I: pbuilder: network access will be disabled during build I: Current time: Sat Jan 20 18:43:22 +14 2024 I: pbuilder-time-stamp: 1705725802 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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: using eatmydata during job I: Copying source file I: copying [jellyfish_2.3.0-15.dsc] I: copying [./jellyfish_2.3.0.orig.tar.gz] I: copying [./jellyfish_2.3.0-15.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Sep 28 20:08:02 2022 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./jellyfish_2.3.0-15.dsc: no acceptable signature found dpkg-source: info: extracting jellyfish in jellyfish-2.3.0 dpkg-source: info: unpacking jellyfish_2.3.0.orig.tar.gz dpkg-source: info: unpacking jellyfish_2.3.0-15.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying manpage_whatis_entry.patch dpkg-source: info: applying reproducible.patch dpkg-source: info: applying portability.patch dpkg-source: info: applying fix_replacement_of_-L_option.patch dpkg-source: info: applying test_needs_bash dpkg-source: info: applying python3 dpkg-source: info: applying fix-32-bit.patch dpkg-source: info: applying fix-autoreconf.patch dpkg-source: info: applying gcc-12.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/31279/tmp/hooks/D01_modify_environment starting debug: Running on ionos2-i386. 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 Jan 20 04:43 /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/31279/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/31279/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]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=7 ' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=428fab9d4211420287481985d7694223 LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-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=31279 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.EpRgtYaS/pbuilderrc_vG0E --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.EpRgtYaS/b2 --logfile b2/build.log jellyfish_2.3.0-15.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-17-686-pae #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) i686 GNU/Linux I: ls -l /bin total 6036 -rwxr-xr-x 1 root root 1408088 Apr 23 2023 bash -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 42920 Sep 20 2022 cat -rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 79816 Sep 20 2022 chown -rwxr-xr-x 1 root root 162024 Sep 20 2022 cp -rwxr-xr-x 1 root root 136916 Jan 5 2023 dash -rwxr-xr-x 1 root root 137160 Sep 20 2022 date -rwxr-xr-x 1 root root 100364 Sep 20 2022 dd -rwxr-xr-x 1 root root 108940 Sep 20 2022 df -rwxr-xr-x 1 root root 162152 Sep 20 2022 dir -rwxr-xr-x 1 root root 87760 Mar 23 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 38760 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 34664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 84272 Mar 23 2023 findmnt -rwsr-xr-x 1 root root 30240 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 218680 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip -rwxr-xr-x 1 root root 21916 Dec 19 2022 hostname -rwxr-xr-x 1 root root 75756 Sep 20 2022 ln -rwxr-xr-x 1 root root 55600 Mar 23 2023 login -rwxr-xr-x 1 root root 162152 Sep 20 2022 ls -rwxr-xr-x 1 root root 214568 Mar 23 2023 lsblk -rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod -rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 63016 Mar 23 2023 more -rwsr-xr-x 1 root root 58912 Mar 23 2023 mount -rwxr-xr-x 1 root root 13856 Mar 23 2023 mountpoint -rwxr-xr-x 1 root root 157932 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 22308 Jul 28 23:46 run-parts -rwxr-xr-x 1 root root 133224 Jan 5 2023 sed lrwxrwxrwx 1 root root 9 Jan 20 04:43 sh -> /bin/bash -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty -rwsr-xr-x 1 root root 83492 Mar 23 2023 su -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync -rwxr-xr-x 1 root root 598456 Apr 6 2023 tar -rwxr-xr-x 1 root root 13860 Jul 28 23:46 tempfile -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch -rwxr-xr-x 1 root root 34664 Sep 20 2022 true -rwxr-xr-x 1 root root 17892 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 30236 Mar 23 2023 umount -rwxr-xr-x 1 root root 38760 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir -rwxr-xr-x 1 root root 71216 Mar 23 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/31279/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: i386 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), d-shlibs, autoconf-archive, yaggo, pkg-config, bc, time, procps, swig, python3-all-dev, dh-python, perl, chrpath, libhts-dev, dos2unix, samtools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18156 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 d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on autoconf-archive; however: Package autoconf-archive is not installed. pbuilder-satisfydepends-dummy depends on yaggo; however: Package yaggo is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on bc; however: Package bc is not installed. pbuilder-satisfydepends-dummy depends on time; however: Package time is not installed. pbuilder-satisfydepends-dummy depends on procps; however: Package procps is not installed. pbuilder-satisfydepends-dummy depends on swig; however: Package swig is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on dos2unix; however: Package dos2unix is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools 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} autoconf-archive{a} automake{a} autopoint{a} autotools-dev{a} bc{a} bsdextrautils{a} ca-certificates{a} chrpath{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dos2unix{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libbsd0{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libedit2{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl5{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librtmp1{a} libruby{a} libruby3.1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} openssl{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python3{a} python3-all{a} python3-all-dev{a} python3-dev{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} rake{a} readline-common{a} ruby{a} ruby-net-telnet{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} rubygems-integration{a} samtools{a} sensible-utils{a} swig{a} swig4.0{a} time{a} yaggo{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-lato javascript-common libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget zip 0 packages upgraded, 106 newly installed, 0 to remove and 0 not upgraded. Need to get 52.0 MB of archives. After unpacking 192 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main i386 autoconf-archive all 20220903-3 [775 kB] Get: 2 http://deb.debian.org/debian bookworm/main i386 libpython3.11-minimal i386 3.11.2-6 [813 kB] Get: 3 http://deb.debian.org/debian bookworm/main i386 libexpat1 i386 2.5.0-1 [103 kB] Get: 4 http://deb.debian.org/debian bookworm/main i386 python3.11-minimal i386 3.11.2-6 [2130 kB] Get: 5 http://deb.debian.org/debian bookworm/main i386 python3-minimal i386 3.11.2-1+b1 [26.3 kB] Get: 6 http://deb.debian.org/debian bookworm/main i386 media-types all 10.0.0 [26.1 kB] Get: 7 http://deb.debian.org/debian bookworm/main i386 readline-common all 8.2-1.3 [69.0 kB] Get: 8 http://deb.debian.org/debian bookworm/main i386 libreadline8 i386 8.2-1.3 [171 kB] Get: 9 http://deb.debian.org/debian bookworm/main i386 libpython3.11-stdlib i386 3.11.2-6 [1799 kB] Get: 10 http://deb.debian.org/debian bookworm/main i386 python3.11 i386 3.11.2-6 [572 kB] Get: 11 http://deb.debian.org/debian bookworm/main i386 libpython3-stdlib i386 3.11.2-1+b1 [9308 B] Get: 12 http://deb.debian.org/debian bookworm/main i386 python3 i386 3.11.2-1+b1 [26.3 kB] Get: 13 http://deb.debian.org/debian bookworm/main i386 libproc2-0 i386 2:4.0.2-3 [63.7 kB] Get: 14 http://deb.debian.org/debian bookworm/main i386 procps i386 2:4.0.2-3 [706 kB] Get: 15 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 16 http://deb.debian.org/debian bookworm/main i386 openssl i386 3.0.11-1~deb12u2 [1423 kB] Get: 17 http://deb.debian.org/debian bookworm/main i386 ca-certificates all 20230311 [153 kB] Get: 18 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB] Get: 19 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB] Get: 20 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB] Get: 21 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB] Get: 22 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 23 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB] Get: 24 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB] Get: 25 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB] Get: 26 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB] Get: 27 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB] Get: 28 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB] Get: 29 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 30 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 31 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB] Get: 32 http://deb.debian.org/debian bookworm/main i386 bc i386 1.07.1-3 [111 kB] Get: 33 http://deb.debian.org/debian bookworm/main i386 chrpath i386 0.16-2+b1 [17.5 kB] Get: 34 http://deb.debian.org/debian bookworm/main i386 d-shlibs all 0.104 [18.6 kB] Get: 35 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 36 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB] Get: 37 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB] Get: 38 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 39 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B] Get: 40 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 41 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 42 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB] Get: 43 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB] Get: 44 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB] Get: 45 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.3~deb12u1 [720 kB] Get: 46 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB] Get: 47 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 48 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 49 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB] Get: 50 http://deb.debian.org/debian bookworm/main i386 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 51 http://deb.debian.org/debian bookworm/main i386 python3-distutils all 3.11.2-3 [131 kB] Get: 52 http://deb.debian.org/debian bookworm/main i386 dh-python all 5.20230130+deb12u1 [104 kB] Get: 