https://launchpad.net/ubuntu/+archive/test-rebuild-20220617-kinetic/+build/24036498 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lgw01-amd64-036 5.4.0-120-generic #136-Ubuntu SMP Fri Jun 10 13:40:48 UTC 2022 x86_64 Buildd toolchain package versions: launchpad-buildd_215~563~ubuntu20.04.1 python3-lpbuildd_215~563~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.4 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 23 Jun 04:22:11 ntpdate[1820]: adjust time server 10.211.37.1 offset 0.002006 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24036498 --image-type chroot /home/buildd/filecache-default/4d18961cd05542d5def75b14497015b674c37821 Creating target for build PACKAGEBUILD-24036498 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24036498 Starting target for build PACKAGEBUILD-24036498 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24036498 'deb http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic main' 'deb http://ftpmaster.internal/ubuntu kinetic main universe' Overriding sources.list in build-PACKAGEBUILD-24036498 RUN: /usr/share/launchpad-buildd/bin/in-target add-trusted-keys --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24036498 Adding trusted keys to build-PACKAGEBUILD-24036498 pub rsa1024/1E9377A2BA9EF27F 2009-10-22 [SC] Key fingerprint = 60C3 1780 3A41 BA51 845E 371A 1E93 77A2 BA9E F27F uid Launchpad Toolchain builds RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24036498 Updating target for build PACKAGEBUILD-24036498 Get:1 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic InRelease [23.8 kB] Get:2 http://ftpmaster.internal/ubuntu kinetic InRelease [267 kB] Get:3 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 Packages [9632 B] Get:4 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main Translation-en [4132 B] Get:5 http://ftpmaster.internal/ubuntu kinetic/main amd64 Packages [1398 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic/main Translation-en [510 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/universe amd64 Packages [14.3 MB] Get:8 http://ftpmaster.internal/ubuntu kinetic/universe Translation-en [5729 kB] Fetched 22.2 MB in 4s (6246 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: libgprofng0 util-linux-extra The following packages will be upgraded: adduser apt base-files binutils binutils-common binutils-x86-64-linux-gnu bsdutils cpp-11 dpkg dpkg-dev e2fsprogs fakeroot g++-11 gcc-11 gcc-11-base gcc-12-base init init-system-helpers libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libbinutils libblkid1 libcap-ng0 libcc1-0 libcom-err2 libctf-nobfd0 libctf0 libdb5.3 libdpkg-perl libext2fs2 libfakeroot libgcc-11-dev libgcc-s1 libgcrypt20 libgnutls30 libgomp1 libgpg-error0 libip4tc2 libitm1 libkeyutils1 liblsan0 liblzma5 libmount1 libncurses6 libncursesw6 libpng16-16 libquadmath0 libreadline8 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libss2 libssl3 libstdc++-11-dev libstdc++6 libsystemd0 libtinfo6 libtsan0 libubsan1 libudev1 libuuid1 libzstd1 login logsave lto-disabled-list mawk mount ncurses-base ncurses-bin openssl passwd pinentry-curses policyrcd-script-zg2 readline-common systemd systemd-sysv util-linux xz-utils 83 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 79.7 MB of archives. After this operation, 5304 kB of additional disk space will be used. Get:1 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 libctf0 amd64 2.38.50.20220615-4ubuntu1 [103 kB] Get:2 http://ftpmaster.internal/ubuntu kinetic/main amd64 base-files amd64 12.2ubuntu1 [62.6 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic/main amd64 bsdutils amd64 1:2.38-4ubuntu1 [80.7 kB] Get:4 http://ftpmaster.internal/ubuntu kinetic/main amd64 libzstd1 amd64 1.5.2+dfsg-1 [270 kB] Get:5 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 libctf-nobfd0 amd64 2.38.50.20220615-4ubuntu1 [107 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic/main amd64 libatomic1 amd64 12.1.0-2ubuntu1 [10.4 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/main amd64 libubsan1 amd64 12.1.0-2ubuntu1 [969 kB] Get:8 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 binutils-x86-64-linux-gnu amd64 2.38.50.20220615-4ubuntu1 [2476 kB] Get:9 http://ftpmaster.internal/ubuntu kinetic/main amd64 libquadmath0 amd64 12.1.0-2ubuntu1 [152 kB] Get:10 http://ftpmaster.internal/ubuntu kinetic/main amd64 liblsan0 amd64 12.1.0-2ubuntu1 [1060 kB] Get:11 http://ftpmaster.internal/ubuntu kinetic/main amd64 libitm1 amd64 12.1.0-2ubuntu1 [29.5 kB] Get:12 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgomp1 amd64 12.1.0-2ubuntu1 [125 kB] Get:13 http://ftpmaster.internal/ubuntu kinetic/main amd64 gcc-12-base amd64 12.1.0-2ubuntu1 [18.8 kB] Get:14 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgcc-s1 amd64 12.1.0-2ubuntu1 [54.2 kB] Get:15 http://ftpmaster.internal/ubuntu kinetic/main amd64 libcc1-0 amd64 12.1.0-2ubuntu1 [46.6 kB] Get:16 http://ftpmaster.internal/ubuntu kinetic/main amd64 libstdc++6 amd64 12.1.0-2ubuntu1 [679 kB] Get:17 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 libbinutils amd64 2.38.50.20220615-4ubuntu1 [655 kB] Get:18 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgpg-error0 amd64 1.45-2 [69.0 kB] Get:19 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgcrypt20 amd64 1.10.1-2ubuntu1 [524 kB] Get:20 http://ftpmaster.internal/ubuntu kinetic/main amd64 liblzma5 amd64 5.2.5-2.1 [99.2 kB] Get:21 http://ftpmaster.internal/ubuntu kinetic/main amd64 systemd-sysv amd64 249.11-0ubuntu4 [10.2 kB] Get:22 http://ftpmaster.internal/ubuntu kinetic/main amd64 libapparmor1 amd64 3.0.4-2ubuntu3 [38.0 kB] Get:23 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgnutls30 amd64 3.7.6-2ubuntu1 [968 kB] Get:24 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 