I: pbuilder: network access will be disabled during build I: Current time: Sun May 26 20:44:29 +14 2024 I: pbuilder-time-stamp: 1716705869 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [nim-hts_0.3.19+ds-1.dsc] I: copying [./nim-hts_0.3.19+ds.orig.tar.xz] I: copying [./nim-hts_0.3.19+ds-1.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Oct 19 09:36:07 2021 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "nilesh@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./nim-hts_0.3.19+ds-1.dsc: no acceptable signature found dpkg-source: info: extracting nim-hts in nim-hts-0.3.19+ds dpkg-source: info: unpacking nim-hts_0.3.19+ds.orig.tar.xz dpkg-source: info: unpacking nim-hts_0.3.19+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying dontDoNestedTests.patch dpkg-source: info: applying disable-test-with-sourceless-file.patch dpkg-source: info: applying fix-version-comparision.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2309659/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 26 06:44 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2309659/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2309659/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=f12611dad8f043b6884cdb4036cd8592 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2309659 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.F3kQ4mcY/pbuilderrc_Yygr --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.F3kQ4mcY/b2 --logfile b2/build.log nim-hts_0.3.19+ds-1.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 23 11:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2309659/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), nim, libhts-dev, samtools, tabix, bcftools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19700 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 nim; however: Package nim is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on tabix; however: Package tabix is not installed. pbuilder-satisfydepends-dummy depends on bcftools; however: Package bcftools 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} bcftools{a} blt{a} bsdextrautils{a} debhelper{a} dh-autoreconf{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} libbsd0{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libopenjp2-7{a} libpcre3{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libssh2-1t64{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxslt1.1{a} libxss1{a} m4{a} man-db{a} media-types{a} netbase{a} nim{a} po-debconf{a} python-matplotlib-data{a} python3{a} python3-appdirs{a} python3-argcomplete{a} python3-argh{a} python3-attr{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-gffutils{a} python3-importlib-metadata{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-packaging{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-pyfaidx{a} python3-pyparsing{a} python3-reportlab{a} python3-rlpycairo{a} python3-scipy{a} python3-simplejson{a} python3-six{a} python3-sympy{a} python3-tk{a} python3-tz{a} python3-ufolib2{a} python3-unicodedata2{a} python3-zipp{a} python3.11{a} python3.11-minimal{a} readline-common{a} samtools{a} sensible-utils{a} sgml-base{a} tabix{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} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-dejavu-extra git isympy-common javascript-common krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx ncbi-blast+ publicsuffix python-biopython-doc python3-bs4 python3-cssselect python3-html5lib python3-olefile python3-pybedtools shared-mime-info wget xdg-user-dirs 0 packages upgraded, 171 newly installed, 0 to remove and 0 not upgraded. Need to get 127 MB of archives. After unpacking 517 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.1-1 [94.1 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 35 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-5 [215 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.8.0-1 [434 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.19+ds-1.1+b1 [448 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 python3-argcomplete all 3.3.0-1 [38.9 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 python3-argh all 0.31.2-1 [26.5 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.2.0-1 [59.9 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 1.0.0-6 [6696 B] Get: 52 http://deb.debian.org/debian trixie/main amd64 python3-importlib-metadata all 4.12.0-1 [24.9 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 python3-pyfaidx all 0.8.1.1-2 [29.0 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 python3-simplejson amd64 3.19.2-1+b1 [69.4 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14-20240330-1 [836 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-10 [5465 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1 [1034 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libfontenc1 amd64 1:1.1.8-1 [23.0 