53 http://deb.debian.org/debian bookworm/main i386 dos2unix i386 7.4.3-1 [432 kB] Get: 54 http://deb.debian.org/debian bookworm/main i386 libbrotli1 i386 1.0.9-2+b6 [275 kB] Get: 55 http://deb.debian.org/debian bookworm/main i386 libbsd0 i386 0.11.7-2 [121 kB] Get: 56 http://deb.debian.org/debian bookworm/main i386 libsasl2-modules-db i386 2.1.28+dfsg-10 [21.4 kB] Get: 57 http://deb.debian.org/debian bookworm/main i386 libsasl2-2 i386 2.1.28+dfsg-10 [62.7 kB] Get: 58 http://deb.debian.org/debian bookworm/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5 [196 kB] Get: 59 http://deb.debian.org/debian bookworm/main i386 libnghttp2-14 i386 1.52.0-1+deb12u1 [80.7 kB] Get: 60 http://deb.debian.org/debian bookworm/main i386 libpsl5 i386 0.21.2-1 [59.3 kB] Get: 61 http://deb.debian.org/debian bookworm/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 62 http://deb.debian.org/debian bookworm/main i386 libssh2-1 i386 1.10.0-3+b1 [187 kB] Get: 63 http://deb.debian.org/debian bookworm/main i386 libcurl3-gnutls i386 7.88.1-10+deb12u4 [417 kB] Get: 64 http://deb.debian.org/debian bookworm/main i386 libcurl4-gnutls-dev i386 7.88.1-10+deb12u4 [532 kB] Get: 65 http://deb.debian.org/debian bookworm/main i386 libdeflate0 i386 1.14-1 [57.5 kB] Get: 66 http://deb.debian.org/debian bookworm/main i386 libdeflate-dev i386 1.14-1 [53.5 kB] Get: 67 http://deb.debian.org/debian bookworm/main i386 libedit2 i386 3.1-20221030-2 [97.2 kB] Get: 68 http://deb.debian.org/debian bookworm/main i386 libexpat1-dev i386 2.5.0-1 [158 kB] Get: 69 http://deb.debian.org/debian bookworm/main i386 libhtscodecs2 i386 1.3.0-4 [67.4 kB] Get: 70 http://deb.debian.org/debian bookworm/main i386 libhts3 i386 1.16+ds-3 [469 kB] Get: 71 http://deb.debian.org/debian bookworm/main i386 liblzma-dev i386 5.4.1-0.2 [272 kB] Get: 72 http://deb.debian.org/debian bookworm/main i386 zlib1g-dev i386 1:1.2.13.dfsg-1 [913 kB] Get: 73 http://deb.debian.org/debian bookworm/main i386 libhts-dev i386 1.16+ds-3 [1585 kB] Get: 74 http://deb.debian.org/debian bookworm/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 75 http://deb.debian.org/debian bookworm/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 76 http://deb.debian.org/debian bookworm/main i386 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 77 http://deb.debian.org/debian bookworm/main i386 libncurses6 i386 6.4-4 [111 kB] Get: 78 http://deb.debian.org/debian bookworm/main i386 libpkgconf3 i386 1.8.1-1 [38.3 kB] Get: 79 http://deb.debian.org/debian bookworm/main i386 libpython3.11 i386 3.11.2-6 [2013 kB] Get: 80 http://deb.debian.org/debian bookworm/main i386 libpython3.11-dev i386 3.11.2-6 [4906 kB] Get: 81 http://deb.debian.org/debian bookworm/main i386 libpython3-dev i386 3.11.2-1+b1 [9580 B] Get: 82 http://deb.debian.org/debian bookworm/main i386 libpython3-all-dev i386 3.11.2-1+b1 [1068 B] Get: 83 http://deb.debian.org/debian bookworm/main i386 rubygems-integration all 1.18 [6704 B] Get: 84 http://deb.debian.org/debian bookworm/main i386 ruby3.1 i386 3.1.2-7 [663 kB] Get: 85 http://deb.debian.org/debian bookworm/main i386 ruby-rubygems all 3.3.15-2 [293 kB] Get: 86 http://deb.debian.org/debian bookworm/main i386 ruby i386 1:3.1 [5872 B] Get: 87 http://deb.debian.org/debian bookworm/main i386 rake all 13.0.6-3 [83.9 kB] Get: 88 http://deb.debian.org/debian bookworm/main i386 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 89 http://deb.debian.org/debian bookworm/main i386 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 90 http://deb.debian.org/debian bookworm/main i386 ruby-xmlrpc all 0.3.2-2 [24.4 kB] Get: 91 http://deb.debian.org/debian bookworm/main i386 ruby-sdbm i386 1.0.0-5+b1 [16.7 kB] Get: 92 http://deb.debian.org/debian bookworm/main i386 libyaml-0-2 i386 0.2.5-1 [55.9 kB] Get: 93 http://deb.debian.org/debian bookworm/main i386 libruby3.1 i386 3.1.2-7 [5459 kB] Get: 94 http://deb.debian.org/debian bookworm/main i386 libruby i386 1:3.1 [4968 B] Get: 95 http://deb.debian.org/debian bookworm/main i386 pkgconf-bin i386 1.8.1-1 [29.8 kB] Get: 96 http://deb.debian.org/debian bookworm/main i386 pkgconf i386 1.8.1-1 [25.9 kB] Get: 97 http://deb.debian.org/debian bookworm/main i386 pkg-config i386 1.8.1-1 [13.7 kB] Get: 98 http://deb.debian.org/debian bookworm/main i386 python3-all i386 3.11.2-1+b1 [1056 B] Get: 99 http://deb.debian.org/debian bookworm/main i386 python3.11-dev i386 3.11.2-6 [615 kB] Get: 100 http://deb.debian.org/debian bookworm/main i386 python3-dev i386 3.11.2-1+b1 [26.2 kB] Get: 101 http://deb.debian.org/debian bookworm/main i386 python3-all-dev i386 3.11.2-1+b1 [1072 B] Get: 102 http://deb.debian.org/debian bookworm/main i386 samtools i386 1.16.1-1 [637 kB] Get: 103 http://deb.debian.org/debian bookworm/main i386 swig4.0 i386 4.1.0-0.2 [1445 kB] Get: 104 http://deb.debian.org/debian bookworm/main i386 swig all 4.1.0-0.2 [321 kB] Get: 105 http://deb.debian.org/debian bookworm/main i386 time i386 1.9-0.2 [50.9 kB] Get: 106 http://deb.debian.org/debian bookworm/main i386 yaggo all 1.5.10-6 [21.2 kB] Fetched 52.0 MB in 6s (8921 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package autoconf-archive. (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 ... 18156 files and directories currently installed.) Preparing to unpack .../autoconf-archive_20220903-3_all.deb ... Unpacking autoconf-archive (20220903-3) ... Selecting previously unselected package libpython3.11-minimal:i386. Preparing to unpack .../libpython3.11-minimal_3.11.2-6_i386.deb ... Unpacking libpython3.11-minimal:i386 (3.11.2-6) ... Selecting previously unselected package libexpat1:i386. 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Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:i386. Preparing to unpack .../3-libreadline8_8.2-1.3_i386.deb ... Unpacking libreadline8:i386 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:i386. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_i386.deb ... Unpacking libpython3.11-stdlib:i386 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_i386.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... 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 ... 20088 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.2-1+b1_i386.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package libproc2-0:i386. Preparing to unpack .../01-libproc2-0_2%3a4.0.2-3_i386.deb ... Unpacking libproc2-0:i386 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../02-procps_2%3a4.0.2-3_i386.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package openssl. Preparing to unpack .../04-openssl_3.0.11-1~deb12u2_i386.deb ... Unpacking openssl (3.0.11-1~deb12u2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../05-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.44-3_i386.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../07-libmagic1_1%3a5.44-3_i386.deb ... Unpacking libmagic1:i386 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.44-3_i386.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-12_i386.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../10-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../11-groff-base_1.22.4-10_i386.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../12-bsdextrautils_2.38.1-5+b1_i386.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../13-libpipeline1_1.5.7-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../14-man-db_2.11.2-2_i386.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../15-m4_1.4.19-3_i386.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../16-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../17-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../18-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 .../19-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package bc. Preparing to unpack .../20-bc_1.07.1-3_i386.deb ... Unpacking bc (1.07.1-3) ... Selecting previously unselected package chrpath. Preparing to unpack .../21-chrpath_0.16-2+b1_i386.deb ... Unpacking chrpath (0.16-2+b1) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../22-d-shlibs_0.104_all.deb ... Unpacking d-shlibs (0.104) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../23-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../24-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../25-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../26-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../27-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../28-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../29-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../30-libelf1_0.188-2.1_i386.deb ... Unpacking libelf1:i386 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../31-dwz_0.15-1_i386.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../32-libicu72_72.1-3_i386.deb ... Unpacking libicu72:i386 (72.1-3) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../33-libxml2_2.9.14+dfsg-1.3~deb12u1_i386.deb ... Unpacking libxml2:i386 (2.9.14+dfsg-1.3~deb12u1) ... Selecting previously unselected package gettext. Preparing to unpack .../34-gettext_0.21-12_i386.