binutils amd64 2.38.50.20220615-4ubuntu1 [3292 B] Get:25 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 binutils-common amd64 2.38.50.20220615-4ubuntu1 [224 kB] Get:26 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 libgprofng0 amd64 2.38.50.20220615-4ubuntu1 [963 kB] Get:27 http://ftpmaster.internal/ubuntu kinetic/main amd64 libip4tc2 amd64 1.8.7-1ubuntu6 [19.7 kB] Get:28 http://ftpmaster.internal/ubuntu kinetic/main amd64 libblkid1 amd64 2.38-4ubuntu1 [103 kB] Get:29 http://ftpmaster.internal/ubuntu kinetic/main amd64 libselinux1 amd64 3.4-1 [77.6 kB] Get:30 http://ftpmaster.internal/ubuntu kinetic/main amd64 libmount1 amd64 2.38-4ubuntu1 [121 kB] Get:31 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsmartcols1 amd64 2.38-4ubuntu1 [50.8 kB] Get:32 http://ftpmaster.internal/ubuntu kinetic/main amd64 login amd64 1:4.11.1+dfsg1-2ubuntu1 [183 kB] Get:33 http://ftpmaster.internal/ubuntu kinetic/main amd64 util-linux-extra amd64 2.38-4ubuntu1 [83.8 kB] Get:34 http://ftpmaster.internal/ubuntu kinetic/main amd64 util-linux amd64 2.38-4ubuntu1 [1069 kB] Get:35 http://ftpmaster.internal/ubuntu kinetic/main amd64 mount amd64 2.38-4ubuntu1 [114 kB] Get:36 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsemanage-common all 3.4-1 [9828 B] Get:37 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsepol2 amd64 3.4-2 [294 kB] Get:38 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsemanage2 amd64 3.4-1 [91.8 kB] Get:39 http://ftpmaster.internal/ubuntu kinetic/main amd64 passwd amd64 1:4.11.1+dfsg1-2ubuntu1 [765 kB] Get:40 http://ftpmaster.internal/ubuntu kinetic/main amd64 adduser all 3.121ubuntu1 [150 kB] Get:41 http://ftpmaster.internal/ubuntu kinetic/main amd64 systemd amd64 249.11-0ubuntu4 [4517 kB] Get:42 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsystemd0 amd64 249.11-0ubuntu4 [314 kB] Get:43 http://ftpmaster.internal/ubuntu kinetic/main amd64 libudev1 amd64 249.11-0ubuntu4 [76.1 kB] Get:44 http://ftpmaster.internal/ubuntu kinetic/main amd64 libapt-pkg6.0 amd64 2.5.0 [896 kB] Get:45 http://ftpmaster.internal/ubuntu kinetic/main amd64 dpkg amd64 1.21.8ubuntu1 [1333 kB] Get:46 http://ftpmaster.internal/ubuntu kinetic/main amd64 ncurses-bin amd64 6.3+20220423-2 [183 kB] Get:47 http://ftpmaster.internal/ubuntu kinetic/main amd64 init-system-helpers all 1.63 [38.7 kB] Get:48 http://ftpmaster.internal/ubuntu kinetic/main amd64 ncurses-base all 6.3+20220423-2 [21.2 kB] Get:49 http://ftpmaster.internal/ubuntu kinetic/main amd64 apt amd64 2.5.0 [1370 kB] Get:50 http://ftpmaster.internal/ubuntu kinetic/main amd64 logsave amd64 1.46.5-2ubuntu2 [9914 B] Get:51 http://ftpmaster.internal/ubuntu kinetic/main amd64 libext2fs2 amd64 1.46.5-2ubuntu2 [205 kB] Get:52 http://ftpmaster.internal/ubuntu kinetic/main amd64 e2fsprogs amd64 1.46.5-2ubuntu2 [585 kB] Get:53 http://ftpmaster.internal/ubuntu kinetic/main amd64 init amd64 1.63 [5674 B] Get:54 http://ftpmaster.internal/ubuntu kinetic/main amd64 libcap-ng0 amd64 0.7.9-4 [12.1 kB] Get:55 http://ftpmaster.internal/ubuntu kinetic/main amd64 libdb5.3 amd64 5.3.28+dfsg1-0.9 [717 kB] Get:56 http://ftpmaster.internal/ubuntu kinetic/main amd64 libncurses6 amd64 6.3+20220423-2 [110 kB] Get:57 http://ftpmaster.internal/ubuntu kinetic/main amd64 libncursesw6 amd64 6.3+20220423-2 [146 kB] Get:58 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RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-24036498 amd64 kinetic -c chroot:build-PACKAGEBUILD-24036498 --arch=amd64 --dist=kinetic --nolog -A mcaller_1.0.3+git20210624.b415090-3.dsc Initiating build PACKAGEBUILD-24036498 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-120-generic #136-Ubuntu SMP Fri Jun 10 13:40:48 UTC 2022 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lgw01-amd64-036.buildd +==============================================================================+ | mcaller 1.0.3+git20210624.b415090-3 (amd64) Thu, 23 Jun 2022 04:22:32 +0000 | +==============================================================================+ Package: mcaller Version: 1.0.3+git20210624.b415090-3 Source Version: 1.0.3+git20210624.b415090-3 Distribution: kinetic Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-24036498/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/mcaller-n6omfR/resolver-TCjVTU' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- mcaller_1.0.3+git20210624.b415090-3.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/mcaller-n6omfR/mcaller-1.0.3+git20210624.b415090' with '<>' I: NOTICE: Log filtering will replace 'build/mcaller-n6omfR' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-python, python3-all, python3-setuptools, python3-seaborn, python3-biopython, python3-numpy, python3-sklearn, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), dh-python, python3-all, python3-setuptools, python3-seaborn, python3-biopython, python3-numpy, python3-sklearn, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [413 B] Get:5 copy:/<>/apt_archive ./ Packages [494 B] Fetched 1864 B in 0s (152 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev blt bsdextrautils debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz file fontconfig-config fonts-dejavu-core fonts-lyx fonts-urw-base35 gettext gettext-base groff-base intltool-debian libarchive-zip-perl libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libdebhelper-perl libdeflate0 libdw1 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libicu71 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 libmagic-mgc libmagic1 libmd0 libmpdec3 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenjp2-7 libpipeline1 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib libqhull-r8.0 libraqm0 libsigsegv2 libsub-override-perl libtcl8.6 libtiff5 