Thu Aug 26 23:33:08 UTC 2021 I: starting to build jellyfish/bullseye/arm64 on jenkins on '2021-08-26 23:32' Thu Aug 26 23:33:08 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_27/24695/console.log Thu Aug 26 23:33:08 UTC 2021 I: Downloading source for bullseye/jellyfish=2.3.0-10 --2021-08-26 23:33:08-- http://cdn-fastly.deb.debian.org/debian/pool/main/j/jellyfish/jellyfish_2.3.0-10.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 3173 (3.1K) Saving to: ‘jellyfish_2.3.0-10.dsc’ 0K ... 100% 2.83M=0.001s 2021-08-26 23:33:08 (2.83 MB/s) - ‘jellyfish_2.3.0-10.dsc’ saved [3173/3173] Thu Aug 26 23:33:08 UTC 2021 I: jellyfish_2.3.0-10.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: 2.3.0-10 Maintainer: Debian Med Packaging Team Uploaders: Shaun Jackman , Andreas Tille , Michael R. Crusoe Homepage: https://www.cbcb.umd.edu/software/jellyfish/ Standards-Version: 4.5.1 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, 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 060f1f4e4f1bece35b4f2886b0df048a37137394 14156 jellyfish_2.3.0-10.debian.tar.xz Checksums-Sha256: 29ead991de90151dbe4a2717f7ac30b3852296c9cbdda8b001121a1f2fa714db 679125 jellyfish_2.3.0.orig.tar.gz 03124b01ea7e8cd20966a6929548f7b4b1e962a3c74d2100e621a730850ce285 14156 jellyfish_2.3.0-10.debian.tar.xz Files: b447a26df0f1e11526129907a9b0acdb 679125 jellyfish_2.3.0.orig.tar.gz 6cea78aed1840960a7f42a870ece839f 14156 jellyfish_2.3.0-10.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmA+LTwRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEP9BAAhXN5a8O7tH8gnSDkWn7aDedHLoEyJiDY 9DY2VaGEl+XU0M1RGLbAeoBhoSP4pCUfZNRs/ZoIPC03pRfO/PNVpNE0r6gQV7DB 11iXb2EeaeBmX+SVbPxq/WniMHEB/olXkZOqZDEJCjcCl1UQ1WYOUvZSO+75zyIx qAWIJGMcYWjpVs8Dd/3PRn4qTKSvKeWvQz55vc1fLXDvoJZiONTAG++EMbnB78ej uZKib/NZmWREXThyXqJbycNEwYWG3RziGyQft4rCAMXc2NNbIh1GWISoayGXIPhV opJalX5MK2+suNYdD2EQrNN1jck7MQ7zxwxCVkZhMr2xGM+XqtPfkdO5hom0DJWh 5C9u4UPJK4tTqcwDEATq1dpo+Zy04+Q7/tSIwsEkdeHteWF7KVItrGL7reUG/osT 1BUcmxICJVTYC6v4zZ6CGlaVLScgubQrFxVNlYmZHOq1d/1Q4bkKPVSLmf0nRg6t OZwrOavZpvH30hCNdEiZQCqDipcT2ozA/3X017JnHItS4l0G33VNLsP1q4G0CGol 0LsA8Xk3r0L8W/9H0+ENNDjYnnRzJoJOivXkh9jYRDPzfp7IGRK3EnVK1GhBdTIu RYbEDxpyyEv3w0dGImaVWJz/1D+L8tPQMrymuJHE6NiCDAkknZRfy/lAOW/38equ kazfStcGsVs= =0ZQL -----END PGP SIGNATURE----- Thu Aug 26 23:33:08 UTC 2021 I: Checking whether the package is not for us Thu Aug 26 23:33:08 UTC 2021 I: Starting 1st build on remote node codethink15-arm64.debian.net. Thu Aug 26 23:33:08 UTC 2021 I: Preparing to do remote build '1' on codethink15-arm64.debian.net. Thu Aug 26 23:53:21 UTC 2021 I: Deleting $TMPDIR on codethink15-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Sep 28 17:56:10 -12 2022 I: pbuilder-time-stamp: 1664430970 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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_2.3.0-10.dsc] I: copying [./jellyfish_2.3.0.orig.tar.gz] I: copying [./jellyfish_2.3.0-10.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.8teO97Ro/trustedkeys.kbx': General error gpgv: Signature made Tue Mar 2 00:19:08 2021 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./jellyfish_2.3.0-10.dsc 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_2.3.0-10.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/5875/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='5875' 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/tmp.9mrsrwZbHh/pbuilderrc_y01w --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.9mrsrwZbHh/b1 --logfile b1/build.log jellyfish_2.3.0-10.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink15-arm64 4.15.0-154-generic #161-Ubuntu SMP Fri Jul 30 13:01:15 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Aug 4 2021 bash -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 14264 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 39832 Sep 22 2020 cat -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash -rwxr-xr-x 1 root root 101384 Sep 22 2020 date -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd -rwxr-xr-x 1 root root 89824 Sep 22 2020 df -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir -rwxr-xr-x 1 root root 76152 Jul 28 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 35632 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 64856 Jul 28 2021 findmnt -rwsr-xr-x 1 root root 34824 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 178400 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 93744 Mar 2 2021 gzip -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln -rwxr-xr-x 1 root root 52720 Feb 7 2020 login -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls -rwxr-xr-x 1 root root 161960 Jul 28 2021 lsblk -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 51368 Jul 28 2021 more -rwsr-xr-x 1 root root 51360 Jul 28 2021 mount -rwxr-xr-x 1 root root 14496 Jul 28 2021 mountpoint -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Sep 23 03:47 sh -> dash -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty -rwsr-xr-x 1 root root 67776 Jul 28 2021 su -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync -rwxr-xr-x 1 root root 535768 Feb 16 2021 tar -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch -rwxr-xr-x 1 root root 31512 Sep 22 2020 true -rwxr-xr-x 1 root root 14264 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 30880 Jul 28 2021 umount -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir -rwxr-xr-x 1 root root 59584 Jul 28 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/5875/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), d-shlibs, 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 ... 