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../35-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../36-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../37-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../38-python3-lib2to3_3.11.2-3_all.deb ... Unpacking python3-lib2to3 (3.11.2-3) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../39-python3-distutils_3.11.2-3_all.deb ... Unpacking python3-distutils (3.11.2-3) ... Selecting previously unselected package dh-python. Preparing to unpack .../40-dh-python_5.20230130+deb12u1_all.deb ... Unpacking dh-python (5.20230130+deb12u1) ... Selecting previously unselected package dos2unix. Preparing to unpack .../41-dos2unix_7.4.3-1_i386.deb ... Unpacking dos2unix (7.4.3-1) ... Selecting previously unselected package libbrotli1:i386. Preparing to unpack .../42-libbrotli1_1.0.9-2+b6_i386.deb ... Unpacking libbrotli1:i386 (1.0.9-2+b6) ... Selecting previously unselected package libbsd0:i386. Preparing to unpack .../43-libbsd0_0.11.7-2_i386.deb ... Unpacking libbsd0:i386 (0.11.7-2) ... Selecting previously unselected package libsasl2-modules-db:i386. Preparing to unpack .../44-libsasl2-modules-db_2.1.28+dfsg-10_i386.deb ... Unpacking libsasl2-modules-db:i386 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:i386. Preparing to unpack .../45-libsasl2-2_2.1.28+dfsg-10_i386.deb ... Unpacking libsasl2-2:i386 (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:i386. Preparing to unpack .../46-libldap-2.5-0_2.5.13+dfsg-5_i386.deb ... Unpacking libldap-2.5-0:i386 (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:i386. Preparing to unpack .../47-libnghttp2-14_1.52.0-1+deb12u1_i386.deb ... Unpacking libnghttp2-14:i386 (1.52.0-1+deb12u1) ... Selecting previously unselected package libpsl5:i386. Preparing to unpack .../48-libpsl5_0.21.2-1_i386.deb ... Unpacking libpsl5:i386 (0.21.2-1) ... Selecting previously unselected package librtmp1:i386. Preparing to unpack .../49-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_i386.deb ... Unpacking librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:i386. Preparing to unpack .../50-libssh2-1_1.10.0-3+b1_i386.deb ... Unpacking libssh2-1:i386 (1.10.0-3+b1) ... Selecting previously unselected package libcurl3-gnutls:i386. Preparing to unpack .../51-libcurl3-gnutls_7.88.1-10+deb12u4_i386.deb ... Unpacking libcurl3-gnutls:i386 (7.88.1-10+deb12u4) ... Selecting previously unselected package libcurl4-gnutls-dev:i386. Preparing to unpack .../52-libcurl4-gnutls-dev_7.88.1-10+deb12u4_i386.deb ... Unpacking libcurl4-gnutls-dev:i386 (7.88.1-10+deb12u4) ... Selecting previously unselected package libdeflate0:i386. Preparing to unpack .../53-libdeflate0_1.14-1_i386.deb ... Unpacking libdeflate0:i386 (1.14-1) ... Selecting previously unselected package libdeflate-dev:i386. Preparing to unpack .../54-libdeflate-dev_1.14-1_i386.deb ... Unpacking libdeflate-dev:i386 (1.14-1) ... Selecting previously unselected package libedit2:i386. Preparing to unpack .../55-libedit2_3.1-20221030-2_i386.deb ... Unpacking libedit2:i386 (3.1-20221030-2) ... Selecting previously unselected package libexpat1-dev:i386. Preparing to unpack .../56-libexpat1-dev_2.5.0-1_i386.deb ... Unpacking libexpat1-dev:i386 (2.5.0-1) ... Selecting previously unselected package libhtscodecs2:i386. Preparing to unpack .../57-libhtscodecs2_1.3.0-4_i386.deb ... Unpacking libhtscodecs2:i386 (1.3.0-4) ... Selecting previously unselected package libhts3:i386. Preparing to unpack .../58-libhts3_1.16+ds-3_i386.deb ... Unpacking libhts3:i386 (1.16+ds-3) ... Selecting previously unselected package liblzma-dev:i386. Preparing to unpack .../59-liblzma-dev_5.4.1-0.2_i386.deb ... Unpacking liblzma-dev:i386 (5.4.1-0.2) ... Selecting previously unselected package zlib1g-dev:i386. Preparing to unpack .../60-zlib1g-dev_1%3a1.2.13.dfsg-1_i386.deb ... Unpacking zlib1g-dev:i386 (1:1.2.13.dfsg-1) ... Selecting previously unselected package libhts-dev:i386. Preparing to unpack .../61-libhts-dev_1.16+ds-3_i386.deb ... Unpacking libhts-dev:i386 (1.16+ds-3) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../62-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../63-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../64-libjs-sphinxdoc_5.3.0-4_all.deb ... Unpacking libjs-sphinxdoc (5.3.0-4) ... Selecting previously unselected package libncurses6:i386. Preparing to unpack .../65-libncurses6_6.4-4_i386.deb ... Unpacking libncurses6:i386 (6.4-4) ... Selecting previously unselected package libpkgconf3:i386. Preparing to unpack .../66-libpkgconf3_1.8.1-1_i386.deb ... Unpacking libpkgconf3:i386 (1.8.1-1) ... Selecting previously unselected package libpython3.11:i386. Preparing to unpack .../67-libpython3.11_3.11.2-6_i386.deb ... Unpacking libpython3.11:i386 (3.11.2-6) ... Selecting previously unselected package libpython3.11-dev:i386. Preparing to unpack .../68-libpython3.11-dev_3.11.2-6_i386.deb ... Unpacking libpython3.11-dev:i386 (3.11.2-6) ... Selecting previously unselected package libpython3-dev:i386. Preparing to unpack .../69-libpython3-dev_3.11.2-1+b1_i386.deb ... Unpacking libpython3-dev:i386 (3.11.2-1+b1) ... Selecting previously unselected package libpython3-all-dev:i386. Preparing to unpack .../70-libpython3-all-dev_3.11.2-1+b1_i386.deb ... Unpacking libpython3-all-dev:i386 (3.11.2-1+b1) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../71-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package ruby3.1. Preparing to unpack .../72-ruby3.1_3.1.2-7_i386.deb ... Unpacking ruby3.1 (3.1.2-7) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../73-ruby-rubygems_3.3.15-2_all.deb ... Unpacking ruby-rubygems (3.3.15-2) ... Selecting previously unselected package ruby. Preparing to unpack .../74-ruby_1%3a3.1_i386.deb ... Unpacking ruby (1:3.1) ... Selecting previously unselected package rake. Preparing to unpack .../75-rake_13.0.6-3_all.deb ... Unpacking rake (13.0.6-3) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../76-ruby-net-telnet_0.2.0-1_all.deb ... Unpacking ruby-net-telnet (0.2.0-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../77-ruby-webrick_1.8.1-1_all.deb ... Unpacking ruby-webrick (1.8.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../78-ruby-xmlrpc_0.3.2-2_all.deb ... Unpacking ruby-xmlrpc (0.3.2-2) ... Selecting previously unselected package ruby-sdbm:i386. Preparing to unpack .../79-ruby-sdbm_1.0.0-5+b1_i386.deb ... Unpacking ruby-sdbm:i386 (1.0.0-5+b1) ... Selecting previously unselected package libyaml-0-2:i386. Preparing to unpack .../80-libyaml-0-2_0.2.5-1_i386.deb ... Unpacking libyaml-0-2:i386 (0.2.5-1) ... Selecting previously unselected package libruby3.1:i386. Preparing to unpack .../81-libruby3.1_3.1.2-7_i386.deb ... Unpacking libruby3.1:i386 (3.1.2-7) ... 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Setting up media-types (10.0.0) ... Setting up libpipeline1:i386 (1.5.7-1) ... Setting up time (1.9-0.2) ... Setting up libpsl5:i386 (0.21.2-1) ... Setting up libicu72:i386 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:i386 (0.2.5-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:i386 (1.0.9-2+b6) ... Setting up libnghttp2-14:i386 (1.52.0-1+deb12u1) ... Setting up libmagic1:i386 (1:5.44-3) ... Setting up libdeflate0:i386 (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up autoconf-archive (20220903-3) ... Setting up file (1:5.44-3) ... Setting up libsasl2-modules-db:i386 (2.1.28+dfsg-10) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:i386 (1.8.1-1) ... Setting up libexpat1-dev:i386 (2.5.0-1) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:i386 (6.4-4) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up libproc2-0:i386 (2:4.0.2-3) ... Setting up autopoint (0.21-12) ... Setting up d-shlibs (0.104) ... Setting up pkgconf-bin (1.8.1-1) ... Setting up libsasl2-2:i386 (2.1.28+dfsg-10) ... Setting up autoconf (2.71-3) ... Setting up ruby-webrick (1.8.1-1) ... Setting up liblzma-dev:i386 (5.4.1-0.2) ... Setting up zlib1g-dev:i386 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up procps (2:4.0.2-3) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:i386 (1.10.0-3+b1) ... Setting up dos2unix (7.4.3-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up swig4.0 (4.1.0-0.2) ... Setting up openssl (3.0.11-1~deb12u2) ... Setting up libbsd0:i386 (0.11.7-2) ... Setting up libdeflate-dev:i386 (1.14-1) ... Setting up libelf1:i386 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up ruby-xmlrpc (0.3.2-2) ... Setting up libxml2:i386 (2.9.14+dfsg-1.3~deb12u1) ... Setting up chrpath (0.16-2+b1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up swig (4.1.0-0.2) ... Setting up libtool (2.4.7-5) ... Setting up libedit2:i386 (3.1-20221030-2) ... Setting up libreadline8:i386 (8.2-1.3) ... Setting up bc (1.07.1-3) ... Setting up libldap-2.5-0:i386 (2.5.13+dfsg-5) ... Setting up pkgconf:i386 (1.8.1-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up pkg-config:i386 (1.8.1-1) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:i386 (3.11.2-6) ... Setting up libcurl3-gnutls:i386 (7.88.1-10+deb12u4) ... Setting up rubygems-integration (1.18) ... Setting up libcurl4-gnutls-dev:i386 (7.88.1-10+deb12u4) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3-stdlib:i386 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libhts3:i386 (1.16+ds-3) ... Setting up libpython3.11:i386 (3.11.2-6) ... Setting up libhts-dev:i386 (1.16+ds-3) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up samtools (1.16.1-1) ... Setting up libpython3.11-dev:i386 (3.11.2-6) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-distutils (3.11.2-3) ... Setting up dh-python (5.20230130+deb12u1) ... Setting up libpython3-dev:i386 (3.11.2-1+b1) ... Setting up python3.11-dev (3.11.2-6) ... Setting up python3-all (3.11.2-1+b1) ... Setting up libpython3-all-dev:i386 (3.11.2-1+b1) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up python3-all-dev (3.11.2-1+b1) ... Setting up rake (13.0.6-3) ... Setting up ruby3.1 (3.1.2-7) ... Setting up libruby3.1:i386 (3.1.2-7) ... Setting up libruby:i386 (1:3.1) ... Setting up ruby (1:3.1) ... Setting up yaggo (1.5.10-6) ... Setting up ruby-sdbm:i386 (1.0.0-5+b1) ... Setting up ruby-rubygems (3.3.15-2) ... Processing triggers for libc-bin (2.36-9+deb12u3) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/31279/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for bookworm I: user script /srv/workspace/pbuilder/31279/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/jellyfish-2.3.0/ && 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 > ../jellyfish_2.3.0-15_source.changes dpkg-buildpackage: info: source package jellyfish dpkg-buildpackage: info: source version 2.3.0-15 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean --with python3 debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/jellyfish-2.3.0' dh_clean if [ -d debian/tmp_save_tests ] ; then \ mv debian/tmp_save_tests/* tests ; \ rmdir debian/tmp_save_tests ; \ fi rm -f tests/compat.sh rm -f swig/python/jellyfish* # swig/python/dna_jellyfish.py rm -f swig/perl5/blib/arch/auto/jellyfish/jellyfish.so rm -f swig/perl5/blib/bin/.exists rm -f swig/perl5/blib/lib/.exists rm -f swig/perl5/blib/lib/auto/jellyfish/.exists rm -f swig/perl5/blib/man1/.exists rm -f swig/perl5/blib/man3/.exists rm -f swig/perl5/blib/script/.exists rm -f swig/perl5/jellyfish.bs rm -f swig/perl5/pm_to_blib rm -rf swig/perl5/MYMETA.json swig/perl5/MYMETA.yml swig/perl5/Makefile swig/perl5/blib/ make[1]: Leaving directory '/build/reproducible-path/jellyfish-2.3.0' debian/rules binary dh binary --with python3 debian/rules override_dh_update_autotools_config make[1]: Entering directory '/build/reproducible-path/jellyfish-2.3.0' # use python configuration from autoconf-archive mv m4/m4-ax_python_devel.m4 /tmp dh_update_autotools_config make[1]: Leaving directory '/build/reproducible-path/jellyfish-2.3.0' dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:8: warning: The macro `AC_PROG_LIBTOOL' is obsolete. configure.ac:8: You should run