2) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up r-bioc-biocgenerics (0.48.1-2) ... Setting up python3-pysam (0.22.0+ds-1+b2) ... Setting up python3-cairo (1.26.0-1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-joblib (1.3.2-2) ... Setting up python3-lz4 (4.0.2+dfsg-1+b3) ... Setting up python3-pytest (7.4.4-3) ... Setting up blt (2.5.3+dfsg-7) ... Setting up python3-all (3.11.8-1) ... Setting up python3-yaml (6.0.1-2) ... Setting up python3-tk:amd64 (3.12.3-1) ... Setting up python3-zipp (1.0.0-6) ... Setting up python3-networkx (2.8.8-2) ... /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:556: SyntaxWarning: invalid octal escape sequence '\420' "graph [edge [ source u'u\4200' target u'u\4200' ] " /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:557: SyntaxWarning: invalid octal escape sequence '\420' + "node [ id u'u\4200' label b ] ]" Setting up python3-fs (2.4.16-4) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-pil.imagetk:amd64 (10.3.0-2) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-numpy (1:1.26.4+ds-8) ... Setting up python3-reportlab (4.2.0-2) ... Setting up r-bioc-dnacopy (1.76.0-1) ... Setting up python3-contourpy (1.0.7-3) ... Setting up dh-python (6.20240422) ... Setting up python3-scipy (1.11.4-6) ... Setting up python3-importlib-metadata (4.12.0-1) ... Setting up pybuild-plugin-pyproject (6.20240422) ... Setting up python3-pomegranate (0.14.8-6) ... Setting up python3-pandas-lib:amd64 (2.1.4+dfsg-8) ... Setting up python3-pandas (2.1.4+dfsg-8) ... Setting up python3-pyfaidx (0.8.1.1-2) ... Setting up python3-fonttools (4.46.0-1) ... Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... Setting up python3-matplotlib (3.6.3-2) ... Processing triggers for libc-bin (2.38-10) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.83+dfsg1-2) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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/reproducible-path/cnvkit-0.9.10/ && 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 > ../cnvkit_0.9.10-2_source.changes dpkg-buildpackage: info: source package cnvkit dpkg-buildpackage: info: source version 0.9.10-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/cnvkit-0.9.10' cd test && /usr/bin/make clean || /bin/true make[2]: Entering directory '/build/reproducible-path/cnvkit-0.9.10/test' # Picard rm -rf build/p*targetcoverage.cnn build/reference-picard.cnn build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns all-scatters.pdf all-diagrams.pdf heatmap-picard.pdf p2-9_2-breaks.txt p2-9_2-genemetrics.txt gender-picard.txt p2-all.cdt p2-all-jtv.txt p2-all.seg p2-9_2.nexus p2-9_2.nexus-ogt p2-all.bed p2-9_2.vcf p2-9_2.theta2.input p2-9_2-segmetrics.cns p2-5_5-segmetrics.cns p*-scatter.pdf p*-diagram.pdf make[2]: Leaving directory '/build/reproducible-path/cnvkit-0.9.10/test' dh_auto_clean make[1]: Leaving directory '/build/reproducible-path/cnvkit-0.9.10' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild dh_auto_build -O--buildsystem=pybuild I: pybuild plugin_pyproject:129: Building wheel for python3.12 with "build" module I: pybuild base:311: python3.12 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit * Building wheel... running bdist_wheel running build running build_py creating build creating build/lib creating build/lib/cnvlib copying cnvlib/diagram.py -> build/lib/cnvlib copying cnvlib/scatter.py -> build/lib/cnvlib copying cnvlib/cnvkit.py -> build/lib/cnvlib copying cnvlib/rna.py -> build/lib/cnvlib copying cnvlib/importers.py -> build/lib/cnvlib copying cnvlib/target.py -> build/lib/cnvlib copying cnvlib/segfilters.py -> build/lib/cnvlib copying cnvlib/samutil.py -> build/lib/cnvlib copying cnvlib/antitarget.py -> build/lib/cnvlib copying cnvlib/cmdutil.py -> build/lib/cnvlib copying cnvlib/call.py -> build/lib/cnvlib copying cnvlib/bintest.py -> build/lib/cnvlib copying cnvlib/descriptives.py -> build/lib/cnvlib copying cnvlib/batch.py -> build/lib/cnvlib copying cnvlib/commands.py -> build/lib/cnvlib copying cnvlib/import_rna.py -> build/lib/cnvlib copying cnvlib/segmetrics.py -> build/lib/cnvlib copying cnvlib/parallel.py -> build/lib/cnvlib copying cnvlib/core.py -> build/lib/cnvlib copying cnvlib/export.py -> build/lib/cnvlib copying cnvlib/cluster.py -> build/lib/cnvlib copying cnvlib/_version.py -> build/lib/cnvlib copying cnvlib/coverage.py -> build/lib/cnvlib copying cnvlib/__init__.py -> build/lib/cnvlib copying cnvlib/access.py -> build/lib/cnvlib copying cnvlib/reference.py -> build/lib/cnvlib copying cnvlib/metrics.py -> build/lib/cnvlib copying cnvlib/heatmap.py -> build/lib/cnvlib copying cnvlib/cnary.py -> build/lib/cnvlib copying cnvlib/params.py -> build/lib/cnvlib copying cnvlib/vary.py -> build/lib/cnvlib copying cnvlib/plots.py -> build/lib/cnvlib copying cnvlib/reports.py -> build/lib/cnvlib copying cnvlib/autobin.py -> build/lib/cnvlib copying cnvlib/fix.py -> build/lib/cnvlib copying cnvlib/smoothing.py -> build/lib/cnvlib creating build/lib/cnvlib/segmentation copying cnvlib/segmentation/cbs.py -> build/lib/cnvlib/segmentation copying cnvlib/segmentation/none.py -> build/lib/cnvlib/segmentation copying cnvlib/segmentation/__init__.py -> build/lib/cnvlib/segmentation copying cnvlib/segmentation/hmm.py -> build/lib/cnvlib/segmentation copying cnvlib/segmentation/flasso.py -> build/lib/cnvlib/segmentation copying cnvlib/segmentation/haar.py -> build/lib/cnvlib/segmentation creating build/lib/skgenome copying skgenome/chromsort.py -> build/lib/skgenome copying skgenome/intersect.py -> build/lib/skgenome copying skgenome/__init__.py -> build/lib/skgenome copying skgenome/merge.py -> build/lib/skgenome copying skgenome/combiners.py -> build/lib/skgenome copying skgenome/subtract.py -> build/lib/skgenome copying skgenome/rangelabel.py -> build/lib/skgenome copying skgenome/subdivide.py -> build/lib/skgenome copying skgenome/gary.py -> build/lib/skgenome creating build/lib/skgenome/tabio copying skgenome/tabio/textcoord.py -> build/lib/skgenome/tabio copying skgenome/tabio/tab.py -> build/lib/skgenome/tabio copying skgenome/tabio/bedio.py -> build/lib/skgenome/tabio copying skgenome/tabio/seqdict.py -> build/lib/skgenome/tabio copying skgenome/tabio/genepred.py -> build/lib/skgenome/tabio copying skgenome/tabio/vcfsimple.py -> build/lib/skgenome/tabio copying skgenome/tabio/picard.py -> build/lib/skgenome/tabio copying skgenome/tabio/seg.py -> build/lib/skgenome/tabio copying skgenome/tabio/__init__.py -> build/lib/skgenome/tabio copying skgenome/tabio/vcfio.py -> build/lib/skgenome/tabio copying skgenome/tabio/util.py -> build/lib/skgenome/tabio copying skgenome/tabio/gff.py -> build/lib/skgenome/tabio running egg_info creating CNVkit.egg-info writing CNVkit.egg-info/PKG-INFO writing dependency_links to CNVkit.egg-info/dependency_links.txt writing entry points to CNVkit.egg-info/entry_points.txt writing requirements to CNVkit.egg-info/requires.txt writing top-level names to CNVkit.egg-info/top_level.txt writing manifest file 'CNVkit.egg-info/SOURCES.txt' reading manifest file 'CNVkit.egg-info/SOURCES.txt' adding license file 'LICENSE' writing manifest file 'CNVkit.egg-info/SOURCES.txt' installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/skgenome copying build/lib/skgenome/chromsort.py -> build/bdist.linux-x86_64/wheel/skgenome copying build/lib/skgenome/intersect.py -> build/bdist.linux-x86_64/wheel/skgenome creating build/bdist.linux-x86_64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/textcoord.py -> build/bdist.linux-x86_64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/tab.py -> build/bdist.linux-x86_64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/bedio.py -> build/bdist.linux-x86_64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/seqdict.py -> build/bdist.linux-x86_64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/genepred.py -> build/bdist.linux-x86_64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/vcfsimple.py -> build/bdist.linux-x86_64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/picard.py -> build/bdist.linux-x86_64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/seg.py -> build/bdist.linux-x86_64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/__init__.py -> build/bdist.linux-x86_64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/vcfio.py -> build/bdist.linux-x86_64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/util.py -> build/bdist.linux-x86_64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/gff.py -> build/bdist.linux-x86_64/wheel/skgenome/tabio