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 71 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2 [144 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b1 [17.0 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.14-1 [784 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get: 86 http://deb.debian.org/debian trixie/main amd64 python3-tk amd64 3.12.3-1 [109 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 python3-pil.imagetk amd64 10.3.0-2 [79.5 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b1 [35.3 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libopenjp2-7 amd64 2.5.0-2+b3 [190 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.80.2-1 [1485 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.1-1+b1 [14.2 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [110 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libwebpmux3 amd64 1.4.0-0.1 [123 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 python3-pil amd64 10.3.0-2 [564 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2 [115 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2 [105 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.0-3+b1 [531 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 python3-cairo amd64 1.26.0-1 [142 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 python3-freetype all 2.4.0-1 [80.3 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 112 http://deb.debian.org/debian trixie/main amd64 python3-reportlab all 4.2.0-2 [1149 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 python3-biopython amd64 1.83+dfsg1-3 [1634 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 python3-gffutils all 0.13-1 [1041 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 fonts-lyx all 2.4.0~RC4-1 [189 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 python-matplotlib-data all 3.6.3-2 [2744 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 python3-six all 1.16.0-6 [16.3 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 python3-dateutil all 2.9.0-2 [79.4 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 python3-contourpy amd64 1.0.7-3 [285 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get: 126 http://deb.debian.org/debian trixie/main amd64 python3-brotli amd64 1.1.0-2+b3 [312 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b1 [29.1 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 python3-scipy amd64 1.11.4-10 [19.5 MB] Get: 130 http://deb.debian.org/debian trixie/main amd64 python3-attr all 23.2.0-2 [65.5 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 python3-sympy all 1.12-7 [3869 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 python3-tz all 2024.1-2 [30.9 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 python3-appdirs all 1.4.4-4 [12.5 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 python3-fs all 2.4.16-4 [95.4 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libxslt1.1 amd64 1.1.35-1+b1 [232 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 python3-lxml amd64 5.1.0-1 [2092 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b3 [25.5 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 python3-unicodedata2 amd64 15.1.0+ds-1+b1 [299 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 python3-fonttools amd64 4.46.0-1 [1623 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 python3-kiwisolver amd64 1.4.5-1 [80.7 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.0-1 [45.5 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libqhull-r8.0 amd64 2020.2-6+b1 [245 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 python3-matplotlib amd64 3.6.3-2 [8167 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 bcftools amd64 1.20-1 [760 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 156 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 libcurl4-gnutls-dev amd64 8.8.0-1 [540 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 libdeflate-dev amd64 1.20-1 [54.5 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 liblzma-dev amd64 5.6.1+really5.4.5-1 [293 kB] Get: 165 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 libhts-dev amd64 1.19+ds-1.1+b1 [1667 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5-2 [104 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 libpcre3 amd64 2:8.39-15+b1 [342 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 nim amd64 1.6.14-3 [4164 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 samtools amd64 1.19.2-1+b1 [645 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 tabix amd64 1.19+ds-1.1+b1 [476 kB] Fetched 127 MB in 11s (11.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (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 ... 19700 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (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 ... 