autoupdate. m4/libtool.m4:100: AC_PROG_LIBTOOL is expanded from... configure.ac:8: the top level configure.ac:65: warning: The macro `AC_TRY_RUN' is obsolete. configure.ac:65: You should run autoupdate. ./lib/autoconf/general.m4:2997: AC_TRY_RUN is expanded from... lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... m4/m4-ax_ext.m4:49: AX_EXT is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... configure.ac:65: the top level configure.ac:107: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:107: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:107: the top level configure.ac:118: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:118: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:118: the top level configure.ac:121: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:121: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:121: the top level configure.ac:124: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:124: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:124: the top level configure.ac:127: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:127: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:127: the top level configure.ac:131: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:131: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:131: the top level configure.ac:135: warning: The macro `SWIG_ENABLE_CXX' is obsolete. configure.ac:135: You should run autoupdate. m4/m4-ax_swig_enable_cxx.m4:48: SWIG_ENABLE_CXX is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... configure.ac:135: the top level configure.ac:145: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:145: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:145: the top level configure.ac:8: installing './compile' configure.ac:2: installing './config.guess' configure.ac:2: installing './config.sub' configure.ac:4: installing './install-sh' configure.ac:4: installing './missing' Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/jellyfish-2.3.0' dh_auto_configure -- --enable-swig --enable-perl-binding --enable-htslib --enable-python-binding PYTHON=/usr/bin/python3 ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-swig --enable-perl-binding --enable-htslib --enable-python-binding PYTHON=/usr/bin/python3 checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports nested variables... (cached) yes checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert i686-pc-linux-gnu file names to i686-pc-linux-gnu format... func_convert_file_noop checking how to convert i686-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for ld... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for shared library run path origin... done checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking 32-bit host C ABI... yes checking for ELF binary format... yes checking for the common suffixes of directories in the library search path... lib,lib,lib checking for htslib... yes checking for samtools... /usr/bin/samtools checking for unix2dos... /usr/bin/unix2dos checking for md5sum... md5sum checking for yaggo... /usr/bin/yaggo checking for x86 cpuid output... unknown checking for x86-AVX xgetbv output... unknown checking for x86 cpuid 0x00000000 output... d:68747541:444d4163:69746e65 checking for x86 cpuid 0x80000000 output... 8000001a:68747541:444d4163:69746e65 checking for x86 cpuid 0x00000001 output... 600f12:3000800:9eb82203:78bfbff checking for x86 cpuid 0x00000007 output... 0:0:0:0 checking for x86 cpuid 0x80000001 output... 600f12:0:3e7:2dd3fbff checking for x86-AVX xgetbv 0x00000000 output... 7:0 checking whether RDRND is supported by the processor... no checking whether BMI1 is supported by the processor... no checking whether BMI2 is supported by the processor... no checking whether ADX is supported by the processor... no checking whether MPX is supported by the processor... no checking whether PREFETCHWT1 is supported by the processor... no checking whether ABM is supported by the processor... yes checking whether ABM is supported by the processor and OS... yes checking whether C++ compiler accepts -mabm... yes checking whether MMX is supported by the processor... yes checking whether MMX is supported by the processor and OS... yes checking whether C++ compiler accepts -mmmx... yes checking whether SSE is supported by the processor... yes checking whether SSE is supported by the processor and OS... yes checking whether C++ compiler accepts -msse... yes checking whether SSE2 is supported by the processor... yes checking whether SSE2 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse2... yes checking whether SSE3 is supported by the processor... yes checking whether SSE3 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse3... yes checking whether SSSE3 is supported by the processor... yes checking whether SSSE3 is supported by the processor and OS... yes checking whether C++ compiler accepts -mssse3... yes checking whether SSE4.1 is supported by the processor... yes checking whether SSE4.1 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse4.1... yes checking whether SSE4.2 is supported by the processor... yes checking whether SSE4.2 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse4.2... yes checking whether SSE4a is supported by the processor... yes checking whether SSE4a is supported by the processor and OS... yes checking whether C++ compiler accepts -msse4a... yes checking whether SHA is supported by the processor... no checking whether AES is supported by the processor... yes checking whether AES is supported by the processor and OS... yes checking whether C++ compiler accepts -maes... yes checking whether AVX is supported by the processor... yes checking whether AVX is supported by the processor and OS... yes checking whether C++ compiler accepts -mavx... yes checking whether FMA3 is supported by the processor... no checking whether FMA4 is supported by the processor... no checking whether XOP is supported by the processor... no checking whether AVX2 is supported by the processor... no checking whether AVX512-F is supported by the processor... no checking whether AVX512-CD is supported by the processor... no checking whether AVX512-PF is supported by the processor... no checking whether AVX512-ER is supported by the processor... no checking whether AVX512-VL is supported by the processor... no checking whether AVX512-BW is supported by the processor... no checking whether AVX512-DQ is supported by the processor... no checking whether AVX512-IFMA is supported by the processor... no checking whether AVX512-VBMI is supported by the processor... no checking for __int128... no checking for std::numeric_limits<__int128>... no checking for _NSGetExecutablePath... no checking for execinfo.h... yes checking for ext/stdio_filebuf.h... yes checking for sys/syscall.h... yes checking for siginfo_t.si_int... yes checking for swig... /usr/bin/swig checking SWIG version... 4.1.0 checking for SWIG library... /usr/share/swig4.0 checking for python... /usr/bin/python3 checking for a version of Python >= '2.1.0'... yes checking for the sysconfig Python package... yes checking for Python include path... -I/usr/include/python3.11 checking for Python library path... -L/usr/lib/i386-linux-gnu -lpython3.11 checking for Python site-packages path... /usr/lib/python3.11/site-packages checking for Python platform specific site-packages path... /usr/lib/python3.11/site-packages checking python extra libraries... -ldl -lm checking python extra linking flags... -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions checking consistency of all components of python development environment... yes checking for perl... /usr/bin/perl checking for Perl prefix... /usr checking for Perl extension include path... /usr/lib/i386-linux-gnu/perl/5.36/CORE checking for Perl extension target directory... /usr/lib/perl/5.36.0 checking for Perl extensions C preprocessor flags... -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include checking for Perl extensions linker flags... -shared -L/usr/local/lib -fstack-protector-strong checking for posix_memalign... yes checking for aligned_alloc... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating compat.sh config.status: creating jellyfish-2.0.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_configure --sourcedirectory=swig/perl5 cd swig/perl5 && /usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=i686-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -lpthread" -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0 -L/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu -ljellyfish-2.0 -lpthread -L/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu Warning (mostly harmless): No library found for -ljellyfish-2.0 Generating a Unix-style Makefile Writing Makefile for jellyfish Writing MYMETA.yml and MYMETA.json dh_auto_configure --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:240: python3.11 setup.py config /build/reproducible-path/jellyfish-2.3.0/swig/python/setup.py:12: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.core import setup, Extension running config mv /tmp/m4-ax_python_devel.m4 m4 make[1]: Leaving directory '/build/reproducible-path/jellyfish-2.3.0' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/jellyfish-2.3.0' mkdir -p debian/tmp_save_tests cp -a tests/* debian/tmp_save_tests dh_auto_build --no-parallel -- all bin/generate_sequence bin/test_all bin/fastq2sam make -j1 all bin/generate_sequence bin/test_all bin/fastq2sam make[2]: Entering directory '/build/reproducible-path/jellyfish-2.3.0' /usr/bin/yaggo --license ./header-license -o sub_commands/count_main_cmdline.hpp sub_commands/count_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/info_main_cmdline.hpp sub_commands/info_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/dump_main_cmdline.hpp sub_commands/dump_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/histo_main_cmdline.hpp sub_commands/histo_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/stats_main_cmdline.hpp sub_commands/stats_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/merge_main_cmdline.hpp sub_commands/merge_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/bc_main_cmdline.hpp sub_commands/bc_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/query_main_cmdline.hpp sub_commands/query_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/cite_main_cmdline.hpp sub_commands/cite_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/mem_main_cmdline.hpp sub_commands/mem_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o jellyfish/generate_sequence_cmdline.hpp jellyfish/generate_sequence_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o jellyfish/fastq2sam_cmdline.hpp jellyfish/fastq2sam_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o unit_tests/test_main_cmdline.hpp unit_tests/test_main_cmdline.yaggo /usr/bin/swig -c++ -python -I./../include -o swig/python/swig_wrap.cpp swig/jellyfish.i /usr/bin/swig -c++ -perl5 -I./../include -o swig/perl5/swig_wrap.cpp swig/jellyfish.i make all-am make[3]: Entering directory '/build/reproducible-path/jellyfish-2.3.0' g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/jellyfish.o sub_commands/jellyfish.