copying build/lib/skgenome/__init__.py -> build/bdist.linux-x86_64/wheel/skgenome copying build/lib/skgenome/merge.py -> build/bdist.linux-x86_64/wheel/skgenome copying build/lib/skgenome/combiners.py -> build/bdist.linux-x86_64/wheel/skgenome copying build/lib/skgenome/subtract.py -> build/bdist.linux-x86_64/wheel/skgenome copying build/lib/skgenome/rangelabel.py -> build/bdist.linux-x86_64/wheel/skgenome copying build/lib/skgenome/subdivide.py -> build/bdist.linux-x86_64/wheel/skgenome copying build/lib/skgenome/gary.py -> build/bdist.linux-x86_64/wheel/skgenome creating build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/diagram.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/scatter.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/cnvkit.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/rna.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/importers.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/target.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/segfilters.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/samutil.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/antitarget.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/cmdutil.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/call.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/bintest.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/descriptives.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/batch.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/commands.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/import_rna.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/segmetrics.py -> build/bdist.linux-x86_64/wheel/cnvlib creating build/bdist.linux-x86_64/wheel/cnvlib/segmentation copying build/lib/cnvlib/segmentation/cbs.py -> build/bdist.linux-x86_64/wheel/cnvlib/segmentation copying build/lib/cnvlib/segmentation/none.py -> build/bdist.linux-x86_64/wheel/cnvlib/segmentation copying build/lib/cnvlib/segmentation/__init__.py -> build/bdist.linux-x86_64/wheel/cnvlib/segmentation copying build/lib/cnvlib/segmentation/hmm.py -> build/bdist.linux-x86_64/wheel/cnvlib/segmentation copying build/lib/cnvlib/segmentation/flasso.py -> build/bdist.linux-x86_64/wheel/cnvlib/segmentation copying build/lib/cnvlib/segmentation/haar.py -> build/bdist.linux-x86_64/wheel/cnvlib/segmentation copying build/lib/cnvlib/parallel.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/core.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/export.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/cluster.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/_version.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/coverage.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/__init__.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/access.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/reference.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/metrics.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/heatmap.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/cnary.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/params.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/vary.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/plots.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/reports.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/autobin.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/fix.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/smoothing.py -> build/bdist.linux-x86_64/wheel/cnvlib running install_egg_info Copying CNVkit.egg-info to build/bdist.linux-x86_64/wheel/CNVkit-0.9.10.