Fri Apr 14 00:26:24 UTC 2023 I: starting to build jellyfish/bookworm/amd64 on jenkins on '2023-04-14 00:26' Fri Apr 14 00:26:24 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_16/26617/console.log Fri Apr 14 00:26:24 UTC 2023 I: Downloading source for bookworm/jellyfish=2.3.0-15 --2023-04-14 00:26:24-- http://cdn-fastly.deb.debian.org/debian/pool/main/j/jellyfish/jellyfish_2.3.0-15.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 3224 (3.1K) [text/prs.lines.tag] Saving to: ‘jellyfish_2.3.0-15.dsc’ 0K ... 100% 29.9M=0s 2023-04-14 00:26:24 (29.9 MB/s) - ‘jellyfish_2.3.0-15.dsc’ saved [3224/3224] Fri Apr 14 00:26:24 UTC 2023 I: jellyfish_2.3.0-15.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: jellyfish Binary: jellyfish, libjellyfish-2.0-2, libjellyfish-2.0-dev, python3-dna-jellyfish, libjellyfish-perl, jellyfish-examples Architecture: amd64 arm64 armel armhf i386 mips64el ppc64el hppa hurd-i386 ia64 kfreebsd-amd64 kfreebsd-i386 riscv64 all Version: 2.3.0-15 Maintainer: Debian Med Packaging Team Uploaders: Shaun Jackman , Andreas Tille , Michael R. Crusoe , Étienne Mollier Homepage: https://github.com/gmarcais/Jellyfish Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/jellyfish Vcs-Git: https://salsa.debian.org/med-team/jellyfish.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@ Build-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 Package-List: jellyfish deb science optional arch=amd64,arm64,armel,armhf,i386,mips64el,ppc64el,hppa,hurd-i386,ia64,kfreebsd-amd64,kfreebsd-i386,riscv64 jellyfish-examples deb science optional arch=all libjellyfish-2.0-2 deb libs optional arch=amd64,arm64,armel,armhf,i386,mips64el,ppc64el,hppa,hurd-i386,ia64,kfreebsd-amd64,kfreebsd-i386,riscv64 libjellyfish-2.0-dev deb libdevel optional arch=amd64,arm64,armel,armhf,i386,mips64el,ppc64el,hppa,hurd-i386,ia64,kfreebsd-amd64,kfreebsd-i386,riscv64 libjellyfish-perl deb perl optional arch=amd64,arm64,armel,armhf,i386,mips64el,ppc64el,hppa,hurd-i386,ia64,kfreebsd-amd64,kfreebsd-i386,riscv64 python3-dna-jellyfish deb python optional arch=amd64,arm64,armel,armhf,i386,mips64el,ppc64el,hppa,hurd-i386,ia64,kfreebsd-amd64,kfreebsd-i386,riscv64 Checksums-Sha1: 4f7f5263e6e097c623531a660ef6158e2fb5e17b 679125 jellyfish_2.3.0.orig.tar.gz dcb7d3cd40572c6cabf719addd384aa9c2f34c5d 15376 jellyfish_2.3.0-15.debian.tar.xz Checksums-Sha256: 29ead991de90151dbe4a2717f7ac30b3852296c9cbdda8b001121a1f2fa714db 679125 jellyfish_2.3.0.orig.tar.gz 9c3b7bccfa8ba49078452b8bd6534295cfa1eb84bd4ab0c5b395b93fae8f8d7c 15376 jellyfish_2.3.0-15.debian.tar.xz Files: b447a26df0f1e11526129907a9b0acdb 679125 jellyfish_2.3.0.orig.tar.gz 0869f7bc0fe3da61452888ad0c293dd3 15376 jellyfish_2.3.0-15.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmM0qaIRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGyvQ/+LdIqzPAjO0e/0FqrTNDOVcY88Cd5DTbX 4wRqju3HjroPvndTTdgWVdafoABGz5zL/FyGKQ4if4mXxb37jE1GVplFc02+8EWw elLo0JwTV8J7yMPQhEn+tRTaPlhhtl+SQWbduWhcTcO8675iPYL2pjcE6nTxRarq PntLh/oagekRyd23SFYrYWd1bzhlU5gil51+IGUG/pym0KYq27xKgb4ZjfIC1gS6 uQE9SQ78KbJFFpfbtyQ0HimBSM/3vS81L97PruBVzaZ+BnchpzD4qx4O5Q7aMlPQ hUh1OpREe1HxVfEcho3ZIf8si2F2v5+Cs1gt1891ZDh84v0rKBZeNa07KsmHKuQr 1d5wBY2NUZj3QIfqGHUXMWevjriPQmGFzyM/CvFOHNptcaeyJdcn3TjSABIXi1gv AskBrxJhDS1CVHw6UoQ5l2X0dKDR7yk0fSqgrtbuqR3mhPncb391VU8h1MkuSKWb z8Wh2mlyNzYNskNugavoeG1JWaQbdzkGL4shj+Z8AVkJ9psgfpwW8EMELrtzjIzY Ap6qu2btDY2dO1j/joKRq7WI+Op1R5KymfciGewZwn7lQx+ATGEY1qG6VJ/ENbix hyi6iilENjoFs9rlBHNlGWURcknT40fFVKbV0tIIw741sYAIWKoK6z8LwRqmpbZ7 ud1Ks+TMSjA= =XmJN -----END PGP SIGNATURE----- Fri Apr 14 00:26:24 UTC 2023 I: Checking whether the package is not for us Fri Apr 14 00:26:24 UTC 2023 I: Starting 1st build on remote node ionos15-amd64.debian.net. Fri Apr 14 00:26:24 UTC 2023 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Fri Apr 14 00:34:26 UTC 2023 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed May 15 18:49:26 -12 2024 I: pbuilder-time-stamp: 1715842166 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: 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 08:08:02 2022 -12 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/114346/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='02ec393e6cd140eea4a5b7e6c35cae78' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='114346' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.sGP9g9ZZ/pbuilderrc_ZwyD --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sGP9g9ZZ/b1 --logfile b1/build.log jellyfish_2.3.0-15.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos15-amd64 6.1.0-0.deb11.5-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.12-1~bpo11+1 (2023-03-05) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Feb 12 2023 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 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 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 2023 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 2023 more -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 18 2022 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Feb 12 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 2023 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/114346/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), 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 ... 19596 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 51.1 MB of archives. After unpacking 200 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 autoconf-archive all 20220903-3 [775 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 12 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 libproc2-0 amd64 2:4.0.2-3 [62.8 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 procps amd64 2:4.0.2-3 [709 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.8-1 [1407 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 bc amd64 1.07.1-3+b1 [110 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 chrpath amd64 0.16-2+b1 [17.1 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 d-shlibs all 0.104 [18.6 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-2 [76.2 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-2 [131 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 dh-python all 5.20230130 [104 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 dos2unix amd64 7.4.3-1 [430 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-7 [380 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 libcurl4-gnutls-dev amd64 7.88.1-7 [480 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libdeflate-dev amd64 1.14-1 [53.3 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 libexpat1-dev amd64 2.5.0-1 [150 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 liblzma-dev amd64 5.4.1-0.2 [260 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 libhts-dev amd64 1.16+ds-3 [1601 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.4-2 [103 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 libpkgconf3 amd64 1.8.1-1 [36.1 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 libpython3.11 amd64 3.11.2-6 [1988 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-dev amd64 3.11.2-6 [4738 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 libpython3-dev amd64 3.11.2-1+b1 [9572 B] Get: 82 http://deb.debian.org/debian bookworm/main amd64 libpython3-all-dev amd64 3.11.2-1+b1 [1068 B] Get: 83 http://deb.debian.org/debian bookworm/main amd64 rubygems-integration all 1.18 [6704 B] Get: 84 http://deb.debian.org/debian bookworm/main amd64 ruby3.1 amd64 3.1.2-6 [663 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 ruby-rubygems all 3.3.15-2 [293 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 ruby amd64 1:3.1 [5868 B] Get: 87 http://deb.debian.org/debian bookworm/main amd64 rake all 13.0.6-3 [83.9 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 ruby-xmlrpc all 0.3.2-2 [24.4 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 ruby-sdbm amd64 1.0.0-5+b1 [15.4 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 libruby3.1 amd64 3.1.2-6 [5402 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 libruby amd64 1:3.1 [4972 B] Get: 95 http://deb.debian.org/debian bookworm/main amd64 pkgconf-bin amd64 1.8.1-1 [29.5 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 pkgconf amd64 1.8.1-1 [25.9 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 pkg-config amd64 1.8.1-1 [13.7 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 python3-all amd64 3.11.2-1+b1 [1056 B] Get: 99 http://deb.debian.org/debian bookworm/main amd64 python3.11-dev amd64 3.11.2-6 [615 kB] Get: 100 http://deb.debian.org/debian bookworm/main amd64 python3-dev amd64 3.11.2-1+b1 [26.2 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 python3-all-dev amd64 3.11.2-1+b1 [1072 B] Get: 102 http://deb.debian.org/debian bookworm/main amd64 samtools amd64 1.16.1-1 [607 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 swig4.0 amd64 4.1.0-0.2 [1388 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 swig all 4.1.0-0.2 [321 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 time amd64 1.9-0.2 [50.8 kB] Get: 106 http://deb.debian.org/debian bookworm/main amd64 yaggo all 1.5.10-6 [21.2 kB] Fetched 51.1 MB in 1s (66.6 MB/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 ... 19596 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:amd64. Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21094 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_amd64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../3-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_amd64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (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 ... 21528 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../01-libproc2-0_2%3a4.0.2-3_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../02-procps_2%3a4.0.2-3_amd64.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_3.0.8-1_amd64.deb ... Unpacking openssl (3.0.8-1) ... 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_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../07-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../10-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../11-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../12-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../13-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../14-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../15-m4_1.4.19-3_amd64.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+b1_amd64.deb ... Unpacking bc (1.07.1-3+b1) ... Selecting previously unselected package chrpath. Preparing to unpack .../21-chrpath_0.16-2+b1_amd64.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:amd64. Preparing to unpack .../30-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../31-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../32-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../33-libxml2_2.9.14+dfsg-1.1+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.1+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../34-gettext_0.21-12_amd64.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_3.11.2-2_all.deb ... Unpacking python3-lib2to3 (3.11.2-2) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../39-python3-distutils_3.11.2-2_all.deb ... Unpacking python3-distutils (3.11.2-2) ... Selecting previously unselected package dh-python. Preparing to unpack .../40-dh-python_5.20230130_all.deb ... Unpacking dh-python (5.20230130) ... Selecting previously unselected package dos2unix. Preparing to unpack .../41-dos2unix_7.4.3-1_amd64.deb ... Unpacking dos2unix (7.4.3-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../42-libbrotli1_1.0.9-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b6) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../43-libbsd0_0.11.7-2_amd64.deb ... Unpacking libbsd0:amd64 (0.11.7-2) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../44-libsasl2-modules-db_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../45-libsasl2-2_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../46-libldap-2.5-0_2.5.13+dfsg-5_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../47-libnghttp2-14_1.52.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.52.0-1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../48-libpsl5_0.21.2-1_amd64.deb ... Unpacking libpsl5:amd64 (0.21.2-1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../49-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../50-libssh2-1_1.10.0-3+b1_amd64.deb ... Unpacking libssh2-1:amd64 (1.10.0-3+b1) ... Selecting previously unselected package libcurl3-gnutls:amd64. Preparing to unpack .../51-libcurl3-gnutls_7.88.1-7_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.88.1-7) ... Selecting previously unselected package libcurl4-gnutls-dev:amd64. 