19646 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 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} 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} libglib2.0-0{a} libhts-dev{a} libhts3{a} libicu67{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libldap-2.4-2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libmpdec3{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libprocps8{a} libpsl5{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.9{a} libpython3.9-dev{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librtmp1{a} libruby2.7{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{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} 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} python3.9{a} python3.9-dev{a} python3.9-minimal{a} rake{a} readline-common{a} ruby{a} ruby-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-rubygems{a} ruby-test-unit{a} ruby-xmlrpc{a} ruby2.7{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 libglib2.0-data libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix shared-mime-info wget xdg-user-dirs zip 0 packages upgraded, 105 newly installed, 0 to remove and 0 not upgraded. Need to get 48.0 MB of archives. After unpacking 167 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-8 [142 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-minimal arm64 3.9.2-1 [797 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libexpat1 arm64 2.2.10-2 [83.1 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 python3.9-minimal arm64 3.9.2-1 [1884 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 python3-minimal arm64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 libmpdec3 arm64 2.5.1-1 [84.4 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 libreadline8 arm64 8.1-1 [160 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-stdlib arm64 3.9.2-1 [1658 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 python3.9 arm64 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 libpython3-stdlib arm64 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 python3 arm64 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 libncurses6 arm64 6.2+20201114-2 [93.2 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 libprocps8 arm64 2:3.3.17-5 [61.9 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 procps arm64 2:3.3.17-5 [497 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 openssl arm64 1.1.1k-1 [829 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 ca-certificates all 20210119 [158 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 bc arm64 1.07.1-2+b2 [107 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 chrpath arm64 0.16-2+b1 [16.0 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 d-shlibs all 0.98 [17.9 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 49 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 50 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 51 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 52 http://deb.debian.org/debian bullseye/main arm64 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 53 http://deb.debian.org/debian bullseye/main arm64 python3-distutils all 3.9.2-1 [143 kB] Get: 54 http://deb.debian.org/debian bullseye/main arm64 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 55 http://deb.debian.org/debian bullseye/main arm64 dos2unix arm64 7.4.1-1 [391 kB] Get: 56 http://deb.debian.org/debian bullseye/main arm64 libbrotli1 arm64 1.0.9-2+b2 [267 kB] Get: 57 http://deb.debian.org/debian bullseye/main arm64 libmd0 arm64 1.0.3-3 [27.9 kB] Get: 58 http://deb.debian.org/debian bullseye/main arm64 libbsd0 arm64 0.11.3-1 [106 kB] Get: 59 http://deb.debian.org/debian bullseye/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2.1 [69.3 kB] Get: 60 http://deb.debian.org/debian bullseye/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2.1 [105 kB] Get: 61 http://deb.debian.org/debian bullseye/main arm64 libldap-2.4-2 arm64 2.4.57+dfsg-3 [222 kB] Get: 62 http://deb.debian.org/debian bullseye/main arm64 libnghttp2-14 arm64 1.43.0-1 [73.8 kB] Get: 63 http://deb.debian.org/debian bullseye/main arm64 libpsl5 arm64 0.21.0-1.2 [57.1 kB] Get: 64 http://deb.debian.org/debian bullseye/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 65 http://deb.debian.org/debian bullseye/main arm64 libssh2-1 arm64 1.9.0-2 [150 kB] Get: 66 http://deb.debian.org/debian bullseye/main arm64 libcurl3-gnutls arm64 7.74.0-1.3+b1 [318 kB] Get: 67 http://deb.debian.org/debian bullseye/main arm64 libcurl4-gnutls-dev arm64 7.74.0-1.3+b1 [419 kB] Get: 68 http://deb.debian.org/debian bullseye/main arm64 libdeflate0 arm64 1.7-1 [47.7 kB] Get: 69 http://deb.debian.org/debian bullseye/main arm64 libdeflate-dev arm64 1.7-1 [44.5 kB] Get: 70 http://deb.debian.org/debian bullseye/main