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/CNVkit-0.9.10.dist-info/WHEEL creating '/build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit/.tmp-uzwj4meo/CNVkit-0.9.10-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'cnvlib/__init__.py' adding 'cnvlib/_version.py' adding 'cnvlib/access.py' adding 'cnvlib/antitarget.py' adding 'cnvlib/autobin.py' adding 'cnvlib/batch.py' adding 'cnvlib/bintest.py' adding 'cnvlib/call.py' adding 'cnvlib/cluster.py' adding 'cnvlib/cmdutil.py' adding 'cnvlib/cnary.py' adding 'cnvlib/cnvkit.py' adding 'cnvlib/commands.py' adding 'cnvlib/core.py' adding 'cnvlib/coverage.py' adding 'cnvlib/descriptives.py' adding 'cnvlib/diagram.py' adding 'cnvlib/export.py' adding 'cnvlib/fix.py' adding 'cnvlib/heatmap.py' adding 'cnvlib/import_rna.py' adding 'cnvlib/importers.py' adding 'cnvlib/metrics.py' adding 'cnvlib/parallel.py' adding 'cnvlib/params.py' adding 'cnvlib/plots.py' adding 'cnvlib/reference.py' adding 'cnvlib/reports.py' adding 'cnvlib/rna.py' adding 'cnvlib/samutil.py' adding 'cnvlib/scatter.py' adding 'cnvlib/segfilters.py' adding 'cnvlib/segmetrics.py' adding 'cnvlib/smoothing.py' adding 'cnvlib/target.py' adding 'cnvlib/vary.py' adding 'cnvlib/segmentation/__init__.py' adding 'cnvlib/segmentation/cbs.py' adding 'cnvlib/segmentation/flasso.py' adding 'cnvlib/segmentation/haar.py' adding 'cnvlib/segmentation/hmm.py' adding 'cnvlib/segmentation/none.py' adding 'skgenome/__init__.py' adding 'skgenome/chromsort.py' adding 'skgenome/combiners.py' adding 'skgenome/gary.py' adding 'skgenome/intersect.py' adding 'skgenome/merge.py' adding 'skgenome/rangelabel.py' adding 'skgenome/subdivide.py' adding 'skgenome/subtract.py' adding 'skgenome/tabio/__init__.py' adding 'skgenome/tabio/bedio.py' adding 'skgenome/tabio/genepred.py' adding 'skgenome/tabio/gff.py' adding 'skgenome/tabio/picard.py' adding 'skgenome/tabio/seg.py' adding 'skgenome/tabio/seqdict.py' adding 'skgenome/tabio/tab.py' adding 'skgenome/tabio/textcoord.py' adding 'skgenome/tabio/util.py' adding 'skgenome/tabio/vcfio.py' adding 'skgenome/tabio/vcfsimple.py' adding 'CNVkit-0.9.10.dist-info/LICENSE' adding 'CNVkit-0.9.10.dist-info/METADATA' adding 'CNVkit-0.9.10.dist-info/WHEEL' adding 'CNVkit-0.9.10.dist-info/entry_points.txt' adding 'CNVkit-0.9.10.dist-info/top_level.txt' adding 'CNVkit-0.9.10.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel Successfully built CNVkit-0.9.10-py3-none-any.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.12 with "installer" module I: pybuild plugin_pyproject:129: Building wheel for python3.11 with "build" module I: pybuild base:311: python3.11 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.11_cnvkit * Building wheel... running bdist_wheel running build running build_py running egg_info writing CNVkit.egg-info/PKG-INFO writing dependency_links to CNVkit.egg-info/dependency_links.txt writing entry points to CNVkit.egg-info/entry_points.txt writing requirements to CNVkit.egg-info/requires.txt writing top-level names to CNVkit.egg-info/top_level.txt reading manifest file 'CNVkit.egg-info/SOURCES.txt' adding license file 'LICENSE' writing manifest file 'CNVkit.egg-info/SOURCES.txt' installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/skgenome copying build/lib/skgenome/chromsort.py -> build/bdist.linux-x86_64/wheel/skgenome copying build/lib/skgenome/intersect.py -> build/bdist.linux-x86_64/wheel/skgenome creating build/bdist.linux-x86_64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/textcoord.py -> build/bdist.linux-x86_64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/tab.py -> build/bdist.linux-x86_64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/bedio.py -> build/bdist.linux-x86_64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/seqdict.py -> build/bdist.linux-x86_64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/genepred.py -> build/bdist.linux-x86_64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/vcfsimple.py -> build/bdist.linux-x86_64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/picard.py -> build/bdist.linux-x86_64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/seg.py -> build/bdist.linux-x86_64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/__init__.py -> build/bdist.linux-x86_64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/vcfio.py -> build/bdist.linux-x86_64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/util.py -> build/bdist.linux-x86_64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/gff.py -> build/bdist.linux-x86_64/wheel/skgenome/tabio copying build/lib/skgenome/__init__.py -> build/bdist.linux-x86_64/wheel/skgenome copying build/lib/skgenome/merge.py -> build/bdist.linux-x86_64/wheel/skgenome copying build/lib/skgenome/combiners.py -> build/bdist.linux-x86_64/wheel/skgenome copying build/lib/skgenome/subtract.py -> build/bdist.linux-x86_64/wheel/skgenome copying build/lib/skgenome/rangelabel.py -> build/bdist.linux-x86_64/wheel/skgenome copying build/lib/skgenome/subdivide.py -> build/bdist.linux-x86_64/wheel/skgenome copying build/lib/skgenome/gary.py -> build/bdist.linux-x86_64/wheel/skgenome creating build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/diagram.