I: pbuilder: network access will be disabled during build I: Current time: Wed Mar 19 23:19:42 -12 2025 I: pbuilder-time-stamp: 1742469582 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [mcaller_1.0.3+git20210624.b415090-3.dsc] I: copying [./mcaller_1.0.3+git20210624.b415090.orig.tar.xz] I: copying [./mcaller_1.0.3+git20210624.b415090-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./mcaller_1.0.3+git20210624.b415090-3.dsc: unsupported subcommand dpkg-source: info: extracting mcaller in mcaller-1.0.3+git20210624.b415090 dpkg-source: info: unpacking mcaller_1.0.3+git20210624.b415090.orig.tar.xz dpkg-source: info: unpacking mcaller_1.0.3+git20210624.b415090-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying shebang.patch dpkg-source: info: applying python2to3.patch dpkg-source: info: applying prefixes.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4107019/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='367fa68489474be18d5e29507db857a1' 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='4107019' 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.AXKLah9E/pbuilderrc_erNc --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.AXKLah9E/b1 --logfile b1/build.log mcaller_1.0.3+git20210624.b415090-3.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-32-cloud-arm64 #1 SMP Debian 6.1.129-1 (2025-03-06) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin I: user script /srv/workspace/pbuilder/4107019/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, python3-all, python3-setuptools, python3-seaborn, python3-biopython, python3-numpy, python3-sklearn dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19898 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-python; however: Package dh-python 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 python3-seaborn; however: Package python3-seaborn is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-sklearn; however: Package python3-sklearn is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} blt{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-lyx{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgcrypt20{a} libgfortran5{a} libglib2.0-0t64{a} libgpg-error0{a} libgraphite2-3{a} libharfbuzz0b{a} libicu76{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} liblapack3{a} liblcms2-2{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libproc2-0{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8t64{a} libsharpyuv0{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libunistring5{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} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} procps{a} python-matplotlib-data{a} python3{a} python3-all{a} python3-attr{a} python3-autocommand{a} python3-biopython{a} python3-brotli{a} python3-cairo{a} python3-chardet{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-fonttools{a} python3-freetype{a} python3-fs{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-joblib{a} python3-kiwisolver{a} python3-lxml{a} python3-lz4{a} python3-matplotlib{a} python3-minimal{a} python3-more-itertools{a} python3-mpmath{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-platformdirs{a} python3-pyparsing{a} python3-pytz{a} python3-reportlab{a} python3-rlpycairo{a} python3-scipy{a} python3-seaborn{a} python3-setuptools{a} python3-sklearn{a} python3-sklearn-lib{a} python3-sympy{a} python3-threadpoolctl{a} python3-tk{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-ufolib2{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} python3.13-tk{a} readline-common{a} sensible-utils{a} sgml-base{a} tk8.6-blt2.5{a} tzdata{a} unicode-data{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-dejavu-extra isympy-common javascript-common libarchive-cpio-perl libglib2.0-data libgpg-error-l10n libltdl-dev libmail-sendmail-perl linux-sysctl-defaults lynx ncbi-blast+ psmisc python-biopython-doc python3-bottleneck python3-bs4 python3-cssselect python3-html5lib python3-jinja2 python3-numexpr python3-odf python3-olefile python3-openpyxl python3-pooch python3-psutil python3-pytest python3-tables python3-yaml shared-mime-info wget xdg-user-dirs 0 packages upgraded, 160 newly installed, 0 to remove and 0 not upgraded. Need to get 135 MB of archives. After unpacking 538 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.2-2 [853 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.7.0-1 [92.8 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.2-2 [1995 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.2-2 [27.1 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025a-2 [259 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.7-1 [21.2 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.2-2 [1888 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.2-2 [746 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.2-2 [10.1 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.2-2 [28.1 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-5 [136 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.1-2 [104 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-19 [361 