arm64 libedit2 arm64 3.1-20191231-2+b1 [92.1 kB] Get: 71 http://deb.debian.org/debian bullseye/main arm64 libexpat1-dev arm64 2.2.10-2 [126 kB] Get: 72 http://deb.debian.org/debian bullseye/main arm64 libglib2.0-0 arm64 2.66.8-1 [1286 kB] Get: 73 http://deb.debian.org/debian bullseye/main arm64 libhts3 arm64 1.11-4 [346 kB] Get: 74 http://deb.debian.org/debian bullseye/main arm64 liblzma-dev arm64 5.2.5-2 [227 kB] Get: 75 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB] Get: 76 http://deb.debian.org/debian bullseye/main arm64 libhts-dev arm64 1.11-4 [3856 kB] Get: 77 http://deb.debian.org/debian bullseye/main arm64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 78 http://deb.debian.org/debian bullseye/main arm64 libjs-underscore all 1.9.1~dfsg-3 [100 kB] Get: 79 http://deb.debian.org/debian bullseye/main arm64 libjs-sphinxdoc all 3.4.3-2 [127 kB] Get: 80 http://deb.debian.org/debian bullseye/main arm64 libpython3.9 arm64 3.9.2-1 [1556 kB] Get: 81 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-dev arm64 3.9.2-1 [3835 kB] Get: 82 http://deb.debian.org/debian bullseye/main arm64 libpython3-dev arm64 3.9.2-3 [21.7 kB] Get: 83 http://deb.debian.org/debian bullseye/main arm64 libpython3-all-dev arm64 3.9.2-3 [1068 B] Get: 84 http://deb.debian.org/debian bullseye/main arm64 rubygems-integration all 1.18 [6704 B] Get: 85 http://deb.debian.org/debian bullseye/main arm64 ruby2.7 arm64 2.7.4-1 [747 kB] Get: 86 http://deb.debian.org/debian bullseye/main arm64 ruby-rubygems all 3.2.5-2 [281 kB] Get: 87 http://deb.debian.org/debian bullseye/main arm64 ruby arm64 1:2.7+2 [11.7 kB] Get: 88 http://deb.debian.org/debian bullseye/main arm64 rake all 13.0.3-1 [84.7 kB] Get: 89 http://deb.debian.org/debian bullseye/main arm64 ruby-minitest all 5.13.0-1 [57.3 kB] Get: 90 http://deb.debian.org/debian bullseye/main arm64 ruby-net-telnet all 0.1.1-2 [12.5 kB] Get: 91 http://deb.debian.org/debian bullseye/main arm64 ruby-power-assert all 1.1.7-2 [11.5 kB] Get: 92 http://deb.debian.org/debian bullseye/main arm64 ruby-test-unit all 3.3.9-1 [86.1 kB] Get: 93 http://deb.debian.org/debian bullseye/main arm64 ruby-xmlrpc all 0.3.0-2 [23.7 kB] Get: 94 http://deb.debian.org/debian bullseye/main arm64 libyaml-0-2 arm64 0.2.2-1 [45.1 kB] Get: 95 http://deb.debian.org/debian bullseye/main arm64 libruby2.7 arm64 2.7.4-1 [4031 kB] Get: 96 http://deb.debian.org/debian bullseye/main arm64 pkg-config arm64 0.29.2-1 [63.6 kB] Get: 97 http://deb.debian.org/debian bullseye/main arm64 python3-all arm64 3.9.2-3 [1056 B] Get: 98 http://deb.debian.org/debian bullseye/main arm64 python3.9-dev arm64 3.9.2-1 [515 kB] Get: 99 http://deb.debian.org/debian bullseye/main arm64 python3-dev arm64 3.9.2-3 [24.8 kB] Get: 100 http://deb.debian.org/debian bullseye/main arm64 python3-all-dev arm64 3.9.2-3 [1064 B] Get: 101 http://deb.debian.org/debian bullseye/main arm64 samtools arm64 1.11-1 [526 kB] Get: 102 http://deb.debian.org/debian bullseye/main arm64 swig4.0 arm64 4.0.2-1 [1295 kB] Get: 103 http://deb.debian.org/debian bullseye/main arm64 swig all 4.0.2-1 [330 kB] Get: 104 http://deb.debian.org/debian bullseye/main arm64 time arm64 1.9-0.1 [50.6 kB] Get: 105 http://deb.debian.org/debian bullseye/main arm64 yaggo all 1.5.10-2 [18.9 kB] Fetched 48.0 MB in 5s (9871 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19646 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8_arm64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../1-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_arm64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../3-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libpython3.9-minimal:arm64. Preparing to unpack .../5-libpython3.9-minimal_3.9.2-1_arm64.deb ... Unpacking libpython3.9-minimal:arm64 (3.9.2-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../6-libexpat1_2.2.10-2_arm64.deb ... Unpacking libexpat1:arm64 (2.2.10-2) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../7-python3.9-minimal_3.9.2-1_arm64.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:arm64 (3.9.2-1) ... Setting up libexpat1:arm64 (2.2.10-2) ... Setting up python3.9-minimal (3.9.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20513 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_arm64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:arm64. Preparing to unpack .../2-libmpdec3_2.5.1-1_arm64.deb ... Unpacking libmpdec3:arm64 (2.5.1-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../3-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../4-libreadline8_8.1-1_arm64.deb ... Unpacking libreadline8:arm64 (8.1-1) ... Selecting previously unselected package libpython3.9-stdlib:arm64. Preparing to unpack .../5-libpython3.9-stdlib_3.9.2-1_arm64.deb ... Unpacking libpython3.9-stdlib:arm64 (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../6-python3.9_3.9.2-1_arm64.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../7-libpython3-stdlib_3.9.2-3_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... 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 ... 20934 files and directories currently installed.) Preparing to unpack .../00-python3_3.9.2-3_arm64.