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/scatter.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/cnvkit.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/rna.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/importers.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/target.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/segfilters.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/samutil.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/antitarget.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/cmdutil.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/call.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/bintest.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/descriptives.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/batch.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/commands.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/import_rna.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/segmetrics.py -> build/bdist.linux-x86_64/wheel/cnvlib creating build/bdist.linux-x86_64/wheel/cnvlib/segmentation copying build/lib/cnvlib/segmentation/cbs.py -> build/bdist.linux-x86_64/wheel/cnvlib/segmentation copying build/lib/cnvlib/segmentation/none.py -> build/bdist.linux-x86_64/wheel/cnvlib/segmentation copying build/lib/cnvlib/segmentation/__init__.py -> build/bdist.linux-x86_64/wheel/cnvlib/segmentation copying build/lib/cnvlib/segmentation/hmm.py -> build/bdist.linux-x86_64/wheel/cnvlib/segmentation copying build/lib/cnvlib/segmentation/flasso.py -> build/bdist.linux-x86_64/wheel/cnvlib/segmentation copying build/lib/cnvlib/segmentation/haar.py -> build/bdist.linux-x86_64/wheel/cnvlib/segmentation copying build/lib/cnvlib/parallel.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/core.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/export.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/cluster.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/_version.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/coverage.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/__init__.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/access.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/reference.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/metrics.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/heatmap.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/cnary.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/params.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/vary.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/plots.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/reports.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/autobin.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/fix.py -> build/bdist.linux-x86_64/wheel/cnvlib copying build/lib/cnvlib/smoothing.py -> build/bdist.linux-x86_64/wheel/cnvlib running install_egg_info Copying CNVkit.egg-info to build/bdist.linux-x86_64/wheel/CNVkit-0.9.10.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/CNVkit-0.9.10.dist-info/WHEEL creating '/build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.11_cnvkit/.tmp-trrjvy7s/CNVkit-0.9.10-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'cnvlib/__init__.py' adding 'cnvlib/_version.py' adding 'cnvlib/access.py' adding 'cnvlib/antitarget.py' adding 'cnvlib/autobin.py' adding 'cnvlib/batch.py' adding 'cnvlib/bintest.py' adding 'cnvlib/call.py' adding 'cnvlib/cluster.py' adding 'cnvlib/cmdutil.py' adding 'cnvlib/cnary.py' adding 'cnvlib/cnvkit.py' adding 'cnvlib/commands.py' adding 'cnvlib/core.py' adding 'cnvlib/coverage.py' adding 'cnvlib/descriptives.py' adding 'cnvlib/diagram.py' adding 'cnvlib/export.py' adding 'cnvlib/fix.py' adding 'cnvlib/heatmap.py' adding 'cnvlib/import_rna.py' adding 'cnvlib/importers.py' adding 'cnvlib/metrics.py' adding 'cnvlib/parallel.py' adding 'cnvlib/params.py' adding 'cnvlib/plots.py' adding 