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/count_main.o sub_commands/count_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/info_main.o sub_commands/info_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/dump_main.o sub_commands/dump_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/histo_main.o sub_commands/histo_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/stats_main.o sub_commands/stats_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/merge_main.o sub_commands/merge_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/bc_main.o sub_commands/bc_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/query_main.o sub_commands/query_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/cite_main.o sub_commands/cite_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/mem_main.o sub_commands/mem_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse 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.libs/libjellyfish-2.0.a lib/rectangular_binary_matrix.o lib/mer_dna.o lib/storage.o lib/allocators_mmap.o lib/misc.o lib/int128.o lib/thread_exec.o lib/jsoncpp.o lib/time.o lib/generator_manager.o libtool: link: ranlib .libs/libjellyfish-2.0.a libtool: link: ( cd ".libs" && rm -f "libjellyfish-2.0.la" && ln -s "../libjellyfish-2.0.la" "libjellyfish-2.0.la" ) /bin/bash ./libtool --tag=CXX --mode=link g++ -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -pthread -L/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu -lhts -R/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o bin/jellyfish sub_commands/jellyfish.o sub_commands/count_main.o sub_commands/info_main.o sub_commands/dump_main.o sub_commands/histo_main.o 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-Wl,/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/lib/i386-linux-gnu/perl/5.36/CORE -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo `test -f 'swig/perl5/swig_wrap.cpp' || echo './'`swig/perl5/swig_wrap.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/lib/i386-linux-gnu/perl/5.36/CORE -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse 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-Werror=format-security -Wno-nonnull -c -o jellyfish/mersenne.o jellyfish/mersenne.cpp g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o jellyfish/backtrace.o jellyfish/backtrace.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o jellyfish/dbg.o jellyfish/dbg.cc /bin/bash ./libtool --tag=CXX --mode=link g++ -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror 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./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_main.o `test -f 'unit_tests/test_main.cc' || echo './'`unit_tests/test_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_misc.o `test -f 'unit_tests/test_misc.cc' || echo './'`unit_tests/test_misc.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_offsets_key_value.o `test -f 'unit_tests/test_offsets_key_value.cc' || echo './'`unit_tests/test_offsets_key_value.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_simple_circular_buffer.o `test -f 'unit_tests/test_simple_circular_buffer.cc' || echo './'`unit_tests/test_simple_circular_buffer.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_rectangular_binary_matrix.o `test -f 'unit_tests/test_rectangular_binary_matrix.cc' || echo './'`unit_tests/test_rectangular_binary_matrix.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_mer_dna.o `test -f 'unit_tests/test_mer_dna.cc' || echo './'`unit_tests/test_mer_dna.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_large_hash_array.o `test -f 'unit_tests/test_large_hash_array.cc' || echo './'`unit_tests/test_large_hash_array.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_mer_overlap_sequence_parser.o `test -f 'unit_tests/test_mer_overlap_sequence_parser.cc' || echo './'`unit_tests/test_mer_overlap_sequence_parser.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_file_header.o `test -f 'unit_tests/test_file_header.cc' || echo './'`unit_tests/test_file_header.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_mer_iterator.o `test -f 'unit_tests/test_mer_iterator.cc' || echo './'`unit_tests/test_mer_iterator.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_hash_counter.o `test -f 'unit_tests/test_hash_counter.cc' || echo './'`unit_tests/test_hash_counter.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_mer_heap.o `test -f 'unit_tests/test_mer_heap.cc' || echo './'`unit_tests/test_mer_heap.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_stream_iterator.o `test -f 'unit_tests/test_stream_iterator.cc' || echo './'`unit_tests/test_stream_iterator.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_token_ring.o `test -f 'unit_tests/test_token_ring.cc' || echo './'`unit_tests/test_token_ring.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_text_dumper.o `test -f 'unit_tests/test_text_dumper.cc' || echo './'`unit_tests/test_text_dumper.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_dumpers.o `test -f 'unit_tests/test_dumpers.cc' || echo './'`unit_tests/test_dumpers.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_mapped_file.o `test -f 'unit_tests/test_mapped_file.cc' || echo './'`unit_tests/test_mapped_file.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_int128.o `test -f 'unit_tests/test_int128.cc' || echo './'`unit_tests/test_int128.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_mer_dna_bloom_counter.o `test -f 'unit_tests/test_mer_dna_bloom_counter.cc' || echo './'`unit_tests/test_mer_dna_bloom_counter.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_whole_sequence_parser.o `test -f 'unit_tests/test_whole_sequence_parser.cc' || echo './'`unit_tests/test_whole_sequence_parser.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_allocators_mmap.o `test -f 'unit_tests/test_allocators_mmap.cc' || echo './'`unit_tests/test_allocators_mmap.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_cooperative_pool2.o `test -f 'unit_tests/test_cooperative_pool2.cc' || echo './'`unit_tests/test_cooperative_pool2.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_generator_manager.o `test -f 'unit_tests/test_generator_manager.cc' || echo './'`unit_tests/test_generator_manager.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_atomic_bits_array.o `test -f 'unit_tests/test_atomic_bits_array.cc' || echo './'`unit_tests/test_atomic_bits_array.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_stdio_filebuf.o `test -f 'unit_tests/test_stdio_filebuf.cc' || echo './'`unit_tests/test_stdio_filebuf.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o jellyfish/bin_test_all-backtrace.o `test -f 'jellyfish/backtrace.cc' || echo './'`jellyfish/backtrace.cc /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -I./unit_tests/gtest -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/gtest/src/libgtest_la-gtest-all.lo `test -f 'unit_tests/gtest/src/gtest-all.cc' || echo './'`unit_tests/gtest/src/gtest-all.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -I./unit_tests/gtest -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c unit_tests/gtest/src/gtest-all.cc -fPIC -DPIC -o unit_tests/gtest/src/.libs/libgtest_la-gtest-all.o unit_tests/gtest/src/gtest-all.cc: In function 'bool testing::internal::StackGrowsDown()': unit_tests/gtest/src/gtest-all.cc:7485:24: warning: 'dummy' may be used uninitialized [-Wmaybe-uninitialized] 7485 | StackLowerThanAddress(&dummy, &result); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ unit_tests/gtest/src/gtest-all.cc:7477:6: note: by argument 1 of type 'const void*' to 'void testing::internal::StackLowerThanAddress(const void*, bool*)' declared here 7477 | void StackLowerThanAddress(const void* ptr, bool* result) { | ^~~~~~~~~~~~~~~~~~~~~ unit_tests/gtest/src/gtest-all.cc:7483:7: note: 'dummy' declared here 7483 | int dummy; | ^~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -I./unit_tests/gtest -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c unit_tests/gtest/src/gtest-all.cc -o unit_tests/gtest/src/libgtest_la-gtest-all.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -I./unit_tests -I./unit_tests/gtest -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -pthread -L/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu -lhts -R/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o libgtest.la unit_tests/gtest/src/libgtest_la-gtest-all.lo libtool: link: ar cr .libs/libgtest.a unit_tests/gtest/src/.libs/libgtest_la-gtest-all.o libtool: link: ranlib .libs/libgtest.a libtool: link: ( cd ".libs" && rm -f "libgtest.la" && ln -s "../libgtest.la" "libgtest.la" ) /bin/bash ./libtool --tag=CXX --mode=link g++ -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -pthread -L/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu -lhts -R/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o bin/test_all unit_tests/bin_test_all-test_main.o unit_tests/bin_test_all-test_misc.o unit_tests/bin_test_all-test_offsets_key_value.o unit_tests/bin_test_all-test_simple_circular_buffer.o unit_tests/bin_test_all-test_rectangular_binary_matrix.o unit_tests/bin_test_all-test_mer_dna.o unit_tests/bin_test_all-test_large_hash_array.o unit_tests/bin_test_all-test_mer_overlap_sequence_parser.o unit_tests/bin_test_all-test_file_header.o unit_tests/bin_test_all-test_mer_iterator.o unit_tests/bin_test_all-test_hash_counter.o unit_tests/bin_test_all-test_mer_heap.o unit_tests/bin_test_all-test_stream_iterator.o unit_tests/bin_test_all-test_token_ring.o unit_tests/bin_test_all-test_text_dumper.o unit_tests/bin_test_all-test_dumpers.o unit_tests/bin_test_all-test_mapped_file.o unit_tests/bin_test_all-test_int128.o unit_tests/bin_test_all-test_mer_dna_bloom_counter.o unit_tests/bin_test_all-test_whole_sequence_parser.o unit_tests/bin_test_all-test_allocators_mmap.o unit_tests/bin_test_all-test_cooperative_pool2.o unit_tests/bin_test_all-test_generator_manager.o