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../01-libncurses6_6.2+20201114-2_arm64.deb ... Unpacking libncurses6:arm64 (6.2+20201114-2) ... Selecting previously unselected package libprocps8:arm64. Preparing to unpack .../02-libprocps8_2%3a3.3.17-5_arm64.deb ... Unpacking libprocps8:arm64 (2:3.3.17-5) ... Selecting previously unselected package procps. Preparing to unpack .../03-procps_2%3a3.3.17-5_arm64.deb ... Unpacking procps (2:3.3.17-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../04-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package openssl. Preparing to unpack .../05-openssl_1.1.1k-1_arm64.deb ... Unpacking openssl (1.1.1k-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../06-ca-certificates_20210119_all.deb ... Unpacking ca-certificates (20210119) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.39-3_arm64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../08-libmagic1_1%3a5.39-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.39-3_arm64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.21-4_arm64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../11-libsigsegv2_2.13-1_arm64.deb ... Unpacking libsigsegv2:arm64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-5_arm64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package bc. Preparing to unpack .../17-bc_1.07.1-2+b2_arm64.deb ... Unpacking bc (1.07.1-2+b2) ... Selecting previously unselected package chrpath. Preparing to unpack .../18-chrpath_0.16-2+b1_arm64.deb ... Unpacking chrpath (0.16-2+b1) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../19-d-shlibs_0.98_all.deb ... Unpacking d-shlibs (0.98) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../20-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../21-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../22-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../23-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 .../24-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../25-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../26-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../27-libelf1_0.183-1_arm64.deb ... Unpacking libelf1:arm64 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../28-dwz_0.13+20210201-1_arm64.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:arm64. Preparing to unpack .../29-libicu67_67.1-7_arm64.deb ... Unpacking libicu67:arm64 (67.1-7) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../30-libxml2_2.9.10+dfsg-6.7_arm64.deb ... Unpacking libxml2:arm64 (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../31-gettext_0.21-4_arm64.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../32-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../33-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../34-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../35-python3-lib2to3_3.9.2-1_all.deb ... Unpacking python3-lib2to3 (3.9.2-1) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../36-python3-distutils_3.9.2-1_all.deb ... Unpacking python3-distutils (3.9.2-1) ... Selecting previously unselected package dh-python. Preparing to unpack .../37-dh-python_4.20201102+nmu1_all.deb ... Unpacking dh-python (4.20201102+nmu1) ... Selecting previously unselected package dos2unix. Preparing to unpack .../38-dos2unix_7.4.1-1_arm64.deb ... Unpacking dos2unix (7.4.1-1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../39-libbrotli1_1.0.9-2+b2_arm64.deb ... Unpacking libbrotli1:arm64 (1.0.9-2+b2) ... Selecting previously unselected package libmd0:arm64. Preparing to unpack .../40-libmd0_1.0.3-3_arm64.deb ... Unpacking libmd0:arm64 (1.0.3-3) ... Selecting previously unselected package libbsd0:arm64. Preparing to unpack .../41-libbsd0_0.11.3-1_arm64.deb ... Unpacking libbsd0:arm64 (0.11.3-1) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../42-libsasl2-modules-db_2.1.27+dfsg-2.1_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.27+dfsg-2.1) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../43-libsasl2-2_2.1.27+dfsg-2.1_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.27+dfsg-2.1) ... Selecting previously unselected package libldap-2.4-2:arm64. Preparing to unpack .../44-libldap-2.4-2_2.4.57+dfsg-3_arm64.deb ... Unpacking libldap-2.4-2:arm64 (2.4.57+dfsg-3) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../45-libnghttp2-14_1.43.0-1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.43.0-1) ... Selecting previously unselected package libpsl5:arm64. Preparing to unpack .../46-libpsl5_0.21.0-1.2_arm64.deb ... Unpacking libpsl5:arm64 (0.21.0-1.2) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../47-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:arm64. Preparing to unpack .../48-libssh2-1_1.9.0-2_arm64.deb ... Unpacking libssh2-1:arm64 (1.9.0-2) ... Selecting previously unselected package libcurl3-gnutls:arm64. Preparing to unpack .../49-libcurl3-gnutls_7.74.0-1.3+b1_arm64.deb ... Unpacking libcurl3-gnutls:arm64 (7.74.0-1.3+b1) ... Selecting previously unselected package libcurl4-gnutls-dev:arm64. Preparing to unpack .../50-libcurl4-gnutls-dev_7.74.0-1.3+b1_arm64.deb ... Unpacking libcurl4-gnutls-dev:arm64 (7.74.0-1.3+b1) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../51-libdeflate0_1.7-1_arm64.deb ... Unpacking libdeflate0:arm64 (1.7-1) ... Selecting previously unselected package libdeflate-dev:arm64. Preparing to unpack .../52-libdeflate-dev_1.7-1_arm64.deb ... Unpacking libdeflate-dev:arm64 (1.7-1) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../53-libedit2_3.1-20191231-2+b1_arm64.deb ... Unpacking libedit2:arm64 (3.1-20191231-2+b1) ... Selecting previously unselected package libexpat1-dev:arm64. Preparing to unpack .../54-libexpat1-dev_2.2.10-2_arm64.deb ... Unpacking libexpat1-dev:arm64 (2.2.10-2) ... Selecting previously unselected package libglib2.0-0:arm64. Preparing to unpack .../55-libglib2.0-0_2.66.8-1_arm64.deb ... Unpacking libglib2.0-0:arm64 (2.66.8-1) ... Selecting previously unselected package libhts3:arm64. Preparing to unpack .../56-libhts3_1.11-4_arm64.deb ... Unpacking libhts3:arm64 (1.11-4) ... Selecting previously unselected package liblzma-dev:arm64. Preparing to unpack .../57-liblzma-dev_5.2.5-2_arm64.deb ... Unpacking liblzma-dev:arm64 (5.2.5-2) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../58-zlib1g-dev_1%3a1.2.11.dfsg-2_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.2.11.dfsg-2) ... Selecting previously unselected package libhts-dev:arm64. Preparing to unpack .../59-libhts-dev_1.11-4_arm64.deb ... Unpacking libhts-dev:arm64 (1.11-4) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../60-libjs-jquery_3.5.1+dfsg+~3.5.5-7_all.deb ... Unpacking libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../61-libjs-underscore_1.9.1~dfsg-3_all.deb ... Unpacking libjs-underscore (1.9.1~dfsg-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../62-libjs-sphinxdoc_3.4.3-2_all.deb ... Unpacking libjs-sphinxdoc (3.4.3-2) ... Selecting previously unselected package libpython3.9:arm64. Preparing to unpack .../63-libpython3.9_3.9.2-1_arm64.deb ... Unpacking libpython3.9:arm64 (3.9.2-1) ... Selecting previously unselected package libpython3.9-dev:arm64. Preparing to unpack .../64-libpython3.9-dev_3.9.2-1_arm64.deb ... Unpacking libpython3.9-dev:arm64 (3.9.2-1) ... Selecting previously unselected package libpython3-dev:arm64. Preparing to unpack .../65-libpython3-dev_3.9.2-3_arm64.deb ... Unpacking libpython3-dev:arm64 (3.9.2-3) ... Selecting previously unselected package libpython3-all-dev:arm64. Preparing to unpack .../66-libpython3-all-dev_3.9.2-3_arm64.deb ... Unpacking libpython3-all-dev:arm64 (3.9.2-3) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../67-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package ruby2.7. Preparing to unpack .../68-ruby2.7_2.7.4-1_arm64.deb ... Unpacking ruby2.7 (2.7.4-1) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../69-ruby-rubygems_3.2.5-2_all.deb ... Unpacking ruby-rubygems (3.2.5-2) ... Selecting previously unselected package ruby. Preparing to unpack .../70-ruby_1%3a2.7+2_arm64.deb ... Unpacking ruby (1:2.7+2) ... Selecting previously unselected package rake. Preparing to unpack .../71-rake_13.0.3-1_all.deb ... Unpacking rake (13.0.3-1) ... Selecting previously unselected package ruby-minitest. Preparing to unpack .../72-ruby-minitest_5.13.0-1_all.deb ... Unpacking ruby-minitest (5.13.0-1) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../73-ruby-net-telnet_0.1.1-2_all.deb ... Unpacking ruby-net-telnet (0.1.1-2) ... Selecting previously unselected package ruby-power-assert. Preparing to unpack .../74-ruby-power-assert_1.1.7-2_all.deb ... Unpacking ruby-power-assert (1.1.7-2) ... Selecting previously unselected package ruby-test-unit. Preparing to unpack .../75-ruby-test-unit_3.3.9-1_all.deb ... Unpacking ruby-test-unit (3.3.9-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../76-ruby-xmlrpc_0.3.0-2_all.deb ... Unpacking ruby-xmlrpc (0.3.0-2) ... Selecting previously unselected package libyaml-0-2:arm64. Preparing to unpack .../77-libyaml-0-2_0.2.2-1_arm64.deb ... Unpacking libyaml-0-2:arm64 (0.2.2-1) ... Selecting previously unselected package libruby2.7:arm64. Preparing to unpack .../78-libruby2.7_2.7.4-1_arm64.deb ... Unpacking libruby2.7:arm64 (2.7.4-1) ... Selecting previously unselected package pkg-config. Preparing to unpack .../79-pkg-config_0.29.2-1_arm64.deb ... Unpacking pkg-config (0.29.2-1) ... Selecting previously unselected package python3-all. Preparing to unpack .../80-python3-all_3.9.2-3_arm64.deb ... Unpacking python3-all (3.9.2-3) ... Selecting previously unselected package python3.9-dev. Preparing to unpack .../81-python3.9-dev_3.9.2-1_arm64.deb ... Unpacking python3.9-dev (3.9.2-1) ... Selecting previously unselected package python3-dev. Preparing to unpack .../82-python3-dev_3.9.2-3_arm64.deb ... Unpacking python3-dev (3.9.2-3) ... Selecting previously unselected package python3-all-dev. Preparing to unpack .../83-python3-all-dev_3.9.2-3_arm64.deb ... Unpacking python3-all-dev (3.9.2-3) ... Selecting previously unselected package samtools. Preparing to unpack .../84-samtools_1.11-1_arm64.deb ... Unpacking samtools (1.11-1) ... Selecting previously unselected package swig4.0. Preparing to unpack .../85-swig4.0_4.0.2-1_arm64.deb ... Unpacking swig4.0 (4.0.2-1) ... Selecting previously unselected package swig. Preparing to unpack .../86-swig_4.0.2-1_all.deb ... Unpacking