20016 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../5-libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (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 ... 21008 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../003-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../004-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../005-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../006-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../007-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../008-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../009-bsdextrautils_2.40.1-1_amd64.deb ... Unpacking bsdextrautils (2.40.1-1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../010-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../011-man-db_2.12.1-1_amd64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../012-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../013-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../014-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../015-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../016-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../017-libbrotli1_1.1.0-2+b3_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b3) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../018-libkrb5support0_1.20.1-6+b1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../019-libcom-err2_1.47.1-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../020-libk5crypto3_1.20.1-6+b1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../021-libkeyutils1_1.6.3-3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../022-libkrb5-3_1.20.1-6+b1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../023-libgssapi-krb5-2_1.20.1-6+b1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../024-libsasl2-modules-db_2.1.28+dfsg1-6_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../025-libsasl2-2_2.1.28+dfsg1-6_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../026-libldap-2.5-0_2.5.17+dfsg-1_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../027-libnghttp2-14_1.61.0-1+b1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.61.0-1+b1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../028-libpsl5t64_0.21.2-1.1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../029-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../030-libssh2-1t64_1.11.0-5_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.0-5) ... Selecting previously unselected package libcurl3t64-gnutls:amd64. Preparing to unpack .../031-libcurl3t64-gnutls_8.8.0-1_amd64.deb ... Unpacking libcurl3t64-gnutls:amd64 (8.8.0-1) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../032-libdeflate0_1.20-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.20-1) ... Selecting previously unselected package libhtscodecs2:amd64. Preparing to unpack .../033-libhtscodecs2_1.6.0-1+b1_amd64.deb ... Unpacking libhtscodecs2:amd64 (1.6.0-1+b1) ... Selecting previously unselected package libhts3t64:amd64. Preparing to unpack .../034-libhts3t64_1.19+ds-1.1+b1_amd64.deb ... Unpacking libhts3t64:amd64 (1.19+ds-1.1+b1) ... Selecting previously unselected package python3-argcomplete. Preparing to unpack .../035-python3-argcomplete_3.3.0-1_all.deb ... Unpacking python3-argcomplete (3.3.0-1) ... Selecting previously unselected package python3-argh. Preparing to unpack .../036-python3-argh_0.31.2-1_all.deb ... 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Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... Setting up libxau6:amd64 (1:1.0.9-1+b1) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-4+b1) ... Setting up bsdextrautils (2.40.1-1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up fonts-lyx (2.4.0~RC4-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:amd64 (1.1.0-2+b3) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.61.0-1+b1) ... Setting up libdeflate0:amd64 (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libqhull-r8.0:amd64 (2020.2-6+b1) ... Setting up libcom-err2:amd64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libjbig0:amd64 (2.1-6.1+b1) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up libkrb5support0:amd64 (1.20.1-6+b1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Sun May 26 06:48:29 UTC 2024. Universal Time is now: Sun May 26 06:48:29 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... Setting up libpcre3:amd64 (2:8.39-15+b1) ... Setting up libfontenc1:amd64 (1:1.1.8-1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:amd64 (2.80.2-1) ... No schema files found: doing nothing. Setting up libblas3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjpeg62-turbo:amd64 (1:2.1.5-3) ... Setting up libx11-data (2:1.8.7-1) ... 