unit_tests/bin_test_all-test_atomic_bits_array.o unit_tests/bin_test_all-test_stdio_filebuf.o jellyfish/bin_test_all-backtrace.o libgtest.la libjellyfish-2.0.la libtool: link: g++ -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/test_all unit_tests/bin_test_all-test_main.o unit_tests/bin_test_all-test_misc.o unit_tests/bin_test_all-test_offsets_key_value.o unit_tests/bin_test_all-test_simple_circular_buffer.o unit_tests/bin_test_all-test_rectangular_binary_matrix.o unit_tests/bin_test_all-test_mer_dna.o unit_tests/bin_test_all-test_large_hash_array.o unit_tests/bin_test_all-test_mer_overlap_sequence_parser.o unit_tests/bin_test_all-test_file_header.o unit_tests/bin_test_all-test_mer_iterator.o unit_tests/bin_test_all-test_hash_counter.o unit_tests/bin_test_all-test_mer_heap.o unit_tests/bin_test_all-test_stream_iterator.o unit_tests/bin_test_all-test_token_ring.o unit_tests/bin_test_all-test_text_dumper.o unit_tests/bin_test_all-test_dumpers.o unit_tests/bin_test_all-test_mapped_file.o unit_tests/bin_test_all-test_int128.o unit_tests/bin_test_all-test_mer_dna_bloom_counter.o unit_tests/bin_test_all-test_whole_sequence_parser.o unit_tests/bin_test_all-test_allocators_mmap.o unit_tests/bin_test_all-test_cooperative_pool2.o unit_tests/bin_test_all-test_generator_manager.o unit_tests/bin_test_all-test_atomic_bits_array.o unit_tests/bin_test_all-test_stdio_filebuf.o jellyfish/bin_test_all-backtrace.o -L/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu ./.libs/libgtest.a -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o jellyfish/fastq2sam.o jellyfish/fastq2sam.cc /bin/bash ./libtool --tag=CXX --mode=link g++ -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -pthread -L/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu -lhts -R/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o bin/fastq2sam jellyfish/fastq2sam.o libjellyfish-2.0.la libtool: link: g++ -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/fastq2sam jellyfish/fastq2sam.o -L/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu make[2]: Leaving directory '/build/reproducible-path/jellyfish-2.3.0' dh_auto_install -- install-data make -j1 install DESTDIR=/build/reproducible-path/jellyfish-2.3.0/debian/tmp AM_UPDATE_INFO_DIR=no install-data make[2]: Entering directory '/build/reproducible-path/jellyfish-2.3.0' make install-am make[3]: Entering directory '/build/reproducible-path/jellyfish-2.3.0' make[4]: Entering directory '/build/reproducible-path/jellyfish-2.3.0' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; }) libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/lib/i386-linux-gnu' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/bin' /bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/bin' libtool: warning: 'libjellyfish-2.0.la' has not been installed in '/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c bin/.libs/jellyfish /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/bin/jellyfish /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/allocators_mmap.hpp include/jellyfish/backtrace.hpp include/jellyfish/atomic_gcc.hpp include/jellyfish/large_hash_array.hpp include/jellyfish/err.hpp include/jellyfish/misc.hpp include/jellyfish/offsets_key_value.hpp include/jellyfish/int128.hpp include/jellyfish/rectangular_binary_matrix.hpp include/jellyfish/mer_dna.hpp include/jellyfish/storage.hpp include/jellyfish/simple_circular_buffer.hpp include/jellyfish/circular_buffer.hpp include/jellyfish/atomic_field.hpp include/jellyfish/compare_and_swap.hpp include/jellyfish/divisor.hpp include/jellyfish/large_hash_iterator.hpp include/jellyfish/jellyfish.hpp include/jellyfish/thread_exec.hpp include/jellyfish/stream_iterator.hpp include/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish/whole_sequence_parser.hpp include/jellyfish/parser_common.hpp include/jellyfish/sam_format.hpp include/jellyfish/binary_dumper.hpp include/jellyfish/sorted_dumper.hpp include/jellyfish/text_dumper.hpp include/jellyfish/dumper.hpp include/jellyfish/time.hpp include/jellyfish/mer_heap.hpp include/jellyfish/token_ring.hpp include/jellyfish/locks_pthread.hpp include/jellyfish/file_header.hpp include/jellyfish/generic_file_header.hpp include/jellyfish/json.h include/jellyfish/hash_counter.hpp include/jellyfish/mapped_file.hpp include/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish/bloom_common.hpp include/jellyfish/bloom_counter2.hpp '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/bloom_filter.hpp include/jellyfish/cooperative_pool.hpp include/jellyfish/cooperative_pool2.hpp include/jellyfish/stream_manager.hpp include/jellyfish/generator_manager.hpp include/jellyfish/cpp_array.hpp include/jellyfish/mer_iterator.hpp include/jellyfish/atomic_bits_array.hpp include/jellyfish/stdio_filebuf.hpp include/jellyfish/mer_qual_iterator.hpp '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/share/man/man1/jellyfish.1' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0; /bin/sh "/build/reproducible-path/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.36.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/reproducible-path/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/12/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu -L/usr/lib/i386-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/i686-linux-gnu/12 -L/usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/12/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-linux-gnu/12/crtendS.o /usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/crtn.o -msse -mfpmath=sse -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.so.0.0.0T /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.so.0.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so.0 || { rm -f jellyfish.so.0 && ln -s jellyfish.so.0.0.0 jellyfish.so.0; }; }) libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so || { rm -f jellyfish.so && ln -s jellyfish.so.0.0.0 jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.lai /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.36.0' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' libtool: warning: relinking 'swig/python/_dna_jellyfish.la' libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0; /bin/sh "/build/reproducible-path/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3.11/site-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/reproducible-path/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/12/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu -L/usr/lib/i386-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/i686-linux-gnu/12 -L/usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/12/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-linux-gnu/12/crtendS.o /usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/crtn.o -msse -mfpmath=sse -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,_dna_jellyfish.so.0 -o swig/python/.libs/_dna_jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.so.0.0.0T /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0 || { rm -f _dna_jellyfish.so.0 && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0; }; }) libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so || { rm -f _dna_jellyfish.so && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.lai /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.la libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3.11/site-packages/dna_jellyfish' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' make[4]: Leaving directory '/build/reproducible-path/jellyfish-2.3.0' make[3]: Leaving directory '/build/reproducible-path/jellyfish-2.3.0' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/allocators_mmap.hpp include/jellyfish/backtrace.hpp include/jellyfish/atomic_gcc.hpp include/jellyfish/large_hash_array.hpp include/jellyfish/err.hpp include/jellyfish/misc.hpp include/jellyfish/offsets_key_value.hpp include/jellyfish/int128.hpp include/jellyfish/rectangular_binary_matrix.hpp include/jellyfish/mer_dna.hpp include/jellyfish/storage.hpp include/jellyfish/simple_circular_buffer.hpp include/jellyfish/circular_buffer.hpp include/jellyfish/atomic_field.hpp include/jellyfish/compare_and_swap.hpp include/jellyfish/divisor.hpp include/jellyfish/large_hash_iterator.hpp include/jellyfish/jellyfish.hpp include/jellyfish/thread_exec.hpp include/jellyfish/stream_iterator.hpp include/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish/whole_sequence_parser.hpp include/jellyfish/parser_common.hpp include/jellyfish/sam_format.hpp include/jellyfish/binary_dumper.hpp include/jellyfish/sorted_dumper.hpp include/jellyfish/text_dumper.hpp include/jellyfish/dumper.hpp include/jellyfish/time.hpp include/jellyfish/mer_heap.hpp include/jellyfish/token_ring.hpp include/jellyfish/locks_pthread.hpp include/jellyfish/file_header.hpp include/jellyfish/generic_file_header.hpp include/jellyfish/json.h include/jellyfish/hash_counter.hpp include/jellyfish/mapped_file.hpp include/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish/bloom_common.hpp include/jellyfish/bloom_counter2.hpp '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/bloom_filter.hpp include/jellyfish/cooperative_pool.hpp include/jellyfish/cooperative_pool2.hpp include/jellyfish/stream_manager.hpp include/jellyfish/generator_manager.hpp include/jellyfish/cpp_array.hpp include/jellyfish/mer_iterator.hpp include/jellyfish/atomic_bits_array.hpp include/jellyfish/stdio_filebuf.hpp include/jellyfish/mer_qual_iterator.hpp '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/share/man/man1/jellyfish.1' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; }) libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/lib/i386-linux-gnu' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0; /bin/sh "/build/reproducible-path/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.36.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/reproducible-path/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/12/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu -L/usr/lib/i386-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/i686-linux-gnu/12 -L/usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/12/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-linux-gnu/12/crtendS.o /usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/crtn.o -msse -mfpmath=sse -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.so.0.0.0T /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.so.0.