swig (4.0.2-1) ... Selecting previously unselected package time. Preparing to unpack .../87-time_1.9-0.1_arm64.deb ... Unpacking time (1.9-0.1) ... Selecting previously unselected package yaggo. Preparing to unpack .../88-yaggo_1.5.10-2_all.deb ... Unpacking yaggo (1.5.10-2) ... Setting up media-types (4.0.0) ... Setting up libpipeline1:arm64 (1.5.3-1) ... Setting up time (1.9-0.1) ... Setting up libpsl5:arm64 (0.21.0-1.2) ... Setting up bsdextrautils (2.36.1-8) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:arm64 (67.1-7) ... Setting up ruby-power-assert (1.1.7-2) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:arm64 (0.2.2-1) ... Setting up libglib2.0-0:arm64 (2.66.8-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:arm64 (1.0.9-2+b2) ... Setting up libnghttp2-14:arm64 (1.43.0-1) ... Setting up libmagic1:arm64 (1:5.39-3) ... Setting up libdeflate0:arm64 (1.7-1) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libsasl2-modules-db:arm64 (2.1.27+dfsg-2.1) ... Setting up ruby-minitest (5.13.0-1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libexpat1-dev:arm64 (2.2.10-2) ... Setting up ruby-test-unit (3.3.9-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:arm64 (6.2+20201114-2) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libsigsegv2:arm64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up pkg-config (0.29.2-1) ... Setting up d-shlibs (0.98) ... Setting up libsasl2-2:arm64 (2.1.27+dfsg-2.1) ... Setting up liblzma-dev:arm64 (5.2.5-2) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-2) ... Setting up libmd0:arm64 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libmpdec3:arm64 (2.5.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:arm64 (1.9.0-2) ... Setting up dos2unix (7.4.1-1) ... Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Setting up swig4.0 (4.0.2-1) ... Setting up openssl (1.1.1k-1) ... Setting up libbsd0:arm64 (0.11.3-1) ... Setting up libdeflate-dev:arm64 (1.7-1) ... Setting up libelf1:arm64 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up ruby-xmlrpc (0.3.0-2) ... Setting up libxml2:arm64 (2.9.10+dfsg-6.7) ... Setting up chrpath (0.16-2+b1) ... Setting up libprocps8:arm64 (2:3.3.17-5) ... Setting up libjs-underscore (1.9.1~dfsg-3) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up swig (4.0.2-1) ... Setting up libtool (2.4.6-15) ... Setting up libedit2:arm64 (3.1-20191231-2+b1) ... Setting up libreadline8:arm64 (8.1-1) ... Setting up bc (1.07.1-2+b2) ... Setting up libldap-2.4-2:arm64 (2.4.57+dfsg-3) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:arm64 (7.74.0-1.3+b1) ... Setting up libcurl4-gnutls-dev:arm64 (7.74.0-1.3+b1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libjs-sphinxdoc (3.4.3-2) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up procps (2:3.3.17-5) ... Setting up libpython3.9-stdlib:arm64 (3.9.2-1) ... Setting up libpython3-stdlib:arm64 (3.9.2-3) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libhts3:arm64 (1.11-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhts-dev:arm64 (1.11-4) ... Setting up rubygems-integration (1.18) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up samtools (1.11-1) ... Setting up dh-autoreconf (20) ... Setting up libpython3.9:arm64 (3.9.2-1) ... Setting up python3.9 (3.9.2-1) ... Setting up libpython3.9-dev:arm64 (3.9.2-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up python3.9-dev (3.9.2-1) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up python3-distutils (3.9.2-1) ... Setting up dh-python (4.20201102+nmu1) ... Setting up libpython3-dev:arm64 (3.9.2-3) ... Setting up python3-all (3.9.2-3) ... Setting up libpython3-all-dev:arm64 (3.9.2-3) ... Setting up python3-dev (3.9.2-3) ... Setting up python3-all-dev (3.9.2-3) ... Setting up ruby2.7 (2.7.4-1) ... Setting up ruby-rubygems (3.2.5-2) ... Setting up ruby (1:2.7+2) ... Setting up rake (13.0.3-1) ... Setting up yaggo (1.5.10-2) ... Setting up libruby2.7:arm64 (2.7.4-1) ... Processing triggers for libc-bin (2.31-13) ... Processing triggers for ca-certificates (20210119) ... 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_2.3.0-10_source.changes dpkg-buildpackage: info: source package jellyfish dpkg-buildpackage: info: source version 2.3.0-10 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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 dh_update_autotools_config 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: 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=aarch64-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/aarch64-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... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe 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 we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... 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 aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r 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 how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for ld... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for shared library run path origin... done checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking 32-bit host C ABI... 