libtk8.6 libtool libuchardet0 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxsimd-dev libxslt1.1 libxss1 m4 man-db media-types po-debconf python-matplotlib-data python3 python3-all python3-all-dev python3-appdirs python3-attr python3-beniget python3-biopython python3-brotli python3-cycler python3-dateutil python3-decorator python3-dev python3-distutils python3-fonttools python3-fs python3-gast python3-joblib python3-kiwisolver python3-lib2to3 python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-mpmath python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk python3-pkg-resources python3-ply python3-pyparsing python3-pythran python3-renderpm python3-reportlab python3-reportlab-accel python3-scipy python3-seaborn python3-setuptools python3-six python3-sklearn python3-sklearn-lib python3-sympy python3-threadpoolctl python3-tk python3-tz python3-ufolib2 python3-unicodedata2 python3.10 python3.10-dev python3.10-minimal sgml-base tk8.6-blt2.5 ucf unicode-data w3c-sgml-lib x11-common xml-core zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc blt-demo dh-make flit python3-build python3-tomli python3-installer fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gettext-doc libasprintf-dev libgettextpo-dev groff libboost-doc libboost1.74-doc libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev libboost-contract1.74-dev libboost-coroutine1.74-dev libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev libboost-filesystem1.74-dev libboost-graph1.74-dev libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev libboost-program-options1.74-dev libboost-python1.74-dev libboost-random1.74-dev libboost-regex1.74-dev libboost-serialization1.74-dev libboost-stacktrace1.74-dev libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk libxsimd-doc m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-venv python-attr-doc bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle phylip phyml prank probcons python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml samtools t-coffee wise python-cycler-doc python-lxml-doc dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 gfortran python-numpy-doc python3-pytest python-pandas-doc python3-statsmodels python-pil-doc python-ply-doc python-pyparsing-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc python-scipy-doc python-setuptools-doc python3-dap python-sklearn-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python3.10-venv python3.10-doc binfmt-support sgml-base-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs javascript-common libltdl-dev libmail-sendmail-perl python-biopython-doc ncbi-blast+ python3-pytest python3-simplejson python3-psutil python3-bs4 python3-html5lib python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-xlwt python3-tables python3-jinja2 python3-numba python3-olefile python3-patsy python3-nose isympy-common The following NEW packages will be installed: autoconf automake autopoint autotools-dev blt bsdextrautils debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz file fontconfig-config fonts-dejavu-core fonts-lyx fonts-urw-base35 gettext gettext-base groff-base intltool-debian libarchive-zip-perl libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libdebhelper-perl libdeflate0 libdw1 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libicu71 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 libmagic-mgc libmagic1 libmd0 libmpdec3 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenjp2-7 libpipeline1 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib libqhull-r8.0 libraqm0 libsigsegv2 libsub-override-perl libtcl8.6 libtiff5 libtk8.6 libtool libuchardet0 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxsimd-dev libxslt1.1 libxss1 m4 man-db media-types po-debconf python-matplotlib-data python3 python3-all python3-all-dev python3-appdirs python3-attr python3-beniget python3-biopython python3-brotli python3-cycler python3-dateutil python3-decorator python3-dev python3-distutils python3-fonttools python3-fs python3-gast python3-joblib python3-kiwisolver python3-lib2to3 python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-mpmath python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk python3-pkg-resources python3-ply python3-pyparsing python3-pythran python3-renderpm python3-reportlab python3-reportlab-accel python3-scipy python3-seaborn python3-setuptools python3-six python3-sklearn python3-sklearn-lib python3-sympy python3-threadpoolctl python3-tk python3-tz python3-ufolib2 python3-unicodedata2 python3.10 python3.10-dev python3.10-minimal sbuild-build-depends-main-dummy sgml-base tk8.6-blt2.5 ucf unicode-data w3c-sgml-lib x11-common xml-core zlib1g-dev 0 upgraded, 160 newly installed, 0 to remove and 0 not upgraded. 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Selecting previously unselected package python3-lz4. Preparing to unpack .../134-python3-lz4_4.0.0+dfsg-1_amd64.deb ... Unpacking python3-lz4 (4.0.0+dfsg-1) ... Selecting previously unselected package python3-unicodedata2. Preparing to unpack .../135-python3-unicodedata2_14.0.0+ds-8_amd64.deb ... Unpacking python3-unicodedata2 (14.0.0+ds-8) ... Selecting previously unselected package unicode-data. Preparing to unpack .../136-unicode-data_14.0.0-1.1_all.deb ... Unpacking unicode-data (14.0.0-1.1) ... Selecting previously unselected package python3-fonttools. Preparing to unpack .../137-python3-fonttools_4.32.0-1_amd64.deb ... Unpacking python3-fonttools (4.32.0-1) ... Selecting previously unselected package python3-joblib. Preparing to unpack .../138-python3-joblib_0.17.0-4ubuntu1_all.deb ... Unpacking python3-joblib (0.17.0-4ubuntu1) ... Selecting previously unselected package python3-kiwisolver. Preparing to unpack .../139-python3-kiwisolver_1.3.2-1build1_amd64.deb ... Unpacking python3-kiwisolver (1.3.2-1build1) ... Selecting previously unselected package python3-pyparsing. Preparing to unpack .../140-python3-pyparsing_3.0.7-2_all.deb ... Unpacking python3-pyparsing (3.0.7-2) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../141-python3-packaging_21.3-1_all.deb ... Unpacking python3-packaging (21.3-1) ... Selecting previously unselected package python3-matplotlib. Preparing to unpack .../142-python3-matplotlib_3.5.1-3_amd64.deb ... Unpacking python3-matplotlib (3.5.1-3) ... Selecting previously unselected package python3-pandas-lib:amd64. Preparing to unpack .../143-python3-pandas-lib_1.3.5+dfsg-4_amd64.deb ... Unpacking python3-pandas-lib:amd64 (1.3.5+dfsg-4) ... Selecting previously unselected package python3-pandas. Preparing to unpack .../144-python3-pandas_1.3.5+dfsg-4_all.deb ... Unpacking python3-pandas (1.3.5+dfsg-4) ... Selecting previously unselected package python3-seaborn. 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Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up media-types (8.0.0) ... Setting up libpipeline1:amd64 (1.5.6-1) ... Setting up libgraphite2-3:amd64 (1.3.14-1build2) ... Setting up liblcms2-2:amd64 (2.12~rc1-2build2) ... Setting up libicu71:amd64 (71.1-3) ... Setting up libxau6:amd64 (1:1.0.9-1build5) ... Setting up libboost1.74-dev:amd64 (1.74.0-14ubuntu4) ... Setting up bsdextrautils (2.38-4ubuntu1) ... Setting up libmagic-mgc (1:5.41-4) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:amd64 (2.72.2-2) ... No schema files found: doing nothing. Setting up fonts-lyx (2.3.6.1-1) ... Setting up libdebhelper-perl (13.7.1ubuntu1) ... Setting up libbrotli1:amd64 (1.0.9-2build6) ... Setting up x11-common (1:7.7+23ubuntu2) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libmagic1:amd64 (1:5.41-4) ... Setting up libdeflate0:amd64 (1.10-2) ... Setting up gettext-base (0.21-6) ... Setting up libqhull-r8.0:amd64 (2020.2-4) ... Setting up file (1:5.41-4) ... Setting up fonts-urw-base35 (20200910-1) ... Setting up libjbig0:amd64 (2.1-3.1build3) ... Setting up unicode-data (14.0.0-1.1) ... Setting up libxsimd-dev:amd64 (7.6.0-2) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.10.1-2) ... 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 libexpat1-dev:amd64 (2.4.8-1) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-3) ... Setting up libx11-data (2:1.7.5-1) ... Setting up libsigsegv2:amd64 (2.13-1ubuntu3) ... Setting up libfribidi0:amd64 (1.0.8-2ubuntu3.1) ... Setting up libimagequant0:amd64 (2.17.0-1) ... Setting up libtcl8.6:amd64 (8.6.12+dfsg-1build1) ... Setting up autopoint (0.21-6) ... Setting up fonts-dejavu-core (2.37-2build1) ... Setting up ucf (3.0043) ... Setting up libjpeg-turbo8:amd64 (2.1.2-0ubuntu1) ... Setting up libgfortran5:amd64 (12.1.0-2ubuntu1) ... Setting up libwebp7:amd64 (1.2.2-2) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2ubuntu9) ... Setting up libmd0:amd64 (1.0.4-1build1) ... Setting up libuchardet0:amd64 (0.0.7-1build2) ... Setting up libmpdec3:amd64 (2.5.1-2build2) ... Setting up libopenjp2-7:amd64 (2.4.0-6) ... Setting up libsub-override-perl (0.09-3) ... Setting up libharfbuzz0b:amd64 (2.7.4-1ubuntu4) ... Setting up sgml-base (1.30) ... Setting up libboost-dev:amd64 (1.74.0.3ubuntu7) ... Setting up libjs-jquery (3.6.0+dfsg+~3.5.13-1) ... Setting up python-matplotlib-data (3.5.1-3) ... Setting up libwebpmux3:amd64 (1.2.2-2) ... Setting up libbsd0:amd64 (0.11.6-1) ... Setting up libelf1:amd64 (0.187-1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1) ... Setting up libjs-underscore (1.13.3~dfsg+~1.11.4-1) ... Setting up libjpeg8:amd64 (8c-2ubuntu10) ... Setting up libfile-stripnondeterminism-perl (1.13.0-1) ... Setting up libdw1:amd64 (0.187-1) ... Setting up libxdmcp6:amd64 (1:1.1.3-0ubuntu5) ... Setting up liblapack3:amd64 (3.10.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.14-3ubuntu3) ... Setting up gettext (0.21-6) ... Setting up libopenblas0-pthread:amd64 (0.3.20+ds-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-x86_64-linux-gnu) in auto mode Setting up libtool (2.4.7-4) ... Setting up fontconfig-config (2.13.1-4.4ubuntu1) ... Setting up libwebpdemux2:amd64 (1.2.2-2) ... Setting up m4 (1.4.18-5ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpython3.10-stdlib:amd64 (3.10.5-1) ... Setting up libjs-jquery-ui (1.13.1+dfsg-1) ... Setting up libraqm0:amd64 (0.7.0-4ubuntu1) ... Setting up libjs-sphinxdoc (4.5.0-4) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.13.0-1) ... Setting up dwz (0.14-1build2) ... Setting up libopenblas0:amd64 (0.3.20+ds-2) ... Setting up groff-base (1.22.4-8build1) ... Setting up xml-core (0.18+nmu1) ... Setting up libxslt1.1:amd64 (1.1.34-4build2) ... Setting up debugedit (1:5.0-4build1) ... Setting up libx11-6:amd64 (2:1.7.5-1) ... Setting up libtiff5:amd64 (4.4.0~rc1-1) ... Setting up libfontconfig1:amd64 (2.13.1-4.4ubuntu1) ... Setting up libpython3-stdlib:amd64 (3.10.4-0ubuntu2) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.3-10) ... 