'cnvlib/reference.py' adding 'cnvlib/reports.py' adding 'cnvlib/rna.py' adding 'cnvlib/samutil.py' adding 'cnvlib/scatter.py' adding 'cnvlib/segfilters.py' adding 'cnvlib/segmetrics.py' adding 'cnvlib/smoothing.py' adding 'cnvlib/target.py' adding 'cnvlib/vary.py' adding 'cnvlib/segmentation/__init__.py' adding 'cnvlib/segmentation/cbs.py' adding 'cnvlib/segmentation/flasso.py' adding 'cnvlib/segmentation/haar.py' adding 'cnvlib/segmentation/hmm.py' adding 'cnvlib/segmentation/none.py' adding 'skgenome/__init__.py' adding 'skgenome/chromsort.py' adding 'skgenome/combiners.py' adding 'skgenome/gary.py' adding 'skgenome/intersect.py' adding 'skgenome/merge.py' adding 'skgenome/rangelabel.py' adding 'skgenome/subdivide.py' adding 'skgenome/subtract.py' adding 'skgenome/tabio/__init__.py' adding 'skgenome/tabio/bedio.py' adding 'skgenome/tabio/genepred.py' adding 'skgenome/tabio/gff.py' adding 'skgenome/tabio/picard.py' adding 'skgenome/tabio/seg.py' adding 'skgenome/tabio/seqdict.py' adding 'skgenome/tabio/tab.py' adding 'skgenome/tabio/textcoord.py' adding 'skgenome/tabio/util.py' adding 'skgenome/tabio/vcfio.py' adding 'skgenome/tabio/vcfsimple.py' adding 'CNVkit-0.9.10.dist-info/LICENSE' adding 'CNVkit-0.9.10.dist-info/METADATA' adding 'CNVkit-0.9.10.dist-info/WHEEL' adding 'CNVkit-0.9.10.dist-info/entry_points.txt' adding 'CNVkit-0.9.10.dist-info/top_level.txt' adding 'CNVkit-0.9.10.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel Successfully built CNVkit-0.9.10-py3-none-any.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.11 with "installer" module dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:308: ln -s /build/reproducible-path/cnvkit-0.9.10/data /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit/build/data; I: pybuild base:311: cd /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit/build; python3.12 -m pytest test ============================= test session starts ============================== platform linux -- Python 3.12.3, pytest-7.4.4, pluggy-1.5.0 rootdir: /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit/build configfile: pyproject.toml collected 64 items test/test_cnvlib.py ......... [ 14%] test/test_commands.py ......................... [ 53%] test/test_genome.py ................... [ 82%] test/test_io.py .......... [ 98%] test/test_r.py . [100%] =============================== warnings summary =============================== test/test_commands.py::CommandTests::test_batch /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit/build/cnvlib/coverage.py:198: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1.20240481 0.31062124 0.89178357 0. 0. 0. 1.20240481 0.4 0.2004008 0. 0.4008016 0.4 0.4008016 0. 0. 0. 0.4008016 0. 1.20240481 0. 0. 0. 0. 0.4 ]' has dtype incompatible with int64, please explicitly cast to a compatible dtype first. table.loc[ok_idx, "depth"] = table.loc[ok_idx, "basecount"] / spans[ok_idx] test/test_commands.py::CommandTests::test_batch test/test_commands.py::CommandTests::test_batch /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit/build/cnvlib/reference.py:187: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation. ref_df = pd.concat([ref_df, anti_ref_df], ignore_index=True) test/test_commands.py::CommandTests::test_batch test/test_commands.py::CommandTests::test_batch /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit/build/cnvlib/coverage.py:198: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ 3. 3. 3. 3.09090909 4. 4. 3.77777778 4. 91.75 81.66666667 75.11111111]' has dtype incompatible with int64, please explicitly cast to a compatible dtype first. table.loc[ok_idx, "depth"] = table.loc[ok_idx, "basecount"] / spans[ok_idx] test/test_commands.py::CommandTests::test_coverage test/test_commands.py::CommandTests::test_coverage test/test_commands.py::CommandTests::test_coverage test/test_commands.py::CommandTests::test_coverage /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit/build/cnvlib/coverage.py:198: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[82.5 3.02325581 4. 