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 __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... 4.0.2 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 distutils Python package... yes checking for Python include path... -I/usr/include/python3.9 checking for Python library path... -L/usr/lib -lpython3.9 checking for Python site-packages path... /usr/lib/python3/dist-packages checking python extra libraries... -lcrypt -lpthread -ldl -lutil -lm -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/aarch64-linux-gnu/perl/5.32/CORE checking for Perl extension target directory... /usr/lib/perl/5.32.0 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 && perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu -ljellyfish-2.0 -lpthread -L/build/jellyfish-2.3.0/debian/tmp//usr/lib/aarch64-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:232: python3.9 setup.py config running config 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 -Werror -std=c++11 -g -O2 -fdebug-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 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat 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'./'`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 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-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 -fdebug-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 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-L/build/jellyfish-2.3.0/debian/tmp//usr/lib/aarch64-linux-gnu -lhts -R/build/jellyfish-2.3.0/debian/tmp//usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o libgtest.la unit_tests/gtest/src/libgtest_la-gtest-all.lo libtool: link: ar cr .libs/libgtest.a unit_tests/gtest/src/.libs/libgtest_la-gtest-all.o libtool: link: ranlib .libs/libgtest.a libtool: link: ( cd ".libs" && rm -f "libgtest.la" && ln -s "../libgtest.la" "libgtest.la" ) /bin/bash ./libtool --tag=CXX --mode=link g++ -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-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/aarch64-linux-gnu -lhts -R/build/jellyfish-2.3.0/debian/tmp//usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o bin/test_all unit_tests/bin_test_all-test_main.o unit_tests/bin_test_all-test_misc.o 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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++ -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -pthread -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/aarch64-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/aarch64-linux-gnu g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-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++ -Werror -std=c++11 -g -O2 -fdebug-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/aarch64-linux-gnu -lhts -R/build/jellyfish-2.3.0/debian/tmp//usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o bin/fastq2sam jellyfish/fastq2sam.o libjellyfish-2.0.la libtool: link: g++ -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -pthread -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/aarch64-linux-gnu -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/build/jellyfish-2.3.0/debian/tmp//usr/lib/aarch64-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/aarch64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-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/aarch64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-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/aarch64-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/aarch64-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/aarch64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-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/aarch64-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/5.32.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0' 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++ -Werror -Wno-error -std=c++11 -g -O2 -fdebug-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/5.32.0 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/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/10/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/10 -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/10/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/10/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-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/5.32.0/jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0 && { 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/5.32.0 && { 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/5.32.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.32.0' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-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/dist-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++ -Werror -std=c++11 -g -O2 -fdebug-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/dist-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/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/10/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/10 -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/10/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/10/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-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/dist-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-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/dist-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/dist-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/dist-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3/dist-packages/dna_jellyfish' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-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/perl/5.32.