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Setting up libopenjp2-7:amd64 (2.5.0-2+b3) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up nim (1.6.14-3) ... Setting up libkrb5-3:amd64 (1.20.1-6+b1) ... Setting up libssh2-1t64:amd64 (1.11.0-5) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up python-matplotlib-data (3.6.3-2) ... Setting up libwebpmux3:amd64 (1.4.0-0.1) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up libdeflate-dev:amd64 (1.20-1) ... Setting up tabix (1.19+ds-1.1+b1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up liblapack3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.17.0-2) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:amd64 (1.17.0-2) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... Setting up libxcb-shm0:amd64 (1.17.0-2) ... Setting up libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-4) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:amd64 (1.1.35-1+b1) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2+b1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up libcurl3t64-gnutls:amd64 (8.8.0-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libcurl4-gnutls-dev:amd64 (8.8.0-1) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.18.0-3+b1) ... Setting up libraqm0:amd64 (0.10.1-1+b1) ... Setting up libhts3t64:amd64 (1.19+ds-1.1+b1) ... Setting up libxss1:amd64 (1:1.2.3-1+b1) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up libxft2:amd64 (2.3.6-1+b1) ... Setting up libtk8.6:amd64 (8.6.14-1) ... Setting up libhts-dev:amd64 (1.19+ds-1.1+b1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-freetype (2.4.0-1) ... Setting up python3-tz (2024.1-2) ... Setting up samtools (1.19.2-1+b1) ... Setting up python3-six (1.16.0-6) ... Setting up python3-simplejson (3.19.2-1+b1) ... Setting up python3-pil:amd64 (10.3.0-2) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.0-1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-brotli (1.1.0-2+b3) ... Setting up python3-cycler (0.12.1-1) ... Setting up python3-kiwisolver (1.4.5-1) ... Setting up python3-lxml:amd64 (5.1.0-1) ... Setting up python3-dateutil (2.9.0-2) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-argcomplete (3.3.0-1) ... Setting up python3-appdirs (1.4.4-4) ... Setting up python3-pkg-resources (68.1.2-2) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2309659/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/2309659/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/nim-hts-0.3.19+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../nim-hts_0.3.19+ds-1_source.changes dpkg-buildpackage: info: source package nim-hts dpkg-buildpackage: info: source version 0.3.19+ds-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/nim-hts-0.3.19+ds' dh_auto_clean # remnants from testing rm -f ____t.vcf t.gz ti.txt.gz ti.txt.gz.csi rm -f tests/run tests/HG02002.bam.csi tests/auxtest tests/newsample.vcf tests/outmissing.vcf tests/outv.vcf tests/outz.vcf tests/sample.fa.fai tests/all tests/htstest tests/bgzftest tests/bamtest rm -rf tests/nimcache make[1]: Leaving directory '/build/reproducible-path/nim-hts-0.3.19+ds' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/nim-hts-dev.substvars debian/nim-hts-examples.substvars debian/files rm -fr -- debian/nim-hts-dev/ debian/tmp/ debian/nim-hts-examples/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/nim-hts-0.3.19+ds' dh_auto_build # Regenerate repacked files cat tests/sa.sam | samtools view -Sb - > tests/sa.bam samtools index tests/sa.bam tests/sa.bam.bai cat debian/missing-sources/HG02002.sam | samtools view -Sb - > tests/HG02002.bam samtools index tests/HG02002.bam tests/HG02002.bam.bai tabix tests/test.vcf.gz bcftools index tests/test.bcf make[1]: Leaving directory '/build/reproducible-path/nim-hts-0.3.19+ds' rm -f debian/nim-hts-dev.debhelper.log debian/nim-hts-examples.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/nim-hts-0.3.19+ds' nim c --nimcache:/build/reproducible-path/nim-hts-0.3.19+ds/tests/nimcache tests/all.nim Hint: used config file '/etc/nim/nim.cfg' [Conf] Hint: used config file '/etc/nim/config.nims' [Conf] Hint: used config file '/build/reproducible-path/nim-hts-0.3.19+ds/tests/nim.cfg' [Conf] ............................................................................................................. /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/bam/flag.nim(1, 18) Hint: duplicate import of 'hts_concat'; previous import here: /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/bam.nim(1, 17) [DuplicateModuleImport] . /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/bam/cigar.nim(1, 18) Hint: duplicate import of 'hts_concat'; previous import here: /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/bam/flag.nim(1, 18) [DuplicateModuleImport] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/bam/cigar.nim(2, 8) Hint: duplicate import of 'strutils'; previous import here: /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/bam.nim(4, 8) [DuplicateModuleImport] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/bam/cigar.nim(57, 