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Selecting previously unselected package libhts3:amd64. Preparing to unpack .../58-libhts3_1.16+ds-3_amd64.deb ... Unpacking libhts3:amd64 (1.16+ds-3) ... Selecting previously unselected package liblzma-dev:amd64. Preparing to unpack .../59-liblzma-dev_5.4.1-0.2_amd64.deb ... Unpacking liblzma-dev:amd64 (5.4.1-0.2) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../60-zlib1g-dev_1%3a1.2.13.dfsg-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Selecting previously unselected package libhts-dev:amd64. Preparing to unpack .../61-libhts-dev_1.16+ds-3_amd64.deb ... Unpacking libhts-dev:amd64 (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:amd64. Preparing to unpack .../65-libncurses6_6.4-2_amd64.deb ... Unpacking libncurses6:amd64 (6.4-2) ... Selecting previously unselected package libpkgconf3:amd64. Preparing to unpack .../66-libpkgconf3_1.8.1-1_amd64.deb ... Unpacking libpkgconf3:amd64 (1.8.1-1) ... Selecting previously unselected package libpython3.11:amd64. Preparing to unpack .../67-libpython3.11_3.11.2-6_amd64.deb ... Unpacking libpython3.11:amd64 (3.11.2-6) ... Selecting previously unselected package libpython3.11-dev:amd64. Preparing to unpack .../68-libpython3.11-dev_3.11.2-6_amd64.deb ... Unpacking libpython3.11-dev:amd64 (3.11.2-6) ... Selecting previously unselected package libpython3-dev:amd64. 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Selecting previously unselected package libruby:amd64. Preparing to unpack .../82-libruby_1%3a3.1_amd64.deb ... Unpacking libruby:amd64 (1:3.1) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../83-pkgconf-bin_1.8.1-1_amd64.deb ... Unpacking pkgconf-bin (1.8.1-1) ... Selecting previously unselected package pkgconf:amd64. Preparing to unpack .../84-pkgconf_1.8.1-1_amd64.deb ... Unpacking pkgconf:amd64 (1.8.1-1) ... Selecting previously unselected package pkg-config:amd64. Preparing to unpack .../85-pkg-config_1.8.1-1_amd64.deb ... Unpacking pkg-config:amd64 (1.8.1-1) ... Selecting previously unselected package python3-all. Preparing to unpack .../86-python3-all_3.11.2-1+b1_amd64.deb ... Unpacking python3-all (3.11.2-1+b1) ... Selecting previously unselected package python3.11-dev. Preparing to unpack .../87-python3.11-dev_3.11.2-6_amd64.deb ... Unpacking python3.11-dev (3.11.2-6) ... Selecting previously unselected package python3-dev. Preparing to unpack .../88-python3-dev_3.11.2-1+b1_amd64.deb ... Unpacking python3-dev (3.11.2-1+b1) ... Selecting previously unselected package python3-all-dev. Preparing to unpack .../89-python3-all-dev_3.11.2-1+b1_amd64.deb ... Unpacking python3-all-dev (3.11.2-1+b1) ... Selecting previously unselected package samtools. Preparing to unpack .../90-samtools_1.16.1-1_amd64.deb ... Unpacking samtools (1.16.1-1) ... Selecting previously unselected package swig4.0. Preparing to unpack .../91-swig4.0_4.1.0-0.2_amd64.deb ... Unpacking swig4.0 (4.1.0-0.2) ... Selecting previously unselected package swig. Preparing to unpack .../92-swig_4.1.0-0.2_all.deb ... Unpacking swig (4.1.0-0.2) ... Selecting previously unselected package time. Preparing to unpack .../93-time_1.9-0.2_amd64.deb ... Unpacking time (1.9-0.2) ... Selecting previously unselected package yaggo. Preparing to unpack .../94-yaggo_1.5.10-6_all.deb ... Unpacking yaggo (1.5.10-6) ... Setting up libhtscodecs2:amd64 (1.3.0-4) ... Setting up media-types (10.0.0) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up time (1.9-0.2) ... Setting up libpsl5:amd64 (0.21.2-1) ... Setting up libicu72:amd64 (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:amd64 (0.2.5-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up libnghttp2-14:amd64 (1.52.0-1) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up libdeflate0:amd64 (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:amd64 (2.1.28+dfsg-10) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:amd64 (1.8.1-1) ... Setting up libexpat1-dev:amd64 (2.5.0-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:amd64 (6.4-2) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up libproc2-0:amd64 (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:amd64 (2.1.28+dfsg-10) ... Setting up autoconf (2.71-3) ... Setting up ruby-webrick (1.8.1-1) ... Setting up liblzma-dev:amd64 (5.4.1-0.2) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up procps (2:4.0.2-3) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:amd64 (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 (3.0.8-1) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up libdeflate-dev:amd64 (1.14-1) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up ruby-xmlrpc (0.3.2-2) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.1+b3) ... 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:amd64 (3.1-20221030-2) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up bc (1.07.1-3+b1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up pkgconf:amd64 (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:amd64 (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:amd64 (3.11.2-6) ... Setting up libcurl3-gnutls:amd64 (7.88.1-7) ... Setting up rubygems-integration (1.18) ... Setting up libcurl4-gnutls-dev:amd64 (7.88.1-7) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libhts3:amd64 (1.16+ds-3) ... Setting up libpython3.11:amd64 (3.11.2-6) ... Setting up libhts-dev:amd64 (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:amd64 (3.11.2-6) ... Setting up python3-lib2to3 (3.11.2-2) ... Setting up python3-distutils (3.11.2-2) ... Setting up dh-python (5.20230130) ... Setting up libpython3-dev:amd64 (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:amd64 (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 (3.1.2-6) ... Setting up libruby3.1:amd64 (3.1.2-6) ... Setting up libruby:amd64 (1:3.1) ... Setting up ruby (1:3.1) ... Setting up yaggo (1.5.10-6) ... Setting up ruby-sdbm:amd64 (1.0.0-5+b1) ... Setting up ruby-rubygems (3.3.15-2) ... Processing triggers for libc-bin (2.36-8) ... 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: Running cd /build/jellyfish-2.3.