3.88888889]' has dtype incompatible with int64, please explicitly cast to a compatible dtype first. table.loc[ok_idx, "depth"] = table.loc[ok_idx, "basecount"] / spans[ok_idx] test/test_commands.py: 8 warnings test/test_genome.py: 21 warnings /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit/build/skgenome/gary.py:90: FutureWarning: Passing a DataFrame to DataFrame.from_records is deprecated. Use set_index and/or drop to modify the DataFrame instead. table = pd.DataFrame.from_records(rows, columns=columns) test/test_commands.py::CommandTests::test_target test/test_commands.py::CommandTests::test_target test/test_commands.py::CommandTests::test_target test/test_commands.py::CommandTests::test_target test/test_commands.py::CommandTests::test_target test/test_commands.py::CommandTests::test_target test/test_genome.py::GaryTests::test_total_range_size test/test_genome.py::GaryTests::test_total_range_size /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit/build/skgenome/combiners.py:53: FutureWarning: unique with argument that is not not a Series, Index, ExtensionArray, or np.ndarray is deprecated and will raise in a future version. return sep.join(pd.unique(elems)) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ======================= 64 passed, 46 warnings in 49.10s ======================= I: pybuild pybuild:308: ln -s /build/reproducible-path/cnvkit-0.9.10/data /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.11_cnvkit/build/data; I: pybuild base:311: cd /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.11_cnvkit/build; python3.11 -m pytest test ============================= test session starts ============================== platform linux -- Python 3.11.9, pytest-7.4.4, pluggy-1.5.0 rootdir: /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.11_cnvkit/build configfile: pyproject.toml collected 64 items test/test_cnvlib.py ......... [ 14%] test/test_commands.py ......................... [ 53%] test/test_genome.py ................... [ 82%] test/test_io.py .......... [ 98%] test/test_r.py . [100%] =============================== warnings summary =============================== test/test_commands.py::CommandTests::test_batch /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/coverage.py:198: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1.20240481 0.31062124 0.89178357 0. 0. 0. 1.20240481 0.4 0.2004008 0. 0.4008016 0.4 0.4008016 0. 0. 0. 0.4008016 0. 1.20240481 0. 0. 0. 0. 0.4 ]' has dtype incompatible with int64, please explicitly cast to a compatible dtype first. table.loc[ok_idx, "depth"] = table.loc[ok_idx, "basecount"] / spans[ok_idx] test/test_commands.py::CommandTests::test_batch test/test_commands.py::CommandTests::test_batch /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/reference.py:187: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation. ref_df = pd.concat([ref_df, anti_ref_df], ignore_index=True) test/test_commands.py::CommandTests::test_batch test/test_commands.py::CommandTests::test_batch /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/coverage.py:198: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ 3. 3. 3. 3.09090909 4. 4. 3.77777778 4. 91.75 81.66666667 75.11111111]' has dtype incompatible with int64, please explicitly cast to a compatible dtype first. table.loc[ok_idx, "depth"] = table.loc[ok_idx, "basecount"] / spans[ok_idx] test/test_commands.py::CommandTests::test_coverage test/test_commands.py::CommandTests::test_coverage test/test_commands.py::CommandTests::test_coverage test/test_commands.py::CommandTests::test_coverage /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/coverage.py:198: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[82.5 3.02325581 4. 3.88888889]' has dtype incompatible with int64, please explicitly cast to a compatible dtype first. table.loc[ok_idx, "depth"] = table.loc[ok_idx, "basecount"] / spans[ok_idx] test/test_commands.py: 8 warnings test/test_genome.py: 21 warnings /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.11_cnvkit/build/skgenome/gary.py:90: FutureWarning: Passing a DataFrame to DataFrame.from_records is deprecated. Use set_index and/or drop to modify the DataFrame instead. table = pd.DataFrame.from_records(rows, columns=columns) test/test_commands.py::CommandTests::test_target test/test_commands.py::CommandTests::test_target test/test_commands.py::CommandTests::test_target test/test_commands.py::CommandTests::test_target test/test_commands.py::CommandTests::test_target