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 libopenblas-pthread-dev:amd64 (0.3.20+ds-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/x86_64-linux-gnu/libopenblas.so (libopenblas.so-x86_64-linux-gnu) in auto mode Setting up libpython3.10:amd64 (3.10.5-1) ... Setting up python3.10 (3.10.5-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:amd64 (2:1.3.4-1build1) ... Setting up python3 (3.10.4-0ubuntu2) ... Setting up man-db (2.10.2-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up python3-tz (2022.1-1) ... Setting up python3-six (1.16.0-3ubuntu1) ... Setting up dh-autoreconf (20) ... Setting up libopenblas-dev:amd64 (0.3.20+ds-2) ... Setting up python3-decorator (4.4.2-0ubuntu1) ... Setting up python3-pyparsing (3.0.7-2) ... Setting up python3-brotli (1.0.9-2build6) ... Setting up python3-cycler (0.11.0-1) ... Setting up python3-reportlab-accel:amd64 (3.6.9-1) ... Setting up python3-kiwisolver (1.3.2-1build1) ... Setting up libpython3.10-dev:amd64 (3.10.5-1) ... Setting up python3.10-dev (3.10.5-1) ... Setting up python3-lxml:amd64 (4.8.0-1build1) ... Setting up python3-dateutil (2.8.1-6) ... Setting up libxss1:amd64 (1:1.2.3-1build2) ... Setting up python3-mpmath (1.2.1-2) ... Setting up python3-lib2to3 (3.10.4-0ubuntu2) ... Setting up python3-appdirs (1.4.4-2) ... Setting up python3-pkg-resources (59.6.0-1.2) ... Setting up python3-distutils (3.10.4-0ubuntu2) ... Setting up dh-python (5.20220403) ... Setting up python3-sympy (1.10.1-3) ... Setting up python3-attr (21.2.0-1) ... Setting up libxft2:amd64 (2.3.4-1) ... Setting up libpython3-dev:amd64 (3.10.4-0ubuntu2) ... Setting up python3-renderpm:amd64 (3.6.9-1) ... Setting up python3-setuptools (59.6.0-1.2) ... Setting up python3-joblib (0.17.0-4ubuntu1) ... Setting up python3-lz4 (4.0.0+dfsg-1) ... Setting up python3-unicodedata2 (14.0.0+ds-8) ... Setting up libtk8.6:amd64 (8.6.12-1build1) ... Setting up python3-ply (3.11-5) ... Setting up python3-threadpoolctl (3.1.0-1) ... Setting up python3-gast (0.5.2-2) ... Setting up python3-all (3.10.4-0ubuntu2) ... Setting up debhelper (13.7.1ubuntu1) ... Setting up python3-fs (2.4.12-1) ... Setting up python3-beniget (0.4.1-2) ... Setting up python3-packaging (21.3-1) ... Setting up libpython3-all-dev:amd64 (3.10.4-0ubuntu2) ... Setting up python3-dev (3.10.4-0ubuntu2) ... Setting up python3-numpy (1:1.21.5-1build2) ... Setting up python3-all-dev (3.10.4-0ubuntu2) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1build2) ... Setting up blt (2.5.3+dfsg-4.1build2) ... Setting up python3-pandas-lib:amd64 (1.3.5+dfsg-4) ... Setting up python3-sklearn-lib:amd64 (0.23.2-5ubuntu6) ... Setting up python3-tk:amd64 (3.10.4-0ubuntu2) ... Setting up python3-pandas (1.3.5+dfsg-4) ... Setting up python3-pythran (0.10.0+ds2-8) ... Setting up python3-scipy (1.8.0-1exp2ubuntu1) ... Setting up python3-sklearn (0.23.2-5ubuntu6) ... Setting up python3-fonttools (4.32.0-1) ... Setting up python3-pil:amd64 (9.1.1-1) ... Setting up python3-pil.imagetk:amd64 (9.1.1-1) ... Setting up python3-ufolib2 (0.13.1+dfsg1-1) ... Setting up python3-reportlab (3.6.9-1) ... Setting up python3-matplotlib (3.5.1-3) ... Setting up python3-seaborn (0.11.2-3) ... Processing triggers for libc-bin (2.35-0ubuntu3) ... Processing triggers for sgml-base (1.30) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.79+dfsg-3) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-120-generic #136-Ubuntu SMP Fri Jun 10 13:40:48 UTC 2022 amd64 (x86_64) Toolchain package versions: binutils_2.38.50.20220615-4ubuntu1 dpkg-dev_1.21.8ubuntu1 g++-11_11.3.0-3ubuntu1 gcc-11_11.3.0-3ubuntu1 libc6-dev_2.35-0ubuntu3 libstdc++-11-dev_11.3.0-3ubuntu1 libstdc++6_12.1.0-2ubuntu1 linux-libc-dev_5.15.0-27.28 Package versions: adduser_3.121ubuntu1 advancecomp_2.1-2.1ubuntu2 apt_2.5.0 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-6 autotools-dev_20220109.1 base-files_12.2ubuntu1 base-passwd_3.5.52build1 bash_5.1-6ubuntu1 binutils_2.38.50.20220615-4ubuntu1 binutils-common_2.38.50.20220615-4ubuntu1 binutils-x86-64-linux-gnu_2.38.50.20220615-4ubuntu1 blt_2.5.3+dfsg-4.1build2 bsdextrautils_2.38-4ubuntu1 bsdutils_1:2.38-4ubuntu1 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20211016 coreutils_8.32-4.1ubuntu1 cpp_4:11.2.0-1ubuntu1 cpp-11_11.3.0-3ubuntu1 dash_0.5.11+git20210903+057cd650a4ed-3build1 debconf_1.5.79ubuntu1 debhelper_13.7.1ubuntu1 debianutils_5.7-0.2 debugedit_1:5.0-4build1 dh-autoreconf_20 dh-python_5.20220403 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-0ubuntu2 dpkg_1.21.8ubuntu1 dpkg-dev_1.21.8ubuntu1 dwz_0.14-1build2 e2fsprogs_1.46.5-2ubuntu2 fakeroot_1.29-1ubuntu1 file_1:5.41-4 findutils_4.8.0-1ubuntu3 fontconfig-config_2.13.1-4.4ubuntu1 fonts-dejavu-core_2.37-2build1 fonts-lyx_2.3.6.1-1 fonts-urw-base35_20200910-1 g++_4:11.2.0-1ubuntu1 g++-11_11.3.0-3ubuntu1 gcc_4:11.2.0-1ubuntu1 gcc-11_11.3.0-3ubuntu1 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rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1ubuntu2 sensible-utils_0.0.17 sgml-base_1.30 systemd_249.11-0ubuntu4 systemd-sysv_249.11-0ubuntu4 sysvinit-utils_3.01-1ubuntu1 tar_1.34+dfsg-1build3 tk8.6-blt2.5_2.5.3+dfsg-4.1build2 tzdata_2022a-0ubuntu1 ubuntu-keyring_2021.03.26 ucf_3.0043 unicode-data_14.0.0-1.1 usrmerge_25ubuntu2 util-linux_2.38-4ubuntu1 util-linux-extra_2.38-4ubuntu1 w3c-sgml-lib_1.3-3 x11-common_1:7.7+23ubuntu2 xml-core_0.18+nmu1 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-2ubuntu9 zlib1g-dev_1:1.2.11.dfsg-2ubuntu9 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: mcaller Binary: mcaller Architecture: all Version: 1.0.3+git20210624.b415090-3 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller Homepage: https://github.com/al-mcintyre/mCaller Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/mcaller Vcs-Git: https://salsa.debian.org/med-team/mcaller.git Testsuite: autopkgtest, autopkgtest-pkg-python Build-Depends: debhelper-compat (= 13), dh-python, python3-all, python3-setuptools, python3-seaborn, python3-biopython, python3-numpy, python3-sklearn Package-List: mcaller deb science optional arch=all Checksums-Sha1: 3581db7c90993a4c321d37aad5ddd80b2dc24a40 6612544 mcaller_1.0.3+git20210624.b415090.orig.tar.xz 54f95a50804acace1e1868a52b555644f13d64b7 7488 mcaller_1.0.3+git20210624.b415090-3.debian.tar.xz Checksums-Sha256: bde75bad7b0cf688084a5ad8a3dd792e4c52419d94c6118f6a4a752a15d4521f 6612544 mcaller_1.0.3+git20210624.b415090.orig.tar.xz 