34) Warning: target type is larger than source type [CastSizes] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/bam.nim(248, 34) template/generic instantiation of `bam_get_cigar` from here /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/bam/cigar.nim(52, 46) Warning: target type is larger than source type [CastSizes] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/bam.nim(262, 52) Warning: implicit conversion to 'cstring' from a non-const location: region; this will become a compile time error in the future [CStringConv] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/bam.nim(373, 28) Warning: implicit conversion to 'cstring' from a non-const location: mode; this will become a compile time error in the future [CStringConv] .. /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/bam/auxtags.nim(3, 1) Hint: duplicate import of 'strformat'; previous import here: /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/bam.nim(3, 8) [DuplicateModuleImport] .... /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/vcf.nim(118, 18) Warning: conversion to enum with holes is unsafe: Status(ret) [HoleEnumConv] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/vcf.nim(119, 16) Warning: conversion to enum with holes is unsafe: Status(bcf_hdr_sync(h.hdr)) [HoleEnumConv] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/vcf.nim(181, 16) Warning: conversion to enum with holes is unsafe: Status(bcf_hdr_sync(h.hdr)) [HoleEnumConv] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/vcf.nim(190, 16) Warning: conversion to enum with holes is unsafe: Status(bcf_hdr_sync(h.hdr)) [HoleEnumConv] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/vcf.nim(288, 18) Warning: conversion to enum with holes is unsafe: Status(int(bcf_update_format(f.v.vcf.header.hdr, f.v.c, cstring(key), nil, 0, cint(htype)))) [HoleEnumConv] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/vcf.nim(297, 20) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/vcf.nim(309, 22) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/vcf.nim(320, 22) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/vcf.nim(352, 16) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/vcf.nim(359, 16) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/vcf.nim(366, 16) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/vcf.nim(376, 20) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/vcf.nim(391, 20) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/vcf.nim(405, 20) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/vcf.nim(432, 16) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/vcf.nim(436, 16) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/vcf.nim(441, 16) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/vcf.nim(461, 16) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/vcf.nim(467, 16) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/vcf.nim(527, 23) Warning: conversion to enum with holes is unsafe: BCF_TYPE(fmt.type) [HoleEnumConv] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/vcf.nim(542, 23) Warning: conversion to enum with holes is unsafe: BCF_TYPE(fld.type) [HoleEnumConv] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/vcf.nim(601, 27) Warning: implicit conversion to 'cstring' from a non-const location: v.fname; this will become a compile time error in the future [CStringConv] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/vcf.nim(603, 31) Warning: implicit conversion to 'cstring' from a non-const location: v.fname; this will become a compile time error in the future [CStringConv] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/vcf.nim(645, 30) Warning: implicit conversion to 'cstring' from a non-const location: v.fname; this will become a compile time error in the future [CStringConv] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/vcf.nim(664, 36) Warning: implicit conversion to 'cstring' from a non-const location: `[]`(region) do: 0 .. pred(cidx, 1); this will become a compile time error in the future [CStringConv] /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/vcf.nim(700, 32) Warning: implicit conversion to 'cstring' from a non-const location: v.fname; this will become a compile time error in the future [CStringConv] . /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/fai.nim(38, 24) Warning: See corresponding Defect; IndexError is deprecated [Deprecated] ... /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/csi.nim(17, 51) Warning: implicit conversion to 'cstring' from a non-const location: base_path & ".csi"; this will become a compile time error in the future [CStringConv] ... /build/reproducible-path/nim-hts-0.3.19+ds/tests/auxtest.nim(3, 7) template/generic instantiation of `suite` from here /build/reproducible-path/nim-hts-0.3.19+ds/tests/auxtest.nim(4, 8) template/generic instantiation of `test` from here /build/reproducible-path/nim-hts-0.3.19+ds/tests/auxtest.nim(10, 18) template/generic instantiation of `tag` from here /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/bam/auxtags.nim(53, 7) Warning: unreachable code after 'return' statement or '{.noReturn.