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../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 amd64 debian/rules clean dh clean --with python3 debian/rules override_dh_clean make[1]: Entering directory '/build/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/jellyfish-2.3.0' debian/rules binary dh binary --with python3 debian/rules override_dh_update_autotools_config make[1]: Entering directory '/build/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/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/jellyfish-2.3.0' dh_auto_configure -- --enable-swig --enable-perl-binding --enable-htslib --enable-python-binding PYTHON=/usr/bin/python3 ./configure --build=x86_64-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/x86_64-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... x86_64-pc-linux-gnu checking host system type... x86_64-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 x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-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 -m elf_x86_64) 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 -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) 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 -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) 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 -m elf_x86_64) 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... no 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... 600f12:7000800:9eb82203:78bfbff checking for x86 cpuid 0x00000007 output... 0:0:0:0 checking for x86 cpuid 0x80000001 output... 600f12:0:10be7:2dd3fbff 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... yes checking whether FMA4 is supported by the processor and OS... yes checking whether C++ compiler accepts -mfma4... yes checking whether XOP is supported by the processor... yes checking whether XOP is supported by the processor and OS... yes checking whether C++ compiler accepts -mxop... yes 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... yes checking for std::numeric_limits<__int128>... yes 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/x86_64-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/x86_64-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/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -lpthread" -I/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0 -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-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/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/jellyfish-2.3.0' debian/rules override_dh_auto_build make[1]: Entering directory '/build/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/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/jellyfish-2.3.0' g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/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/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/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/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/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/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/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/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/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/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/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/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/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/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/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/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/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/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/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/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. 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'./'`swig/python/swig_wrap.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/include/python3.11 -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c swig/python/swig_wrap.cpp -fPIC -DPIC -o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/include/python3.11 -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c swig/python/swig_wrap.cpp -o swig/python/swig_python__dna_jellyfish_la-swig_wrap.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. 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-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: link: (cd "swig/python/.libs" && rm -f "_dna_jellyfish.so.0" && ln -s "_dna_jellyfish.so.0.0.0" "_dna_jellyfish.so.0") libtool: link: (cd "swig/python/.libs" && rm -f "_dna_jellyfish.so" && ln -s "_dna_jellyfish.so.0.0.0" "_dna_jellyfish.so") libtool: link: ar cr swig/python/.libs/_dna_jellyfish.a swig/python/swig_python__dna_jellyfish_la-swig_wrap.o libtool: link: ranlib swig/python/.libs/_dna_jellyfish.a libtool: link: ( cd "swig/python/.libs" && rm -f "_dna_jellyfish.la" && ln -s "../_dna_jellyfish.la" "_dna_jellyfish.la" ) /usr/bin/python3 -c 'import py_compile, sys; py_compile.compile(sys.argv[1], sys.argv[2])' swig/python/dna_jellyfish.py swig/python/__init__.pyc make[3]: Leaving directory '/build/jellyfish-2.3.0' g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 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-I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/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/jellyfish-2.3.0/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/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' || 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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/jellyfish-2.3.0/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/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/jellyfish-2.3.0/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/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/jellyfish-2.3.0/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/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/jellyfish-2.3.0/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/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/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/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 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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/jellyfish-2.3.0/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/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/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu ./.libs/libgtest.a -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/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/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -pthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu -lhts -R/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o bin/fastq2sam jellyfish/fastq2sam.o libjellyfish-2.0.la libtool: link: g++ -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/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/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu make[2]: Leaving directory '/build/jellyfish-2.3.0' dh_auto_install -- install-data make -j1 install DESTDIR=/build/jellyfish-2.3.0/debian/tmp AM_UPDATE_INFO_DIR=no install-data make[2]: Entering directory '/build/jellyfish-2.3.0' make install-am make[3]: Entering directory '/build/jellyfish-2.3.0' make[4]: Entering directory '/build/jellyfish-2.3.0' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-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/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-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/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/bin' /bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/build/jellyfish-2.3.0/debian/tmp/usr/bin' libtool: warning: 'libjellyfish-2.0.