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.1-2 [1819 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 python3-numpy arm64 1:2.2.3+ds-5 [3596 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-7 [62.4 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-7 [868 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-2 [337 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-2 [103 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-2 [43.6 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.4-5 [92.0 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-7 [285 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-3 [862 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [984 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.47-1.1 [274 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libfontenc1 arm64 1:1.1.8-1+b2 [22.5 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+24 [217 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 49 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-2.1 [318 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-2.1 [387 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b4 [27.2 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libxft2 arm64 2.3.6-1+b4 [51.6 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libxss1 arm64 1:1.2.3-1+b3 [17.1 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libtk8.6 arm64 8.6.16-1 [741 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-8 [537 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 blt arm64 2.5.3+dfsg-8 [5984 B] Get: 63 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 69 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libicu76 arm64 76.1-3 [9526 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.3+b1 [630 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.1 [920 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20250308 [115 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 fonts-lyx all 2.4.3-1 [190 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.4-1+b1 [483 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.23-1+b1 [42.5 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.16-1 [26.5 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libgpg-error0 arm64 1.51-3 [78.5 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libgcrypt20 arm64 1.11.0-7 [742 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.84.0-2 [1424 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.2.0-1+b1 [442 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3.1 [173 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libopenjp2-7 arm64 2.5.3-2 [190 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libqhull-r8.0 arm64 2020.2-6+b2 [229 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libraqm0 arm64 0.10.2-1 [13.6 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [113 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libwebpmux3 arm64 1.5.0-0.1 [125 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libxslt1.1 arm64 1.1.35-1.2 [221 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 python-matplotlib-data all 3.8.3-7 [2735 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 python3-all arm64 3.13.2-2 [1044 B] Get: 109 http://deb.debian.org/debian unstable/main arm64 python3-attr all 25.1.0-1 [68.7 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 python3.13-tk arm64 3.13.2-2 [105 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 python3-tk arm64 3.13.2-1 [9516 B] Get: 114 http://deb.debian.org/debian unstable/main arm64 python3-pil.imagetk arm64 11.1.0-5+b1 [81.8 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 python3-pil arm64 11.1.0-5+b1 [495 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 python3-cairo arm64 1.27.0-2 [114 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 python3-freetype all 2.5.1-1 [89.3 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 119 http://deb.debian.org/debian unstable/main arm64 python3-reportlab all 4.3.1-1 [1158 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 python3-biopython arm64 1.85+dfsg-2+b1 [1657 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 python3-brotli arm64 1.1.0-2+b7 [300 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 python3-contourpy arm64 1.3.1-1+b1 [190 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 python3-cycler all 0.12.1-1 [9496 B] Get: 126 http://deb.debian.org/debian unstable/main arm64 python3-dateutil all 2.9.0-4 [79.4 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 python3-platformdirs all 4.3.6-1 [16.6 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 python3-fs all 2.4.16-7 [95.2 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 python3-lxml arm64 5.3.1-1+b1 [1139 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 python3-lz4 arm64 4.4.0+dfsg-1+b1 [25.6 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 python3-scipy arm64 1.15.2-6 [14.8 MB] Get: 133 http://deb.debian.org/debian unstable/main arm64 python3-mpmath all 1.3.0-1 [419 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 python3-sympy all 