}' proc [UnreachableCode] /build/reproducible-path/nim-hts-0.3.19+ds/tests/auxtest.nim(3, 7) template/generic instantiation of `suite` from here /build/reproducible-path/nim-hts-0.3.19+ds/tests/auxtest.nim(4, 8) template/generic instantiation of `test` from here /build/reproducible-path/nim-hts-0.3.19+ds/tests/auxtest.nim(13, 19) template/generic instantiation of `tag` from here /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/bam/auxtags.nim(71, 7) Warning: unreachable code after 'return' statement or '{.noReturn.}' proc [UnreachableCode] /build/reproducible-path/nim-hts-0.3.19+ds/tests/auxtest.nim(3, 7) template/generic instantiation of `suite` from here /build/reproducible-path/nim-hts-0.3.19+ds/tests/auxtest.nim(4, 8) template/generic instantiation of `test` from here /build/reproducible-path/nim-hts-0.3.19+ds/tests/auxtest.nim(13, 19) template/generic instantiation of `tag` from here /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/bam/auxtags.nim(74, 7) Warning: unreachable code after 'return' statement or '{.noReturn.}' proc [UnreachableCode] /build/reproducible-path/nim-hts-0.3.19+ds/tests/auxtest.nim(3, 7) template/generic instantiation of `suite` from here /build/reproducible-path/nim-hts-0.3.19+ds/tests/auxtest.nim(4, 8) template/generic instantiation of `test` from here /build/reproducible-path/nim-hts-0.3.19+ds/tests/auxtest.nim(17, 19) template/generic instantiation of `tag` from here /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/bam/auxtags.nim(63, 7) Warning: unreachable code after 'return' statement or '{.noReturn.}' proc [UnreachableCode] /build/reproducible-path/nim-hts-0.3.19+ds/tests/auxtest.nim(3, 7) template/generic instantiation of `suite` from here /build/reproducible-path/nim-hts-0.3.19+ds/tests/auxtest.nim(4, 8) template/generic instantiation of `test` from here /build/reproducible-path/nim-hts-0.3.19+ds/tests/auxtest.nim(17, 19) template/generic instantiation of `tag` from here /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/bam/auxtags.nim(66, 7) Warning: unreachable code after 'return' statement or '{.noReturn.}' proc [UnreachableCode] /build/reproducible-path/nim-hts-0.3.19+ds/tests/auxtest.nim(3, 7) template/generic instantiation of `suite` from here /build/reproducible-path/nim-hts-0.3.19+ds/tests/auxtest.nim(4, 8) template/generic instantiation of `test` from here /build/reproducible-path/nim-hts-0.3.19+ds/tests/auxtest.nim(17, 19) template/generic instantiation of `tag` from here /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/bam/auxtags.nim(74, 7) Warning: unreachable code after 'return' statement or '{.noReturn.}' proc [UnreachableCode] /build/reproducible-path/nim-hts-0.3.19+ds/tests/auxtest.nim(3, 7) template/generic instantiation of `suite` from here /build/reproducible-path/nim-hts-0.3.19+ds/tests/auxtest.nim(25, 8) template/generic instantiation of `test` from here /build/reproducible-path/nim-hts-0.3.19+ds/tests/auxtest.nim(40, 18) template/generic instantiation of `tag` from here /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/bam/auxtags.nim(58, 7) Warning: unreachable code after 'return' statement or '{.noReturn.}' proc [UnreachableCode] . /build/reproducible-path/nim-hts-0.3.19+ds/tests/vcftest.nim(23, 7) template/generic instantiation of `suite` from here /build/reproducible-path/nim-hts-0.3.19+ds/tests/vcftest.nim(46, 8) template/generic instantiation of `test` from here /build/reproducible-path/nim-hts-0.3.19+ds/tests/vcftest.nim(63, 13) template/generic instantiation of `check` from here /build/reproducible-path/nim-hts-0.3.19+ds/src/hts/vcf.nim(448, 16) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/reproducible-path/nim-hts-0.3.19+ds/tests/vcftest.nim(404, 7) Hint: 'current_line' is declared but not used [XDeclaredButNotUsed] /build/reproducible-path/nim-hts-0.3.19+ds/tests/vcftest.nim(406, 7) Hint: 'currentBlock' is declared but not used [XDeclaredButNotUsed] /build/reproducible-path/nim-hts-0.3.19+ds/tests/vcftest.nim(411, 7) Hint: 'block_pos_i' is declared but not used [XDeclaredButNotUsed] ..... CC: ../../../../usr/lib/nim/lib/std/private/digitsutils.nim CC: ../../../../usr/lib/nim/lib/system/assertions.nim CC: ../../../../usr/lib/nim/lib/system/formatfloat.nim CC: ../../../../usr/lib/nim/lib/system/dollars.nim CC: ../../../../usr/lib/nim/lib/system/io.nim CC: ../../../../usr/lib/nim/lib/system.nim CC: ../../../../usr/lib/nim/lib/std/exitprocs.nim CC: ../../../../usr/lib/nim/lib/pure/parseutils.nim CC: ../../../../usr/lib/nim/lib/pure/math.nim CC: ../../../../usr/lib/nim/lib/pure/algorithm.nim CC: ../../../../usr/lib/nim/lib/pure/unicode.nim CC: ../../../../usr/lib/nim/lib/pure/strutils.nim CC: ../../../../usr/lib/nim/lib/pure/streams.nim CC: ../../../../usr/lib/nim/lib/pure/times.nim CC: ../../../../usr/lib/nim/lib/pure/hashes.nim CC: ../../../../usr/lib/nim/lib/pure/collections/sets.nim CC: ../../../../usr/lib/nim/lib/pure/os.nim CC: ../../../../usr/lib/nim/lib/pure/strformat.nim CC: ../../../../usr/lib/nim/lib/pure/terminal.nim CC: ../../../../usr/lib/nim/lib/pure/unittest.nim CC: ../src/hts/private/hts_concat.nim CC: ../src/hts/bam/flag.nim CC: flagtest.nim CC: ../src/hts/bam.nim CC: cigartest.nim CC: htstest.nim CC: ../src/hts/vcf.nim CC: ../src/hts/fai.nim CC: ../src/hts/bgzf.nim CC: ../src/hts/csi.nim CC: ../src/hts/bgzf/bgzi.nim CC: ../src/hts/stats.nim CC: ../src/hts.nim CC: bgzftest.nim CC: faitest.nim CC: auxtest.nim CC: vcftest.nim CC: bamtest.nim CC: statstests.nim CC: vcfiso.nim CC: ../src/hts/files.nim CC: test_files.nim CC: all.nim Hint: [Link] Hint: gc: refc; opt: none (DEBUG BUILD, `-d:release` generates faster code) 84440 lines; 37.194s; 145.406MiB peakmem; proj: /build/reproducible-path/nim-hts-0.3.19+ds/tests/all.nim; out: /build/reproducible-path/nim-hts-0.3.19+ds/tests/all [SuccessX] tests/all [Suite] flag test-suite [OK] test flags [Suite] flag cigar-suite [OK] test op [OK] new cigar [Suite] flag hts-suite [OK] test hts [Suite] bgzf-suite [OK] test-write [OK] test-read [OK] bgzf-iterator [E::bgzf_read_block] Failed to read BGZF block data at offset 0 expected 24944 bytes; hread returned 982 [OK] bgzf-iterator-err [OK] write-with-index [OK] read-new-index [OK] csi-iterator [Suite] fai-suite [OK] fai-read [OK] fai chrom_len [OK] fai indexing [OK] issue26 [OK] close [Suite] aux-test [OK] test aux [OK] tag [OK] drop tag [Suite] vcf suite [E::bcf_hdr_read] Input is not detected as bcf or vcf format [OK] empty file rasies [OK] filter [OK] test writer [OK] vcf write missing format values [OK] iterating over info fields [OK] that adding a new sample and setting values works. [OK] format fields [OK] test empty format [OK] test format setting [OK] add string to header [OK] add info to header [OK] add and set Flag [OK] remove info from header [OK] add format to header [OK] remove format from header [OK] set qual [OK] set id [OK] new from string [Suite] genotypes suite [OK] test alts [OK] unknown alts [OK] contig names [Suite] header record [OK] info test [OK] format test [Suite] vcf alleles [OK] update alleles with low-level setters works [OK] update alleles with high-level setters works [Suite] bug suite [OK] csq reader [OK] re-use same header issue 77 [Suite] speed tests 312078 in .. 14.413676577 seconds [OK] standard format getter [Suite] bam-suite [OK] xam_index [OK] test sa sam [OK] test sa bam [OK] cram writing [OK] set aux [OK] set qname [OK] test from string [Suite] stats suite [OK] test fisher 0.09873714670538818 0.002221433773229274 0.002221433773229274 [OK] binomial [Suite] bugs [OK] vcf/bcf subset alts [Suite] test files [OK] that iteration works [OK] file types [E::hts_open_format] Failed to open file "tests/sadfasdfasdfasdf" : No such file or directory [OK] that bad path gives reasonable error message [OK] readLine make[1]: Leaving directory '/build/reproducible-path/nim-hts-0.3.19+ds' create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/nim-hts-dev.substvars debian/nim-hts-examples.substvars rm -fr -- debian/.debhelper/generated/nim-hts-dev/ debian/nim-hts-dev/ debian/tmp/ debian/.debhelper/generated/nim-hts-examples/ debian/nim-hts-examples/ dh_install install -m0755 -d debian/nim-hts-dev/usr/share/nimble/hts/ cp --reflink=auto -a ./src/hts ./src/hts.nim debian/nim-hts-dev/usr/share/nimble/hts// install -m0755 -d debian/nim-hts-examples/usr/share/doc/nim-hts-examples cp --reflink=auto -a ./debian/missing-sources/HG02002.sam ./debian/tests/run-unit-test ./debian/tests/test1.nim ./debian/tests/test2.nim ./tests/HG02002.bam ./tests/HG02002.bam.bai ./tests/HG02002.bam.csi ./tests/aa.fa ./tests/aa.fa.fai ./tests/all.nim ./tests/auxtest.nim ./tests/bamtest.nim ./tests/bgzftest.nim ./tests/cigartest.nim ./tests/decomposed.vcf ./tests/faitest.nim ./tests/flagtest.nim ./tests/htstest.nim ./tests/newsample.vcf ./tests/outmissing.vcf ./tests/outz.vcf ./tests/run.nim ./tests/sa.bam ./tests/sa.bam.bai ./tests/sa.sam ./tests/sample.fa ./tests/sample.fa.fai ./tests/statstests.nim ./tests/test.bcf ./tests/test.bcf.csi ./tests/test_files ./tests/test_files.nim ./tests/test_readme.nim ./tests/unknown-alts.vcf ./tests/vcfiso.nim ./tests/vcftest.nim debian/nim-hts-examples/usr/share/doc/nim-hts-examples/ dh_installdocs install -m0755 -d debian/nim-hts-dev/usr/share/doc/nim-hts-dev install -p -m0644 debian/copyright debian/nim-hts-dev/usr/share/doc/nim-hts-dev/copyright install -p -m0644 debian/copyright