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c bin/.libs/jellyfish /build/jellyfish-2.3.0/debian/tmp/usr/bin/jellyfish /bin/mkdir -p '/build/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/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/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/jellyfish-2.3.0/debian/tmp/usr/share/man/man1/jellyfish.1' /bin/mkdir -p '/build/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/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/jellyfish-2.3.0; /bin/bash "/build/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/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/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/12/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/12 -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/12/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crtn.o -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/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.so.0.0.0 libtool: install: (cd /build/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/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/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/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: install: ranlib /build/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/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /bin/mkdir -p '/build/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/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/jellyfish-2.3.0; /bin/bash "/build/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/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/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/12/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/12 -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/12/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crtn.o -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/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/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/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/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/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/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/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' make[4]: Leaving directory '/build/jellyfish-2.3.0' make[3]: Leaving directory '/build/jellyfish-2.3.0' /bin/mkdir -p '/build/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/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/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/jellyfish-2.3.0/debian/tmp/usr/share/man/man1/jellyfish.1' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-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/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-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/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /bin/mkdir -p '/build/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/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/jellyfish-2.3.0; /bin/bash "/build/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/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/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/12/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/12 -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/12/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crtn.o -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/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.so.0.0.0 libtool: install: (cd /build/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/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/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/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: install: ranlib /build/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/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /bin/mkdir -p '/build/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/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/jellyfish-2.3.0; /bin/bash "/build/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/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/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/12/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/12 -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/12/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crtn.o -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/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/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/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/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/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/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/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' make[2]: Leaving directory '/build/jellyfish-2.3.0' dh_auto_build --sourcedirectory=swig/perl5 cd swig/perl5 && make -j16 make[2]: Entering directory '/build/jellyfish-2.3.0/swig/perl5' Running Mkbootstrap for jellyfish () g++ -c -std=c++0x -I/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0 -g -O2 -ffile-prefix-map=/build/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/x86_64-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 x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/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/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/jellyfish-2.3.0/.libs /build/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/jellyfish-2.3.0/.pybuild/cpython3_3.11_dna_jellyfish/build running build_ext building '_dna_jellyfish' extension creating build creating build/temp.linux-x86_64-3.11 x86_64-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/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/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-x86_64-3.11/swig_wrap.o -std=c++0x x86_64-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/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.11/swig_wrap.o -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu -L/build/jellyfish-2.3.0/.libs -ljellyfish-2.0 -lpthread -o /build/jellyfish-2.3.0/.pybuild/cpython3_3.11_dna_jellyfish/build/_dna_jellyfish.cpython-311-x86_64-linux-gnu.so -Wl,-rpath,/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu make[1]: Leaving directory '/build/jellyfish-2.3.0' debian/rules override_dh_auto_test make[1]: Entering directory '/build/jellyfish-2.3.0' dh_auto_test make -j16 check "TESTSUITEFLAGS=-j16 --verbose" VERBOSE=1 make[2]: Entering directory '/build/jellyfish-2.3.0' make check-am make[3]: Entering directory '/build/jellyfish-2.3.0' make bin/generate_sequence bin/fastq2sam bin/test_all libgtest.la libgtest_main.la make[4]: Entering directory '/build/jellyfish-2.3.0' make[4]: 'bin/generate_sequence' is up to date. make[4]: 'bin/fastq2sam' is up to date. make[4]: 'bin/test_all' is up to date. make[4]: 'libgtest.la' is up to date. /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 -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/gtest/src/libgtest_main_la-gtest_main.lo `test -f 'unit_tests/gtest/src/gtest_main.cc' || echo './'`unit_tests/gtest/src/gtest_main.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c unit_tests/gtest/src/gtest_main.cc -fPIC -DPIC -o unit_tests/gtest/src/.libs/libgtest_main_la-gtest_main.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c unit_tests/gtest/src/gtest_main.cc -o unit_tests/gtest/src/libgtest_main_la-gtest_main.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -pthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu -lhts -R/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o libgtest_main.la unit_tests/gtest/src/libgtest_main_la-gtest_main.lo libgtest.la libtool: link: (cd .libs/libgtest_main.lax/libgtest.a && ar x "/build/jellyfish-2.3.0/./.libs/libgtest.a") libtool: link: ar cr .libs/libgtest_main.a unit_tests/gtest/src/.libs/libgtest_main_la-gtest_main.o .libs/libgtest_main.lax/libgtest.a/libgtest_la-gtest-all.o libtool: link: ranlib .libs/libgtest_main.a libtool: link: rm -fr .libs/libgtest_main.lax libtool: link: ( cd ".libs" && rm -f "libgtest_main.la" && ln -s "../libgtest_main.la" "libgtest_main.la" ) make[4]: Leaving directory '/build/jellyfish-2.3.0' make check-TESTS make[4]: Entering directory '/build/jellyfish-2.3.0' make[5]: Entering directory '/build/jellyfish-2.3.0' SKIP: tests/big.sh PASS: tests/generate_sequence.sh SKIP: tests/swig_ruby.sh PASS: tests/subset_hashing.sh PASS: tests/swig_python.sh PASS: tests/bloom_filter.sh PASS: tests/bloom_counter.sh PASS: tests/multi_file.sh PASS: tests/sam.sh PASS: tests/large_key.sh PASS: tests/swig_perl.sh PASS: tests/parallel_hashing.sh PASS: tests/merge.sh PASS: tests/small_mers.sh PASS: unit_tests/unit_tests.sh ============================================================================ Testsuite summary for jellyfish 2.3.0 ============================================================================ # TOTAL: 15 # PASS: 13 # SKIP: 2 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/build/jellyfish-2.3.0' make[4]: Leaving directory '/build/jellyfish-2.3.0' make[3]: Leaving directory '/build/jellyfish-2.3.0' make[2]: Leaving directory '/build/jellyfish-2.3.0' make[1]: Leaving directory '/build/jellyfish-2.3.0' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/jellyfish-2.3.0' chrpath --delete bin/.libs/* dh_auto_install -- install-data make -j1 install DESTDIR=/build/jellyfish-2.3.0/debian/tmp AM_UPDATE_INFO_DIR=no install-data make[2]: Entering directory '/build/jellyfish-2.3.0' make install-am make[3]: Entering directory '/build/jellyfish-2.3.0' make[4]: Entering directory '/build/jellyfish-2.3.0' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-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/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-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/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/bin' /bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/build/jellyfish-2.3.0/debian/tmp/usr/bin' libtool: warning: 'libjellyfish-2.0.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c bin/.libs/jellyfish /build/jellyfish-2.3.0/debian/tmp/usr/bin/jellyfish /bin/mkdir -p '/build/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/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/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/jellyfish-2.3.0/debian/tmp/usr/share/man/man1/jellyfish.1' /bin/mkdir -p '/build/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/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/jellyfish-2.3.0; /bin/bash "/build/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/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/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/12/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/12 -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/12/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crtn.o -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/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.so.0.0.0 libtool: install: (cd /build/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/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/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/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: install: ranlib /build/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/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /bin/mkdir -p '/build/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/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/jellyfish-2.3.0; /bin/bash "/build/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/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/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/12/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/12 -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/12/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crtn.o -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/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/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/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/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/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/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/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' make[4]: Leaving directory '/build/jellyfish-2.3.0' make[3]: Leaving directory '/build/jellyfish-2.3.0' /bin/mkdir -p '/build/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/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/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/jellyfish-2.3.0/debian/tmp/usr/share/man/man1/jellyfish.1' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-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/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-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/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /bin/mkdir -p '/build/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/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/jellyfish-2.3.0; /bin/bash "/build/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/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/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/12/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/12 -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/12/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crtn.o -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/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.so.0.0.0 libtool: install: (cd /build/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/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/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/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: install: ranlib /build/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/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /bin/mkdir -p '/build/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/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/jellyfish-2.3.0; /bin/bash "/build/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/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/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/12/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/12 -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/12/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crtn.o -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/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/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/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/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/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/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/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' make[2]: Leaving directory '/build/jellyfish-2.3.0' dh_auto_install --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py install --root /build/jellyfish-2.3.0/debian/python3-dna-jellyfish /build/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/jellyfish-2.3.0/debian/python3-dna-jellyfish creating /build/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr creating /build/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib creating /build/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib/python3.11 creating /build/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib/python3.11/dist-packages copying /build/jellyfish-2.3.0/.pybuild/cpython3_3.11_dna_jellyfish/build/_dna_jellyfish.cpython-311-x86_64-linux-gnu.so -> /build/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib/python3.11/dist-packages copying /build/jellyfish-2.3.0/.pybuild/cpython3_3.11_dna_jellyfish/build/dna_jellyfish.py -> /build/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib/python3.11/dist-packages byte-compiling /build/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/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 -j16 install DESTDIR=/build/jellyfish-2.3.0/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr make[2]: Entering directory '/build/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/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.36/auto/jellyfish/jellyfish.so make[2]: Leaving directory '/build/jellyfish-2.3.0/swig/perl5' ls -l debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so -r-xr-xr-x 1 pbuilder1 pbuilder1 1133952 May 15 18:55 debian/tmp/usr/lib/x86_64-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/x86_64-linux-gnu install -d -m 755 debian/libjellyfish-2.0-2/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a debian/libjellyfish-2.0-dev/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.la debian/libjellyfish-2.0-dev/usr/lib/x86_64-linux-gnu || true mv debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so debian/libjellyfish-2.0-dev/usr/lib/x86_64-linux-gnu mv /build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2 debian/libjellyfish-2.0-2/usr/lib/x86_64-linux-gnu mv /build/jellyfish-2.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 debian/libjellyfish-2.0-2/usr/lib/x86_64-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/x86_64-linux-gnu/*.la chrpath --delete debian/*/usr/lib/python*/dist-packages/_dna_jellyfish*.so make[1]: Leaving directory '/build/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/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/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 'jellyfish' in '../jellyfish_2.3.0-15_amd64.deb'. dpkg-deb: building package 'jellyfish-dbgsym' in '../jellyfish-dbgsym_2.3.0-15_amd64.deb'. dpkg-deb: building package 'libjellyfish-2.0-2' in '../libjellyfish-2.0-2_2.3.0-15_amd64.deb'. dpkg-deb: building package 'libjellyfish-2.0-2-dbgsym' in '../libjellyfish-2.0-2-dbgsym_2.3.0-15_amd64.deb'. dpkg-deb: building package 'python3-dna-jellyfish' in '../python3-dna-jellyfish_2.3.0-15_amd64.deb'. dpkg-deb: building package 'python3-dna-jellyfish-dbgsym' in '../python3-dna-jellyfish-dbgsym_2.3.0-15_amd64.deb'. dpkg-deb: building package 'libjellyfish-2.0-dev' in '../libjellyfish-2.0-dev_2.3.0-15_amd64.deb'. dpkg-deb: building package 'libjellyfish-perl' in '../libjellyfish-perl_2.3.0-15_amd64.deb'. dpkg-deb: building package 'libjellyfish-perl-dbgsym' in '../libjellyfish-perl-dbgsym_2.3.0-15_amd64.deb'. dpkg-deb: building package 'jellyfish-examples' in '../jellyfish-examples_2.3.0-15_all.deb'. dpkg-genbuildinfo --build=binary -O../jellyfish_2.3.0-15_amd64.buildinfo dpkg-genchanges --build=binary -O../jellyfish_2.3.0-15_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/114346 and its subdirectories I: Current time: Wed May 15 18:57:26 -12 2024 I: pbuilder-time-stamp: 1715842646 Fri Apr 14 00:34:26 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Fri Apr 14 00:34:26 UTC 2023 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Fri Apr 14 00:59:35 UTC 2023 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Fri Apr 14 00:59:36 UTC 2023 I: jellyfish_2.3.0-15_amd64.changes: Format: 1.8 Date: Wed, 28 Sep 2022 21:48:56 +0200 Source: jellyfish Binary: jellyfish jellyfish-dbgsym jellyfish-examples libjellyfish-2.0-2 libjellyfish-2.0-2-dbgsym libjellyfish-2.0-dev libjellyfish-perl libjellyfish-perl-dbgsym python3-dna-jellyfish python3-dna-jellyfish-dbgsym Architecture: amd64 all Version: 2.3.0-15 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: jellyfish - count k-mers in DNA sequences jellyfish-examples - count k-mers in DNA sequences (examples for testing) libjellyfish-2.0-2 - count k-mers in DNA sequences (dynamic library of jellyfish) libjellyfish-2.0-dev - count k-mers in DNA sequences (development files of jellyfish) libjellyfish-perl - count k-mers in DNA sequences (Perl bindings of jellyfish) python3-dna-jellyfish - count k-mers in DNA sequences (Python bindings of jellyfish) Closes: 1017261 Changes: jellyfish (2.3.0-15) unstable; urgency=medium . * Fix dh_missing Closes: #1017261 Checksums-Sha1: 2d6f4870d313a6920faf18ebeb746cced961d543 8442780 jellyfish-dbgsym_2.3.0-15_amd64.deb a635444e1265f8c170da736d6406eb5e98d81105 12964 jellyfish-examples_2.3.0-15_all.deb 066f275d280dfe9f0f403252cfb7a731beebd3c8 10253 jellyfish_2.3.0-15_amd64.buildinfo f29e4575f47cbf505e73dbb42f418aca10720f7b 789028 jellyfish_2.3.0-15_amd64.deb c549f5feed7f50d68d98ffefd427ecb2d5081168 545692 libjellyfish-2.0-2-dbgsym_2.3.0-15_amd64.deb e0258a46111befa6e93351bb779520aa4d952d69 62860 libjellyfish-2.0-2_2.3.0-15_amd64.deb 7a5649c808b3db661490f7e36e86ef3fb1a32b28 135272 libjellyfish-2.0-dev_2.3.0-15_amd64.deb bbcaa1a8c249eccda13860da82251bc71379a372 355524 libjellyfish-perl-dbgsym_2.3.0-15_amd64.deb 9d8ca736f2f4a1d32b2b8931510e94d73a9d25b7 53940 libjellyfish-perl_2.3.0-15_amd64.deb 42fb5fcc2224c05988b5b1f13a59d2ce1c73fd10 338128 python3-dna-jellyfish-dbgsym_2.3.0-15_amd64.deb 3f83be69bf8f7fa0743537b3a7050ab8e35b2fb9 53024 python3-dna-jellyfish_2.3.0-15_amd64.deb Checksums-Sha256: 24907f9c5a2b48bfc99403326c69bc050944db0c62bde0c70af724971a8b6b7a 8442780 jellyfish-dbgsym_2.3.0-15_amd64.deb 3c0cccc3f6e059a379fb08934e815e5352993636c3f527fc30251b2504eb97d0 12964 jellyfish-examples_2.3.0-15_all.deb f92652715d0d76beb2a9b5a9a2d47c04a6c72a3c0fe85503b7b242e176984de6 10253 jellyfish_2.3.0-15_amd64.buildinfo c54a28bf6e10ad1be04ef8a9d2e689c74cc23b01aad579b4bf2ffae53b35988c 789028 jellyfish_2.3.0-15_amd64.deb 307831c972b1f413bf2d3c81f0c729da42863b12250d3b87ea12888bffb0bce4 545692 libjellyfish-2.0-2-dbgsym_2.3.0-15_amd64.deb d722b1bbd0f10caeb280f49eaf0cae3ad6a914d3702473daac232c6729df05fe 62860 libjellyfish-2.0-2_2.3.0-15_amd64.deb 2d2b9efb250013c9c161af3bcfbdb58570a74683d83727c39fd9b40bc22d36ba 135272 libjellyfish-2.0-dev_2.3.0-15_amd64.deb 4a0ffb3a28f892cb3a982e874dc67ab108a4fac925af3ee2b3800bad64f67477 355524 libjellyfish-perl-dbgsym_2.3.0-15_amd64.deb 510ce2df2f603a22665ac376c20bee913859cf74cf753061e9d159b16a306830 53940 libjellyfish-perl_2.3.0-15_amd64.deb 3a7368ea7a56c7ca2843a4f42b5348adff084b53284940a6f126db7b87ce8473 338128 python3-dna-jellyfish-dbgsym_2.3.0-15_amd64.deb eedb8938031000d91cd3cc4e22add6680275c3dead676580c89927309ad66ca4 53024 python3-dna-jellyfish_2.3.0-15_amd64.deb Files: 8e88189d31f60781771e4bbf082b913f 8442780 debug optional jellyfish-dbgsym_2.3.0-15_amd64.deb 02d5ceb4636a832fc4a8e27cbc6c2706 12964 science optional jellyfish-examples_2.3.0-15_all.deb b2008c68602486c441622afc1a946c8d 10253 science optional jellyfish_2.3.0-15_amd64.buildinfo 86d6be4337c2eb160757dd204416c1d2 789028 science optional jellyfish_2.3.0-15_amd64.deb a9bb07f14693814e03de2d87ae3184b5 545692 debug optional libjellyfish-2.0-2-dbgsym_2.3.0-15_amd64.deb d96d51228b30ae72a44ebd493d8ed9b0 62860 libs optional libjellyfish-2.0-2_2.3.0-15_amd64.deb 498aaede1e61d5fb9c4bd0f3cb6151ee 135272 libdevel optional libjellyfish-2.0-dev_2.3.0-15_amd64.deb 2896ecba7e218e1756aee825a65c0f33 355524 debug optional libjellyfish-perl-dbgsym_2.3.0-15_amd64.deb b40a489e75bbc0423ea21c5e4aa70784 53940 perl optional libjellyfish-perl_2.3.0-15_amd64.deb cb4ca6e35f2da5cd8c2be10494506a97 338128 debug optional python3-dna-jellyfish-dbgsym_2.3.0-15_amd64.deb 57e0fd3c1df129d8aba5d741f8074e97 53024 python optional python3-dna-jellyfish_2.3.0-15_amd64.deb Fri Apr 14 00:59:37 UTC 2023 I: diffoscope 240 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.sGP9g9ZZ/jellyfish_2.3.0-15.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.sGP9g9ZZ/jellyfish_2.3.0-15.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.sGP9g9ZZ/jellyfish_2.3.0-15.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.sGP9g9ZZ/b1/jellyfish_2.3.0-15_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.sGP9g9ZZ/b2/jellyfish_2.3.0-15_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.664s) 0.664s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.343s) 0.343s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.001s) 0.001s 1 call specialize Fri Apr 14 00:59:39 UTC 2023 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists. Fri Apr 14 00:59:39 UTC 2023 I: jellyfish from bookworm built successfully and reproducibly on amd64. Fri Apr 14 00:59:45 UTC 2023 I: Submitting .buildinfo files to external archives: Fri Apr 14 00:59:45 UTC 2023 I: Submitting 12K b1/jellyfish_2.3.0-15_amd64.buildinfo.asc Fri Apr 14 00:59:46 UTC 2023 I: Submitting 12K b2/jellyfish_2.3.0-15_amd64.buildinfo.asc Fri Apr 14 00:59:47 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Apr 14 00:59:47 UTC 2023 I: Done submitting .buildinfo files. Fri Apr 14 00:59:47 UTC 2023 I: Removing signed jellyfish_2.3.0-15_amd64.buildinfo.asc files: removed './b1/jellyfish_2.3.0-15_amd64.buildinfo.asc' removed './b2/jellyfish_2.3.0-15_amd64.buildinfo.asc'