4207438d211679ddbf852aef098fe6a9c98a5331d38f5c9f88c8009bf51667ec 7488 mcaller_1.0.3+git20210624.b415090-3.debian.tar.xz Files: 6d969880db638213a6e7389af1322483 6612544 mcaller_1.0.3+git20210624.b415090.orig.tar.xz c21227868dc517732860621d1140e1ae 7488 mcaller_1.0.3+git20210624.b415090-3.debian.tar.xz Dgit: 09a50931020529c246a06d938d43d3d692f34d17 debian archive/debian/1.0.3+git20210624.b415090-3 https://git.dgit.debian.org/mcaller -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmJpwywUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdp3hRAApkoygpWS3goFgMLJ4Psv8Ssrktsp kBdbJeN5pf9tDbYisX9uN9e4dQbKDEYgUXYmPhI45joXH6vFYlh90mLhJWCmf7WA Qub7f/1U/QV56DTlkAG7zHutP5Dinbf5BxIAIFZGVupqmrSIf2+xMa+THObobJF1 MduWETE4NFr62dGOVQgCcD9CipBC9IUUJAmrhQI4gEgUc2goigvU/0tcgbluAdAm J29lOOYRyY9Sw2IJFTS3JGIN+9KLE24ipK9RGSaT1wAKUW44LpVtjoibjDGZaZ9L mFfP/Z15HS9oxY/5dIfwmnxLuK2d5km6HIcCPKhw9aozs4M0unjjX6FbP2MmyU9P xi1yCNWyegGcLuIpkVSqxyj5efylY9vBpxO5w6gqc4RCiV4z40bqTrSAu7IBAwct 6jnFimdBZ77mlzZqVt3m/MXnHxhTOi7Oo6ZU/DvRpzQdzKX9eI1utLl+poaxCB9Y 0CnZqcvMheHi8J5lmhXy/bEUbyLmKQo4TTOX1TEFMzJGZzKPGI6uznEvevmBkYBP PCJPd0OqNu/KAn18S2vIrf58c9D4m/NnOB7wlBPpGHKHW9vEnqYVJWQ9e1S+rAGK 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LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-24036498 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-24036498 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-24036498 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -b -rfakeroot dpkg-buildpackage: info: source package mcaller dpkg-buildpackage: info: source version 1.0.3+git20210624.b415090-3 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean #rm -f model_NN_6_m6A.pkl testdata/masonread1.eventalign.diffs.6 testdata/masonread1.eventalign.diffs.6.train rm -rf __pycache__ rm -f model_NN_6_m6A.pkl make[1]: Leaving directory '/<>' dh_clean debian/rules binary dh binary --with python3 dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_test make[1]: Entering directory '/<>' cp -a testdata testdata_save ./mCaller.py -p testdata/test_positions_A.txt -r testdata/pb_ecoli_polished_assembly.fasta -e testdata/masonread1.eventalign.tsv -d r95_twobase_model_NN_6_m6A.pkl -f testdata/masonread1.fastq testdata/ 1 contigs 1 threads thread finished processing...: 35 observations 35 positions 0 regions with multiple methylated bases 0 observations with skips included 8 observations with too many skips Finished extracting signals ./mCaller.py -p testdata/test_positions_m6A.txt -r testdata/pb_ecoli_polished_assembly.fasta -e testdata/masonread1.eventalign.tsv -d r95_twobase_model_NN_6_m6A.pkl -f testdata/masonread1.fastq testdata/ 1 contigs 1 threads thread finished processing...: 9 observations 9 positions 0 regions with multiple methylated bases 0 observations with skips included 2 observations with too many skips Finished extracting signals ./mCaller.py -p testdata/test_positions.txt -r testdata/pb_ecoli_polished_assembly.fasta -e testdata/masonread1.eventalign.tsv -t 4 --train -f testdata/masonread1.fastq testdata/ 1 contigs 4 threads thread finished processing...: 28 observations 28 positions 0 regions with multiple methylated bases 0 observations with skips included 6 observations with too many skips thread finished processing...: 9 observations 9 positions 0 regions with multiple methylated bases 0 observations with skips included 4 observations with too many skips Error: could not find sequence for reference contig li thread finished processing...: 16 observations 16 positions 0 regions with multiple methylated bases 0 observations with skips included 6 observations with too many skips thread finished processing...: 44 observations 44 positions 1 regions with multiple methylated bases 0 observations with skips included 10 observations with too many skips Finished extracting signals Merging files... Training... ['A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A'] [[-1.44, -5.03, 1.4449999999999998, 0.4000000000000001, -0.588, -0.55, 7.055265349382997], [-1.4433333333333334, -0.020000000000000018, -0.0366666666666667, -0.5499999999999999, 0.64, -2.71, 7.055265349382997], [-1.23, -1.635, -0.24, 1.1033333333333333, -2.215, -2.93, 7.055265349382997], [-0.21, 0.07500000000000001, -1.3083333333333333, 4.15, -0.3, -0.21500000000000002, 7.055265349382997], [-1.355, -0.34, -1.8633333333333333, -1.87, -1.2650000000000001, -1.22, 7.055265349382997], [-5.64, -3.6, -5.13, -0.255, 0.4, 0.73, 7.055265349382997], [-1.1400000000000001, 0.94, -4.55, 2.0, -0.34, -2.71, 7.055265349382997], [1.02, -2.38, 0.915, 0.05, 1.75, 0.8875000000000001, 7.055265349382997], [-0.56, -3.505, 1.02, -1.55, -0.7139999999999999, -0.4825, 7.055265349382997], [3.49, 1.3, -1.4949999999999999, -2.3, -1.2, -0.62, 7.055265349382997]] ['AAATGMGATTT', 'AGTAGMTTGAT', 'ACTTAMCCGGT', 'AGCATMTTTAT', 'GTTATMTGCAA', 'GGTAAMAATTT', 'GTGACMGTTTT', 'GGCTTMTTTTA', 'GGATGMAAGAA', 'ATATTMTGCAT'] NN general model scores: 1.0,1.0,1.0,0.5,0.5 Cross validation accuracy: 0.80 (+/- 0.49) Finished training rm -rf testdata mv testdata_save testdata make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/mcaller/ dh_install dh_installdocs dh_installchangelogs dh_installman dh_python3 dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package mcaller: substitution variable ${python3:Depends} used, but is not defined dh_md5sums dh_builddeb INFO: pkgstriptranslations version 149 pkgstriptranslations: processing mcaller (in debian/mcaller); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/mcaller/DEBIAN/control, package mcaller, directory debian/mcaller pkgstripfiles: Running PNG optimization (using 4 cpus) for package mcaller ... pkgstripfiles: No PNG files. dpkg-deb: building package 'mcaller' in '../mcaller_1.0.3+git20210624.b415090-3_all.deb'. dpkg-genbuildinfo --build=binary -O../mcaller_1.0.3+git20210624.b415090-3_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../mcaller_1.0.3+git20210624.b415090-3_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) -------------------------------------------------------------------------------- Build finished at 2022-06-23T04:24:01Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ mcaller_1.0.3+git20210624.b415090-3_amd64.changes: -------------------------------------------------- Format: 1.8 Date: Thu, 28 Apr 2022 00:24:38 +0200 Source: mcaller Binary: mcaller Built-For-Profiles: noudeb Architecture: all Version: 1.0.3+git20210624.b415090-3 Distribution: kinetic Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Étienne Mollier Description: mcaller - find methylation in nanopore reads Changes: mcaller (1.0.3+git20210624.b415090-3) unstable; urgency=medium . * Team upload. * d/t/control: declare test unsupported on S390x Checksums-Sha1: 746c8cc9ee394f5e6c909379dac37b235d247858 19314 mcaller_1.0.3+git20210624.b415090-3_all.deb 90a2c857ed59c925f32dd6d33cf0388076bd5e12 10027 mcaller_1.0.3+git20210624.b415090-3_amd64.buildinfo Checksums-Sha256: 1b7e9626873de3d1a54bb3d5418149b972e3efb1f9d2be7d4f420a9818dd00dd 19314 mcaller_1.0.3+git20210624.b415090-3_all.deb 410a7e9ebd88e19d81ac720ff8c92086f537807ae655844a4a3410d1497db841 10027 mcaller_1.0.3+git20210624.b415090-3_amd64.buildinfo Files: e9ae9292af048b9e3184bfd2b53f1c95 19314 science optional mcaller_1.0.3+git20210624.b415090-3_all.deb c2f98a9452f0e735ae8cdebf63f13ddb 10027 science optional mcaller_1.0.3+git20210624.b415090-3_amd64.buildinfo /<>/mcaller_1.0.3+git20210624.b415090-3_amd64.changes.new could not be renamed to /<>/mcaller_1.0.3+git20210624.b415090-3_amd64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: mcaller Binary: mcaller Architecture: all Version: 1.0.3+git20210624.b415090-3 Checksums-Md5: e9ae9292af048b9e3184bfd2b53f1c95 19314 mcaller_1.0.3+git20210624.b415090-3_all.deb Checksums-Sha1: 746c8cc9ee394f5e6c909379dac37b235d247858 19314 mcaller_1.0.3+git20210624.b415090-3_all.deb Checksums-Sha256: 1b7e9626873de3d1a54bb3d5418149b972e3efb1f9d2be7d4f420a9818dd00dd 19314 mcaller_1.0.3+git20210624.b415090-3_all.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Thu, 23 Jun 2022 04:24:00 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1.3), autopoint (= 0.21-6), autotools-dev (= 20220109.1), base-files (= 12.2ubuntu1), base-passwd (= 3.5.52build1), bash (= 5.1-6ubuntu1), binutils (= 2.38.50.20220615-4ubuntu1), binutils-common (= 2.38.50.20220615-4ubuntu1), binutils-x86-64-linux-gnu (= 2.38.50.20220615-4ubuntu1), blt (= 2.5.3+dfsg-4.1build2), bsdextrautils (= 2.38-4ubuntu1), bsdutils (= 1:2.38-4ubuntu1), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), coreutils (= 8.32-4.1ubuntu1), cpp (= 4:11.2.0-1ubuntu1), cpp-11 (= 11.3.0-3ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-3build1), debconf (= 1.5.79ubuntu1), debhelper (= 13.7.1ubuntu1), debianutils (= 5.7-0.2), debugedit (= 1:5.0-4build1), dh-autoreconf (= 20), dh-python (= 5.20220403), dh-strip-nondeterminism (= 1.13.0-1), diffutils (= 1:3.8-0ubuntu2), dpkg (= 1.21.8ubuntu1), dpkg-dev (= 1.21.8ubuntu1), 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2020.2-4), libquadmath0 (= 12.1.0-2ubuntu1), libraqm0 (= 0.7.0-4ubuntu1), libreadline8 (= 8.1.2-1.2), libseccomp2 (= 2.5.4-1ubuntu1), libselinux1 (= 3.4-1), libsigsegv2 (= 2.13-1ubuntu3), libsmartcols1 (= 2.38-4ubuntu1), libsqlite3-0 (= 3.38.5-1), libssl3 (= 3.0.3-5ubuntu3), libstdc++-11-dev (= 11.3.0-3ubuntu1), libstdc++6 (= 12.1.0-2ubuntu1), libsub-override-perl (= 0.09-3), libsystemd0 (= 249.11-0ubuntu4), libtcl8.6 (= 8.6.12+dfsg-1build1), libtiff5 (= 4.4.0~rc1-1), libtinfo6 (= 6.3+20220423-2), libtirpc-common (= 1.3.2-2build1), libtirpc-dev (= 1.3.2-2build1), libtirpc3 (= 1.3.2-2build1), libtk8.6 (= 8.6.12-1build1), libtool (= 2.4.7-4), libtsan0 (= 11.3.0-3ubuntu1), libubsan1 (= 12.1.0-2ubuntu1), libuchardet0 (= 0.0.7-1build2), libudev1 (= 249.11-0ubuntu4), libunistring2 (= 1.0-1), libuuid1 (= 2.38-4ubuntu1), libwebp7 (= 1.2.2-2), libwebpdemux2 (= 1.2.2-2), libwebpmux3 (= 1.2.2-2), libx11-6 (= 2:1.7.5-1), libx11-data (= 2:1.7.5-1), libxau6 (= 1:1.0.9-1build5), libxcb1 (= 1.14-3ubuntu3), libxdmcp6 (= 1:1.1.3-0ubuntu5), libxext6 (= 2:1.3.4-1build1), libxft2 (= 2.3.4-1), libxml2 (= 2.9.14+dfsg-1), libxrender1 (= 1:0.9.10-1.1), libxsimd-dev (= 7.6.0-2), libxslt1.1 (= 1.1.34-4build2), libxss1 (= 1:1.2.3-1build2), libzstd1 (= 1.5.2+dfsg-1), linux-libc-dev (= 5.15.0-27.28), login (= 1:4.11.1+dfsg1-2ubuntu1), lsb-base (= 11.1.0ubuntu4), lto-disabled-list (= 27), m4 (= 1.4.18-5ubuntu2), make (= 4.3-4.1build1), man-db (= 2.10.2-1), mawk (= 1.3.4.20200120-3.1), media-types (= 8.0.0), ncurses-base (= 6.3+20220423-2), ncurses-bin (= 6.3+20220423-2), patch (= 2.7.6-7build2), perl (= 5.34.0-3ubuntu1), perl-base (= 5.34.0-3ubuntu1), perl-modules-5.34 (= 5.34.0-3ubuntu1), po-debconf (= 1.0.21+nmu1), procps (= 2:3.3.17-6ubuntu2), python-matplotlib-data (= 3.5.1-3), python3 (= 3.10.4-0ubuntu2), python3-all (= 3.10.4-0ubuntu2), python3-all-dev (= 3.10.4-0ubuntu2), python3-appdirs (= 1.4.4-2), python3-attr (= 21.2.0-1), python3-beniget (= 0.4.1-2), python3-biopython (= 1.79+dfsg-3), python3-brotli (= 1.0.9-2build6), python3-cycler (= 0.11.0-1), python3-dateutil (= 2.8.1-6), python3-decorator (= 4.4.2-0ubuntu1), python3-dev (= 3.10.4-0ubuntu2), python3-distutils (= 3.10.4-0ubuntu2), python3-fonttools (= 4.32.0-1), python3-fs (= 2.4.12-1), python3-gast (= 0.5.2-2), python3-joblib (= 0.17.0-4ubuntu1), python3-kiwisolver (= 1.3.2-1build1), python3-lib2to3 (= 3.10.4-0ubuntu2), python3-lxml (= 4.8.0-1build1), python3-lz4 (= 4.0.0+dfsg-1), python3-matplotlib (= 