1.13.3-5 [4148 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.0 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 unicode-data all 15.1.0-1 [8547 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 python3-fonttools arm64 4.55.3-2+b1 [1381 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 75.8.0-1 [222 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 75.8.0-1 [724 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 148 http://deb.debian.org/debian unstable/main arm64 python3-joblib all 1.4.2-3 [216 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 python3-kiwisolver arm64 1.4.7-3+b1 [57.8 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 python3-matplotlib arm64 3.8.3-7+b1 [22.9 MB] Get: 153 http://deb.debian.org/debian unstable/main arm64 python3-pytz all 2025.1-3 [150 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 python3-tz all 2025.1-3 [4004 B] Get: 155 http://deb.debian.org/debian unstable/main arm64 python3-pandas-lib arm64 2.2.3+dfsg-8+b1 [3872 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 python3-pandas all 2.2.3+dfsg-8 [3097 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 python3-seaborn all 0.13.2-5 [215 kB] Get: 158 http://deb.debian.org/debian unstable/main arm64 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 python3-sklearn-lib arm64 1.4.2+dfsg-8 [3408 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 python3-sklearn all 1.4.2+dfsg-8 [2248 kB] Fetched 135 MB in 1s (215 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19898 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.2-2_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.2-2) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.7.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.7.0-1) ... 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-2_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.2-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-2_arm64.deb ... Unpacking python3.13 (3.13.2-2) ... 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Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-7) ... Setting up libgcrypt20:arm64 (1.11.0-7) ... Setting up libqhull-r8.0:arm64 (2020.2-6+b2) ... Setting up libxcb-shm0:arm64 (1.17.0-2+b1) ... Setting up file (1:5.46-2) ... Setting up libjbig0:arm64 (2.1-6.1+b2) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Mar 20 11:20:10 UTC 2025. Universal Time is now: Thu Mar 20 11:20:10 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... Setting up libfontenc1:arm64 (1:1.1.8-1+b2) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.12.1-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libjpeg62-turbo:arm64 (1:2.1.5-3.1) ... Setting up libx11-data (2:1.8.10-2) ... 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Setting up sgml-base (1.31) ... Setting up libicu76:arm64 (76.1-3) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up python-matplotlib-data (3.8.3-7) ... Setting up libwebpmux3:arm64 (1.5.0-0.1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.3+b1) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up liblapack3:arm64 (3.12.1-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.23.1-1) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b4) ... Setting up libtool (2.5.4-4) ... Setting up fontconfig-config (2.15.0-2.1) ... Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... Setting up libxext6:arm64 (2:1.3.4-1+b3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libglib2.0-0t64:arm64 (2.84.0-2) ... No schema files found: doing nothing. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:arm64 (1.1.35-1.2) ... Setting up libharfbuzz0b:arm64 (10.2.0-1+b1) ... Setting up libxss1:arm64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:arm64 (2.15.0-2.1) ... Setting up libpython3.13-stdlib:arm64 (3.13.2-2) ... Setting up libpython3-stdlib:arm64 (3.13.2-2) ... Setting up libxft2:arm64 (2.3.6-1+b4) ... Setting up python3.13 (3.13.2-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:arm64 (8.6.16-1) ... Setting up python3 (3.13.2-2) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-freetype (2.5.1-1) ... Setting up xfonts-utils (1:7.7+7) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.18.4-1+b1) ... Setting up python3.13-tk (3.13.2-2) ... Setting up python3-platformdirs (4.3.6-1) ... Setting up python3-fs (2.4.16-7) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.2-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-brotli (1.1.0-2+b7) ... Setting up libraqm0:arm64 (0.10.2-1) ... Setting up python3-cycler (0.12.1-1) ... Setting up python3-kiwisolver (1.4.7-3+b1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-numpy (1:2.2.3+ds-5) ... Setting up python3-lxml:arm64 (5.3.1-1+b1) ... Setting up python3-dateutil (2.9.0-4) ... Setting up python3-contourpy (1.3.1-1+b1) ... Setting up python3-mpmath (1.3.0-1) ... Setting up dh-python (6.20250308) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up python3-sympy (1.13.3-5) ... Setting up python3-attr (25.1.0-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... Setting up python3-scipy (1.15.2-6) ... Setting up python3-cairo (1.27.0-2) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3-joblib (1.4.2-3) ... Setting up python3-lz4 (4.4.0+dfsg-1+b1) ... Setting up blt (2.5.3+dfsg-8) ... Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-8+b1) ... Setting up python3-typeguard (4.4.2-1) ... Setting up python3-threadpoolctl (3.1.0-1) ... Setting up python3-sklearn-lib:arm64 (1.4.2+dfsg-8) ... Setting up python3-all (3.13.2-2) ... Setting up python3-tk:arm64 (3.13.2-1) ... Setting up debhelper (13.24.1) ... Setting up python3-pytz (2025.1-3) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-tz (2025.1-3) ... Setting up python3-pil:arm64 (11.1.0-5+b1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pandas (2.2.3+dfsg-8) ... Setting up python3-pil.imagetk:arm64 (11.1.0-5+b1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-sklearn (1.4.2+dfsg-8) ... Setting up python3-reportlab (4.3.1-1) ... Setting up python3-pkg-resources (75.8.0-1) ... Setting up python3-setuptools (75.8.0-1) ... Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... Setting up python3-fonttools (4.55.3-2+b1) ... Setting up python3-matplotlib (3.8.3-7+b1) ... Setting up python3-seaborn (0.13.2-5) ... Processing triggers for libc-bin (2.41-6) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.85+dfsg-2+b1) ... 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/mcaller-1.0.3+git20210624.b415090/ && 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 > ../mcaller_1.0.3+git20210624.b415090-3_source.changes dpkg-buildpackage: info: source package mcaller dpkg-buildpackage: info: source version 1.0.3+git20210624.b415090-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --with python3 debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/mcaller-1.0.3+git20210624.b415090' 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 '/build/reproducible-path/mcaller-1.0.3+git20210624.b415090' 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 '/build/reproducible-path/mcaller-1.0.3+git20210624.b415090' 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...: 9 observations 9 positions 0 regions with multiple methylated bases 0 observations with skips included 4 observations with too many skips 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...: 44 observations 44 positions 1 regions with multiple methylated bases 0 observations with skips included 10 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 Finished extracting signals Merging files... Training... ['A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A'] [[np.float64(-0.18999999999999992), np.float64(-1.6799999999999997), np.float64(-2.3), np.float64(0.56), np.float64(-1.41), np.float64(1.48), np.float64(7.055265349382997)], [np.float64(-1.1300000000000001), np.float64(-1.67), np.float64(-1.1), np.float64(-0.5774999999999999), np.float64(0.42), np.float64(1.0225), np.float64(7.055265349382997)], [np.float64(0.0050000000000000044), np.float64(-0.29500000000000004), np.float64(-0.54), np.float64(3.96), np.float64(1.47), np.float64(0.06499999999999995), np.float64(7.055265349382997)], [np.float64(3.255), np.float64(3.925), np.float64(0.03999999999999998), np.float64(-0.15599999999999997), np.float64(-1.01), np.float64(1.3533333333333333), np.float64(7.055265349382997)], [np.float64(-0.07999999999999996), np.float64(-1.3666666666666665), np.float64(0.84), np.float64(-0.5449999999999999), np.float64(-3.22), np.float64(-1.53), np.float64(7.055265349382997)], [np.float64(-1.74), np.float64(-2.56), np.float64(-2.0774999999999997), np.float64(1.84), np.float64(-0.09999999999999998), np.float64(-0.3), np.float64(7.055265349382997)], [np.float64(1.92), np.float64(2.75), np.float64(1.59), np.float64(1.6433333333333333), np.float64(1.59), np.float64(1.27), np.float64(7.055265349382997)], [np.float64(-1.44), np.float64(-5.03), np.float64(1.4449999999999998), np.float64(0.4000000000000001), np.float64(-0.588), np.float64(-0.55), np.float64(7.055265349382997)], [np.float64(-1.4433333333333334), np.float64(-0.020000000000000018), np.float64(-0.0366666666666667), np.float64(-0.5499999999999999), np.float64(0.64), np.float64(-2.71), np.float64(7.055265349382997)], [np.float64(-1.23), np.float64(-1.635), np.float64(-0.24), np.float64(1.1033333333333333), np.float64(-2.215), np.float64(-2.93), np.float64(7.055265349382997)]] ['GGATTMTTTCA', 'CTGGAMAAAGC', 'GGGCCMTTACC', 'GGTGGMTGAAT', 'GGTTAMCGCGT', 'TGTGGMGAAAC', 'AGAACMCTTTC', 'AAATGMGATTT', 'AGTAGMTTGAT', 'ACTTAMCCGGT'] NN general model scores: 0.75,0.5,0.5,1.0,0.5 Cross validation accuracy: 0.65 (+/- 0.40) Finished training rm -rf testdata mv testdata_save testdata make[1]: Leaving directory '/build/reproducible-path/mcaller-1.0.3+git20210624.b415090' 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 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_arm64.buildinfo dpkg-genchanges --build=binary -O../mcaller_1.0.3+git20210624.b415090-3_arm64.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/4107019 and its subdirectories I: Current time: Wed Mar 19 23:22:01 -12 2025 I: pbuilder-time-stamp: 1742469721