debian/nim-hts-examples/usr/share/doc/nim-hts-examples/copyright dh_installchangelogs install -m0755 -d debian/nim-hts-dev/usr/share/doc/nim-hts-dev install -p -m0644 debian/.debhelper/generated/nim-hts-dev/dh_installchangelogs.dch.trimmed debian/nim-hts-dev/usr/share/doc/nim-hts-dev/changelog.Debian install -p -m0644 ./CHANGES.md debian/nim-hts-dev/usr/share/doc/nim-hts-dev/changelog install -m0755 -d debian/nim-hts-examples/usr/share/doc/nim-hts-examples install -p -m0644 debian/.debhelper/generated/nim-hts-examples/dh_installchangelogs.dch.trimmed debian/nim-hts-examples/usr/share/doc/nim-hts-examples/changelog.Debian install -p -m0644 ./CHANGES.md debian/nim-hts-examples/usr/share/doc/nim-hts-examples/changelog dh_perl dh_link dh_strip_nondeterminism dh_compress cd debian/nim-hts-dev cd debian/nim-hts-examples chmod a-x usr/share/doc/nim-hts-dev/changelog usr/share/doc/nim-hts-dev/changelog.Debian chmod a-x usr/share/doc/nim-hts-examples/HG02002.bam usr/share/doc/nim-hts-examples/HG02002.bam.bai usr/share/doc/nim-hts-examples/HG02002.sam usr/share/doc/nim-hts-examples/changelog usr/share/doc/nim-hts-examples/changelog.Debian usr/share/doc/nim-hts-examples/newsample.vcf usr/share/doc/nim-hts-examples/outmissing.vcf usr/share/doc/nim-hts-examples/outz.vcf usr/share/doc/nim-hts-examples/sa.bam usr/share/doc/nim-hts-examples/sa.bam.bai usr/share/doc/nim-hts-examples/sa.sam usr/share/doc/nim-hts-examples/test.bcf usr/share/doc/nim-hts-examples/unknown-alts.vcf usr/share/doc/nim-hts-examples/vcftest.nim gzip -9nf usr/share/doc/nim-hts-dev/changelog usr/share/doc/nim-hts-dev/changelog.Debian gzip -9nf usr/share/doc/nim-hts-examples/HG02002.bam usr/share/doc/nim-hts-examples/HG02002.bam.bai usr/share/doc/nim-hts-examples/HG02002.sam usr/share/doc/nim-hts-examples/changelog usr/share/doc/nim-hts-examples/changelog.Debian usr/share/doc/nim-hts-examples/newsample.vcf usr/share/doc/nim-hts-examples/outmissing.vcf usr/share/doc/nim-hts-examples/outz.vcf usr/share/doc/nim-hts-examples/sa.bam usr/share/doc/nim-hts-examples/sa.bam.bai usr/share/doc/nim-hts-examples/sa.sam usr/share/doc/nim-hts-examples/test.bcf usr/share/doc/nim-hts-examples/unknown-alts.vcf usr/share/doc/nim-hts-examples/vcftest.nim cd '/build/reproducible-path/nim-hts-0.3.19+ds' cd '/build/reproducible-path/nim-hts-0.3.19+ds' dh_fixperms find debian/nim-hts-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/nim-hts-examples ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/nim-hts-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/nim-hts-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/nim-hts-examples/usr/share/doc -type f -a -true -a ! -regex 'debian/nim-hts-examples/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/nim-hts-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/nim-hts-examples/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/nim-hts-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/nim-hts-examples -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 dh_missing dh_installdeb install -m0755 -d debian/nim-hts-dev/DEBIAN install -m0755 -d debian/nim-hts-examples/DEBIAN dh_gencontrol install -m0755 -d debian/nim-hts-dev/DEBIAN echo misc:Depends= >> debian/nim-hts-dev.substvars echo misc:Pre-Depends= >> debian/nim-hts-dev.substvars dpkg-gencontrol -pnim-hts-dev -ldebian/changelog -Tdebian/nim-hts-dev.substvars -cdebian/control -Pdebian/nim-hts-dev install -m0755 -d debian/nim-hts-examples/DEBIAN echo misc:Depends= >> debian/nim-hts-examples.substvars echo misc:Pre-Depends= >> debian/nim-hts-examples.substvars dpkg-gencontrol -pnim-hts-examples -ldebian/changelog -Tdebian/nim-hts-examples.substvars -cdebian/control -Pdebian/nim-hts-examples chmod 0644 -- debian/nim-hts-dev/DEBIAN/control chmod 0644 -- debian/nim-hts-examples/DEBIAN/control dh_md5sums install -m0755 -d debian/nim-hts-dev/DEBIAN install -m0755 -d debian/nim-hts-examples/DEBIAN cd debian/nim-hts-examples >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/nim-hts-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/nim-hts-examples/DEBIAN/md5sums chmod 0644 -- debian/nim-hts-dev/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/nim-hts-dev .. dpkg-deb --root-owner-group --build debian/nim-hts-examples .. dpkg-deb: building package 'nim-hts-dev' in '../nim-hts-dev_0.3.19+ds-1_all.deb'. dpkg-deb: building package 'nim-hts-examples' in '../nim-hts-examples_0.3.19+ds-1_all.deb'. dpkg-genbuildinfo --build=binary -O../nim-hts_0.3.19+ds-1_amd64.buildinfo dpkg-genchanges --build=binary -O../nim-hts_0.3.19+ds-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2309659/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2309659/tmp/hooks/B01_cleanup finished 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/2309659 and its subdirectories I: Current time: Sun May 26 20:59:32 +14 2024 I: pbuilder-time-stamp: 1716706772