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so.0 || { rm -f jellyfish.so.0 && ln -s jellyfish.so.0.0.0 jellyfish.so.0; }; }) libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so || { rm -f jellyfish.so && ln -s jellyfish.so.0.0.0 jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.lai /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.36.0' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' libtool: warning: relinking 'swig/python/_dna_jellyfish.la' libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0; /bin/sh "/build/reproducible-path/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3.11/site-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/reproducible-path/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/12/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu -L/usr/lib/i386-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/i686-linux-gnu/12 -L/usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/12/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-linux-gnu/12/crtendS.o /usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/crtn.o -msse -mfpmath=sse -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,_dna_jellyfish.so.0 -o swig/python/.libs/_dna_jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.so.0.0.0T /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0 || { rm -f _dna_jellyfish.so.0 && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0; }; }) libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so || { rm -f _dna_jellyfish.so && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.lai /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.la libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3.11/site-packages/dna_jellyfish' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' make[2]: Leaving directory '/build/reproducible-path/jellyfish-2.3.0' dh_auto_build --sourcedirectory=swig/perl5 cd swig/perl5 && make -j7 make[2]: Entering directory '/build/reproducible-path/jellyfish-2.3.0/swig/perl5' Running Mkbootstrap for jellyfish () g++ -c -std=c++0x -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.0.1\" -DXS_VERSION=\"0.0.1\" -fPIC "-I/usr/lib/i386-linux-gnu/perl/5.36/CORE" swig_wrap.cpp chmod 644 "jellyfish.bs" "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- jellyfish.bs blib/arch/auto/jellyfish/jellyfish.bs 644 rm -f blib/arch/auto/jellyfish/jellyfish.so i686-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -lpthread -shared -L/usr/local/lib -fstack-protector-strong swig_wrap.o -o blib/arch/auto/jellyfish/jellyfish.so \ -lpthread \ chmod 755 blib/arch/auto/jellyfish/jellyfish.so make[2]: Leaving directory '/build/reproducible-path/jellyfish-2.3.0/swig/perl5' dh_auto_build --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py build build_ext -L/build/reproducible-path/jellyfish-2.3.0/.libs /build/reproducible-path/jellyfish-2.3.0/swig/python/setup.py:12: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.core import setup, Extension running build running build_py copying dna_jellyfish.py -> /build/reproducible-path/jellyfish-2.3.0/.pybuild/cpython3_3.11_dna_jellyfish/build running build_ext building '_dna_jellyfish' extension creating build creating build/temp.linux-i386-3.11 i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0 -I/usr/include/python3.11 -c swig_wrap.cpp -o build/temp.linux-i386-3.11/swig_wrap.o -std=c++0x i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -lpthread -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-3.11/swig_wrap.o -L/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu -L/build/reproducible-path/jellyfish-2.3.0/.libs -ljellyfish-2.0 -lpthread -o /build/reproducible-path/jellyfish-2.3.0/.pybuild/cpython3_3.11_dna_jellyfish/build/_dna_jellyfish.cpython-311-i386-linux-gnu.so -Wl,-rpath,/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu make[1]: Leaving directory '/build/reproducible-path/jellyfish-2.3.0' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/jellyfish-2.3.0' echo "Test data are to big for 32bit architectures thus no testing is done" Test data are to big for 32bit architectures thus no testing is done make[1]: Leaving directory '/build/reproducible-path/jellyfish-2.3.0' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/jellyfish-2.3.0' chrpath --delete bin/.libs/* dh_auto_install -- install-data make -j1 install DESTDIR=/build/reproducible-path/jellyfish-2.3.0/debian/tmp AM_UPDATE_INFO_DIR=no install-data make[2]: Entering directory '/build/reproducible-path/jellyfish-2.3.0' make install-am make[3]: Entering directory '/build/reproducible-path/jellyfish-2.3.0' make[4]: Entering directory '/build/reproducible-path/jellyfish-2.3.0' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; }) libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/lib/i386-linux-gnu' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/bin' /bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/bin' libtool: warning: 'libjellyfish-2.0.la' has not been installed in '/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c bin/.libs/jellyfish /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/bin/jellyfish /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/allocators_mmap.hpp include/jellyfish/backtrace.hpp include/jellyfish/atomic_gcc.hpp include/jellyfish/large_hash_array.hpp include/jellyfish/err.hpp include/jellyfish/misc.hpp include/jellyfish/offsets_key_value.hpp include/jellyfish/int128.hpp include/jellyfish/rectangular_binary_matrix.hpp include/jellyfish/mer_dna.hpp include/jellyfish/storage.hpp include/jellyfish/simple_circular_buffer.hpp include/jellyfish/circular_buffer.hpp include/jellyfish/atomic_field.hpp include/jellyfish/compare_and_swap.hpp include/jellyfish/divisor.hpp include/jellyfish/large_hash_iterator.hpp include/jellyfish/jellyfish.hpp include/jellyfish/thread_exec.hpp include/jellyfish/stream_iterator.hpp include/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish/whole_sequence_parser.hpp include/jellyfish/parser_common.hpp include/jellyfish/sam_format.hpp include/jellyfish/binary_dumper.hpp include/jellyfish/sorted_dumper.hpp include/jellyfish/text_dumper.hpp include/jellyfish/dumper.hpp include/jellyfish/time.hpp include/jellyfish/mer_heap.hpp include/jellyfish/token_ring.hpp include/jellyfish/locks_pthread.hpp include/jellyfish/file_header.hpp include/jellyfish/generic_file_header.hpp include/jellyfish/json.h include/jellyfish/hash_counter.hpp include/jellyfish/mapped_file.hpp include/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish/bloom_common.hpp include/jellyfish/bloom_counter2.hpp '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/bloom_filter.hpp include/jellyfish/cooperative_pool.hpp include/jellyfish/cooperative_pool2.hpp include/jellyfish/stream_manager.hpp include/jellyfish/generator_manager.hpp include/jellyfish/cpp_array.hpp include/jellyfish/mer_iterator.hpp include/jellyfish/atomic_bits_array.hpp include/jellyfish/stdio_filebuf.hpp include/jellyfish/mer_qual_iterator.hpp '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/share/man/man1/jellyfish.1' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0; /bin/sh "/build/reproducible-path/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.36.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/reproducible-path/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/12/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu -L/usr/lib/i386-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/i686-linux-gnu/12 -L/usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/12/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-linux-gnu/12/crtendS.o /usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/crtn.o -msse -mfpmath=sse -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.so.0.0.0T /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.so.0.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so.0 || { rm -f jellyfish.so.0 && ln -s jellyfish.so.0.0.0 jellyfish.so.0; }; }) libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so || { rm -f jellyfish.so && ln -s jellyfish.so.0.0.0 jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.lai /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.36.0' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' libtool: warning: relinking 'swig/python/_dna_jellyfish.la' libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0; /bin/sh "/build/reproducible-path/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3.11/site-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/reproducible-path/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/12/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu -L/usr/lib/i386-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/i686-linux-gnu/12 -L/usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/12/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-linux-gnu/12/crtendS.o /usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/crtn.o -msse -mfpmath=sse -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,_dna_jellyfish.so.0 -o swig/python/.libs/_dna_jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.so.0.0.0T /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0 || { rm -f _dna_jellyfish.so.0 && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0; }; }) libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so || { rm -f _dna_jellyfish.so && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.lai /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.la libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3.11/site-packages/dna_jellyfish' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' make[4]: Leaving directory '/build/reproducible-path/jellyfish-2.3.0' make[3]: Leaving directory '/build/reproducible-path/jellyfish-2.3.0' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/allocators_mmap.hpp include/jellyfish/backtrace.hpp include/jellyfish/atomic_gcc.hpp include/jellyfish/large_hash_array.hpp include/jellyfish/err.hpp include/jellyfish/misc.hpp include/jellyfish/offsets_key_value.hpp include/jellyfish/int128.hpp include/jellyfish/rectangular_binary_matrix.hpp include/jellyfish/mer_dna.hpp include/jellyfish/storage.hpp include/jellyfish/simple_circular_buffer.hpp include/jellyfish/circular_buffer.hpp include/jellyfish/atomic_field.hpp include/jellyfish/compare_and_swap.hpp include/jellyfish/divisor.hpp include/jellyfish/large_hash_iterator.hpp include/jellyfish/jellyfish.hpp include/jellyfish/thread_exec.hpp include/jellyfish/stream_iterator.hpp include/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish/whole_sequence_parser.hpp include/jellyfish/parser_common.hpp include/jellyfish/sam_format.hpp include/jellyfish/binary_dumper.hpp include/jellyfish/sorted_dumper.hpp include/jellyfish/text_dumper.hpp include/jellyfish/dumper.hpp include/jellyfish/time.hpp include/jellyfish/mer_heap.hpp include/jellyfish/token_ring.hpp include/jellyfish/locks_pthread.hpp include/jellyfish/file_header.hpp include/jellyfish/generic_file_header.hpp include/jellyfish/json.h include/jellyfish/hash_counter.hpp include/jellyfish/mapped_file.hpp include/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish/bloom_common.hpp include/jellyfish/bloom_counter2.hpp '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/bloom_filter.hpp include/jellyfish/cooperative_pool.hpp include/jellyfish/cooperative_pool2.hpp include/jellyfish/stream_manager.hpp include/jellyfish/generator_manager.hpp include/jellyfish/cpp_array.hpp include/jellyfish/mer_iterator.hpp include/jellyfish/atomic_bits_array.hpp include/jellyfish/stdio_filebuf.hpp include/jellyfish/mer_qual_iterator.hpp '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/share/man/man1/jellyfish.1' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; }) libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/lib/i386-linux-gnu' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0; /bin/sh "/build/reproducible-path/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.36.