test/test_commands.py::CommandTests::test_target test/test_genome.py::GaryTests::test_total_range_size test/test_genome.py::GaryTests::test_total_range_size /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.11_cnvkit/build/skgenome/combiners.py:53: FutureWarning: unique with argument that is not not a Series, Index, ExtensionArray, or np.ndarray is deprecated and will raise in a future version. return sep.join(pd.unique(elems)) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ======================= 64 passed, 46 warnings in 50.62s ======================= create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/cnvkit-0.9.10' for script in `find scripts -name "*.py"` ; do \ dh_install ${script} /usr/bin; \ done dh_auto_install I: pybuild plugin_pyproject:178: Copying package built for python3.12 to destdir I: pybuild plugin_pyproject:178: Copying package built for python3.11 to destdir make[1]: Leaving directory '/build/reproducible-path/cnvkit-0.9.10' dh_install -O--buildsystem=pybuild dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild I: dh_python3 tools:113: replacing shebang in debian/cnvkit/usr/bin/genome_instability_index.py dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'cnvkit' in '../cnvkit_0.9.10-2_all.deb'. dpkg-genbuildinfo --build=binary -O../cnvkit_0.9.10-2_amd64.buildinfo dpkg-genchanges --build=binary -O../cnvkit_0.9.10-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1283422 and its subdirectories I: Current time: Tue Jun 17 19:09:43 -12 2025 I: pbuilder-time-stamp: 1750230583 Thu May 16 00:46:44 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Thu May 16 00:46:44 UTC 2024 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Thu May 16 01:41:55 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Thu May 16 01:41:56 UTC 2024 I: cnvkit_0.9.10-2_amd64.changes: Format: 1.8 Date: Mon, 08 Apr 2024 10:42:20 +0200 Source: cnvkit Binary: cnvkit Architecture: all Version: 0.9.10-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: cnvkit - Copy number variant detection from targeted DNA sequencing Changes: cnvkit (0.9.10-2) unstable; urgency=medium . * No-change rebuild of the package from experimental for unstable. Checksums-Sha1: 9f8206e9507ce5847e881fb0d0fc87a28ee90b13 19501620 cnvkit_0.9.10-2_all.deb f2d887e272ea20aebd39543910ec154e8643724b 10585 cnvkit_0.9.10-2_amd64.buildinfo Checksums-Sha256: bf1fd75c757a204fb8123b69285b16b389dfc0c840d3941227ff8c7f89a602e3 19501620 cnvkit_0.9.10-2_all.deb 05645d7a8acc8170ab8280c71a83abdb1ba5446647b5be5a15cd26c14ed0bee6 10585 cnvkit_0.9.10-2_amd64.buildinfo Files: 34bc5101407f83474714510d690c42f5 19501620 science optional cnvkit_0.9.10-2_all.deb 97dcd941deba207252d72941d27d420a 10585 science optional cnvkit_0.9.10-2_amd64.buildinfo Thu May 16 01:41:57 UTC 2024 I: diffoscope 266 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_4-20738.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.imKBoxJK/cnvkit_0.9.10-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.imKBoxJK/cnvkit_0.9.10-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.imKBoxJK/cnvkit_0.9.10-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.imKBoxJK/b1/cnvkit_0.9.10-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.imKBoxJK/b2/cnvkit_0.9.10-2_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.547s) 0.547s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.213s) 0.213s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 866ms CPU time consumed: 864ms Thu May 16 01:41:58 UTC 2024 I: diffoscope 266 found no differences in the changes files, and a .buildinfo file also exists. Thu May 16 01:41:58 UTC 2024 I: cnvkit from trixie built successfully and reproducibly on amd64. Thu May 16 01:42:00 UTC 2024 I: Submitting .buildinfo files to external archives: Thu May 16 01:42:00 UTC 2024 I: Submitting 12K b1/cnvkit_0.9.10-2_amd64.buildinfo.asc Thu May 16 01:42:01 UTC 2024 I: Submitting 12K b2/cnvkit_0.9.10-2_amd64.buildinfo.asc Thu May 16 01:42:01 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu May 16 01:42:01 UTC 2024 I: Done submitting .buildinfo files. Thu May 16 01:42:02 UTC 2024 I: Removing signed cnvkit_0.9.10-2_amd64.buildinfo.asc files: removed './b1/cnvkit_0.9.10-2_amd64.buildinfo.asc' removed './b2/cnvkit_0.9.10-2_amd64.buildinfo.asc'