3.5.1-3), python3-minimal (= 3.10.4-0ubuntu2), python3-mpmath (= 1.2.1-2), python3-numpy (= 1:1.21.5-1build2), python3-packaging (= 21.3-1), python3-pandas (= 1.3.5+dfsg-4), python3-pandas-lib (= 1.3.5+dfsg-4), python3-pil (= 9.1.1-1), python3-pil.imagetk (= 9.1.1-1), python3-pkg-resources (= 59.6.0-1.2), python3-ply (= 3.11-5), python3-pyparsing (= 3.0.7-2), python3-pythran (= 0.10.0+ds2-8), python3-renderpm (= 3.6.9-1), python3-reportlab (= 3.6.9-1), python3-reportlab-accel (= 3.6.9-1), python3-scipy (= 1.8.0-1exp2ubuntu1), python3-seaborn (= 0.11.2-3), python3-setuptools (= 59.6.0-1.2), python3-six (= 1.16.0-3ubuntu1), python3-sklearn (= 0.23.2-5ubuntu6), python3-sklearn-lib (= 0.23.2-5ubuntu6), python3-sympy (= 1.10.1-3), python3-threadpoolctl (= 3.1.0-1), python3-tk (= 3.10.4-0ubuntu2), python3-tz (= 2022.1-1), python3-ufolib2 (= 0.13.1+dfsg1-1), python3-unicodedata2 (= 14.0.0+ds-8), python3.10 (= 3.10.5-1), python3.10-dev (= 3.10.5-1), python3.10-minimal (= 3.10.5-1), readline-common (= 8.1.2-1.2), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.8-1ubuntu2), sensible-utils (= 0.0.17), sgml-base (= 1.30), sysvinit-utils (= 3.01-1ubuntu1), tar (= 1.34+dfsg-1build3), tk8.6-blt2.5 (= 2.5.3+dfsg-4.1build2), tzdata (= 2022a-0ubuntu1), ucf (= 3.0043), unicode-data (= 14.0.0-1.1), util-linux (= 2.38-4ubuntu1), util-linux-extra (= 2.38-4ubuntu1), w3c-sgml-lib (= 1.3-3), x11-common (= 1:7.7+23ubuntu2), xml-core (= 0.18+nmu1), xz-utils (= 5.2.5-2.1), zlib1g (= 1:1.2.11.dfsg-2ubuntu9), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu9) Environment: DEB_BUILD_OPTIONS="noautodbgsym parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1651098278" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ mcaller_1.0.3+git20210624.b415090-3_all.deb ------------------------------------------- new Debian package, version 2.0. size 19314 bytes: control archive=1057 bytes. 771 bytes, 21 lines control 957 bytes, 14 lines md5sums Package: mcaller Version: 1.0.3+git20210624.b415090-3 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 83 Depends: python3, python3-sklearn, python3-h5py, python3-biopython, python3-matplotlib, python3-seaborn, python3-numpy, python3-pysam, python3-scipy, python3-pandas Recommends: nanopolish | poretools Suggests: graphmap, bwa Section: science Priority: optional Homepage: https://github.com/al-mcintyre/mCaller Description: find methylation in nanopore reads H | H-C-aller | H . This program is designed to call m6A from nanopore data using the differences between measured and expected currents. drwxr-xr-x root/root 0 2022-04-27 22:24 ./ drwxr-xr-x root/root 0 2022-04-27 22:24 ./usr/ drwxr-xr-x root/root 0 2022-04-27 22:24 ./usr/bin/ lrwxrwxrwx root/root 0 2022-04-27 22:24 ./usr/bin/compare_genomes -> ../share/mCaller/compare_genomes.py lrwxrwxrwx root/root 0 2022-04-27 22:24 ./usr/bin/mCaller -> ../share/mCaller/mCaller.py lrwxrwxrwx root/root 0 2022-04-27 22:24 ./usr/bin/make_bed -> ../share/mCaller/make_bed.py drwxr-xr-x root/root 0 2022-04-27 22:24 ./usr/lib/ drwxr-xr-x root/root 0 2022-04-27 22:24 ./usr/lib/debian-med/ drwxr-xr-x root/root 0 2022-04-27 22:24 ./usr/lib/debian-med/bin/ lrwxrwxrwx root/root 0 2022-04-27 22:24 ./usr/lib/debian-med/bin/compare_genomes.py -> ../../../share/mCaller/compare_genomes.py lrwxrwxrwx root/root 0 2022-04-27 22:24 ./usr/lib/debian-med/bin/mCaller.py -> ../../../share/mCaller/mCaller.py lrwxrwxrwx root/root 0 2022-04-27 22:24 ./usr/lib/debian-med/bin/make_bed.py -> ../../../share/mCaller/make_bed.py drwxr-xr-x root/root 0 2022-04-27 22:24 ./usr/share/ drwxr-xr-x root/root 0 2022-04-27 22:24 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-04-27 22:24 ./usr/share/doc/mcaller/ -rw-r--r-- root/root 364 2022-04-27 22:24 ./usr/share/doc/mcaller/changelog.Debian.gz -rw-r--r-- root/root 1341 2022-04-27 22:24 ./usr/share/doc/mcaller/copyright drwxr-xr-x root/root 0 2022-04-27 22:24 ./usr/share/lintian/ drwxr-xr-x root/root 0 2022-04-27 22:24 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 68 2022-04-27 22:24 ./usr/share/lintian/overrides/mcaller drwxr-xr-x root/root 0 2022-04-27 22:24 ./usr/share/mCaller/ -rwxr-xr-x root/root 2484 2022-04-27 22:24 ./usr/share/mCaller/compare_genomes.py -rw-r--r-- root/root 15821 2022-04-27 22:24 ./usr/share/mCaller/extract_contexts.py -rw-r--r-- root/root 1054 2021-06-24 22:04 ./usr/share/mCaller/load_mCaller_data.py -rwxr-xr-x root/root 9419 2022-04-27 22:24 ./usr/share/mCaller/mCaller.py -rwxr-xr-x root/root 10403 2022-04-27 22:24 ./usr/share/mCaller/make_bed.py -rw-r--r-- root/root 4007 2022-04-27 22:24 ./usr/share/mCaller/plotlib.py -rw-r--r-- root/root 625 2021-06-24 22:04 ./usr/share/mCaller/read_qual.py -rw-r--r-- root/root 5701 2022-04-27 22:24 ./usr/share/mCaller/train_model.py drwxr-xr-x root/root 0 2022-04-27 22:24 ./usr/share/man/ drwxr-xr-x root/root 0 2022-04-27 22:24 ./usr/share/man/man1/ -rw-r--r-- root/root 512 2022-04-27 22:24 ./usr/share/man/man1/compare_genomes.1.gz -rw-r--r-- root/root 1280 2022-04-27 22:24 ./usr/share/man/man1/mCaller.1.gz -rw-r--r-- root/root 1105 2022-04-27 22:24 ./usr/share/man/man1/make_bed.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 15236 Build-Time: 9 Distribution: kinetic Host Architecture: amd64 Install-Time: 78 Job: mcaller_1.0.3+git20210624.b415090-3.dsc Machine Architecture: amd64 Package: mcaller Package-Time: 89 Source-Version: 1.0.3+git20210624.b415090-3 Space: 15236 Status: successful Version: 1.0.3+git20210624.b415090-3 -------------------------------------------------------------------------------- Finished at 2022-06-23T04:24:01Z Build needed 00:01:29, 15236k disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24036498 Scanning for processes to kill in build PACKAGEBUILD-24036498