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/reproducible-path/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/12/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu -L/usr/lib/i386-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/i686-linux-gnu/12 -L/usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/12/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-linux-gnu/12/crtendS.o /usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/crtn.o -msse -mfpmath=sse -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.so.0.0.0T /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.so.0.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so.0 || { rm -f jellyfish.so.0 && ln -s jellyfish.so.0.0.0 jellyfish.so.0; }; }) libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so || { rm -f jellyfish.so && ln -s jellyfish.so.0.0.0 jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.lai /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.36.0' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' libtool: warning: relinking 'swig/python/_dna_jellyfish.la' libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0; /bin/sh "/build/reproducible-path/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -I/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/include -msse -mfpmath=sse -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3.11/site-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/reproducible-path/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/12/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu -L/usr/lib/i386-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/i686-linux-gnu/12 -L/usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/12/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-linux-gnu/12/crtendS.o /usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/crtn.o -msse -mfpmath=sse -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,_dna_jellyfish.so.0 -o swig/python/.libs/_dna_jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.so.0.0.0T /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0 || { rm -f _dna_jellyfish.so.0 && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0; }; }) libtool: install: (cd /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so || { rm -f _dna_jellyfish.so && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.lai /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.la libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3.11/site-packages/dna_jellyfish' /bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' make[2]: Leaving directory '/build/reproducible-path/jellyfish-2.3.0' dh_auto_install --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py install --root /build/reproducible-path/jellyfish-2.3.0/debian/python3-dna-jellyfish /build/reproducible-path/jellyfish-2.3.0/swig/python/setup.py:12: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.core import setup, Extension running install running build running build_py running build_ext running install_lib creating /build/reproducible-path/jellyfish-2.3.0/debian/python3-dna-jellyfish creating /build/reproducible-path/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr creating /build/reproducible-path/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib creating /build/reproducible-path/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib/python3.11 creating /build/reproducible-path/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib/python3.11/dist-packages copying /build/reproducible-path/jellyfish-2.3.0/.pybuild/cpython3_3.11_dna_jellyfish/build/_dna_jellyfish.cpython-311-i386-linux-gnu.so -> /build/reproducible-path/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib/python3.11/dist-packages copying /build/reproducible-path/jellyfish-2.3.0/.pybuild/cpython3_3.11_dna_jellyfish/build/dna_jellyfish.py -> /build/reproducible-path/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib/python3.11/dist-packages byte-compiling /build/reproducible-path/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib/python3.11/dist-packages/dna_jellyfish.py to dna_jellyfish.cpython-311.pyc running install_egg_info Writing /build/reproducible-path/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib/python3.11/dist-packages/dna_jellyfish-0.0.1.egg-info dh_auto_install --sourcedirectory=swig/perl5 cd swig/perl5 && make -j7 install DESTDIR=/build/reproducible-path/jellyfish-2.3.0/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr make[2]: Entering directory '/build/reproducible-path/jellyfish-2.3.0/swig/perl5' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- jellyfish.bs blib/arch/auto/jellyfish/jellyfish.bs 644 Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/perl5/5.36/auto/jellyfish/jellyfish.so make[2]: Leaving directory '/build/reproducible-path/jellyfish-2.3.0/swig/perl5' ls -l debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so -r-xr-xr-x 1 pbuilder2 pbuilder2 1065768 Jan 20 04:51 debian/tmp/usr/lib/i386-linux-gnu/perl5/5.36/auto/jellyfish/jellyfish.so if [ ! -e debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so ] ; then sleep 1; fi chmod +w debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so chrpath --delete debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so dh_install d-shlibmove --commit \ --multiarch \ --devunversioned \ --movedev "debian/tmp/usr/include/jellyfish*/jellyfish/*.hpp" usr/include/jellyfish \ --movedev "debian/tmp/usr/include/jellyfish*/jellyfish/*.h" usr/include/jellyfish \ --movedev config.h usr/include/jellyfish \ debian/tmp/usr/lib/*/libjellyfish-*.so Library package automatic movement utility set -e install -d -m 755 debian/libjellyfish-2.0-dev/usr/lib/i386-linux-gnu install -d -m 755 debian/libjellyfish-2.0-2/usr/lib/i386-linux-gnu mv debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-2.0.a debian/libjellyfish-2.0-dev/usr/lib/i386-linux-gnu mv debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-2.0.la debian/libjellyfish-2.0-dev/usr/lib/i386-linux-gnu || true mv debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-2.0.so debian/libjellyfish-2.0-dev/usr/lib/i386-linux-gnu mv /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-2.0.so.2 debian/libjellyfish-2.0-2/usr/lib/i386-linux-gnu mv /build/reproducible-path/jellyfish-2.3.0/debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-2.0.so.2.0.0 debian/libjellyfish-2.0-2/usr/lib/i386-linux-gnu PKGDEV=libjellyfish-2.0-dev PKGSHL=libjellyfish-2.0-2 install -d -m 755 debian/libjellyfish-2.0-dev/usr/include/jellyfish mv debian/tmp/usr/include/jellyfish*/jellyfish/*.hpp debian/libjellyfish-2.0-dev/usr/include/jellyfish install -d -m 755 debian/libjellyfish-2.0-dev/usr/include/jellyfish mv debian/tmp/usr/include/jellyfish*/jellyfish/*.h debian/libjellyfish-2.0-dev/usr/include/jellyfish install -d -m 755 debian/libjellyfish-2.0-dev/usr/include/jellyfish mv config.h debian/libjellyfish-2.0-dev/usr/include/jellyfish sed -i "/dependency_libs/ s/'.*'/''/" ./debian/libjellyfish-2.0-dev/usr/lib/i386-linux-gnu/*.la chrpath --delete debian/*/usr/lib/python*/dist-packages/_dna_jellyfish*.so make[1]: Leaving directory '/build/reproducible-path/jellyfish-2.3.0' dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_python3 dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms debian/rules override_dh_missing make[1]: Entering directory '/build/reproducible-path/jellyfish-2.3.0' # Python files are just installed rm -rf debian/tmp/usr/lib/python3/dist-packages # Necessary Perl files are just installed rm -rf debian/tmp/usr/lib/perl/5.* dh_missing make[1]: Leaving directory '/build/reproducible-path/jellyfish-2.3.0' dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package jellyfish-examples: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'python3-dna-jellyfish-dbgsym' in '../python3-dna-jellyfish-dbgsym_2.3.0-15_i386.deb'. dpkg-deb: building package 'libjellyfish-2.0-2' in '../libjellyfish-2.0-2_2.3.0-15_i386.deb'. dpkg-deb: building package 'libjellyfish-perl-dbgsym' in '../libjellyfish-perl-dbgsym_2.3.0-15_i386.deb'. dpkg-deb: building package 'jellyfish' in '../jellyfish_2.3.0-15_i386.deb'. dpkg-deb: building package 'libjellyfish-2.0-dev' in '../libjellyfish-2.0-dev_2.3.0-15_i386.deb'. dpkg-deb: building package 'libjellyfish-2.0-2-dbgsym' in '../libjellyfish-2.0-2-dbgsym_2.3.0-15_i386.deb'. dpkg-deb: building package 'libjellyfish-perl' in '../libjellyfish-perl_2.3.0-15_i386.deb'. dpkg-deb: building package 'jellyfish-examples' in '../jellyfish-examples_2.3.0-15_all.deb'. dpkg-deb: building package 'python3-dna-jellyfish' in '../python3-dna-jellyfish_2.3.0-15_i386.deb'. dpkg-deb: building package 'jellyfish-dbgsym' in '../jellyfish-dbgsym_2.3.0-15_i386.deb'. dpkg-genbuildinfo --build=binary -O../jellyfish_2.3.0-15_i386.buildinfo dpkg-genchanges --build=binary -O../jellyfish_2.3.0-15_i386.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: user script /srv/workspace/pbuilder/31279/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/31279/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/31279 and its subdirectories I: Current time: Sat Jan 20 18:51:36 +14 2024 I: pbuilder-time-stamp: 1705726296