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0' 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++ -Werror -Wno-error -std=c++11 -g -O2 -fdebug-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/5.32.0 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/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/10/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/10 -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/10/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/10/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-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/5.32.0/jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0 && { 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/5.32.0 && { 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/5.32.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.32.0' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-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/dist-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++ -Werror -std=c++11 -g -O2 -fdebug-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/dist-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/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/10/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/10 -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/10/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/10/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-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/dist-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-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/dist-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/dist-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/dist-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3/dist-packages/dna_jellyfish' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish' make[2]: Leaving directory '/build/jellyfish-2.3.0' dh_auto_build --sourcedirectory=swig/perl5 cd swig/perl5 && make -j8 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 -fdebug-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/aarch64-linux-gnu/perl/5.32/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 aarch64-linux-gnu-gcc -g -O2 -fdebug-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:232: /usr/bin/python3 setup.py build build_ext -L/build/jellyfish-2.3.0/.libs running build running build_py copying dna_jellyfish.py -> /build/jellyfish-2.3.0/.pybuild/cpython3_3.9_dna_jellyfish/build running build_ext building '_dna_jellyfish' extension creating build creating build/temp.linux-arm64-3.9 aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-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/python3.9 -c swig_wrap.cpp -o build/temp.linux-arm64-3.9/swig_wrap.o -std=c++0x aarch64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -lpthread -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.9/swig_wrap.o -L/build/jellyfish-2.3.0/debian/tmp//usr/lib/aarch64-linux-gnu -L/build/jellyfish-2.3.0/.libs -ljellyfish-2.0 -lpthread -o /build/jellyfish-2.3.0/.pybuild/cpython3_3.9_dna_jellyfish/build/_dna_jellyfish.cpython-39-aarch64-linux-gnu.so -Wl,-rpath,/build/jellyfish-2.3.0/debian/tmp//usr/lib/aarch64-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 -j8 check 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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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/aarch64-linux-gnu -lhts -R/build/jellyfish-2.3.0/debian/tmp//usr/lib/aarch64-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 PASS: tests/subset_hashing.sh PASS: tests/bloom_filter.sh PASS: tests/bloom_counter.sh PASS: tests/small_mers.sh PASS: tests/large_key.sh SKIP: tests/swig_ruby.sh PASS: tests/sam.sh PASS: tests/multi_file.sh PASS: tests/merge.sh PASS: tests/swig_python.sh PASS: tests/parallel_hashing.sh PASS: tests/swig_perl.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/aarch64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-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/aarch64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-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/aarch64-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/aarch64-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/aarch64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-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/aarch64-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/5.32.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0' 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++ -Werror -Wno-error -std=c++11 -g -O2 -fdebug-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/5.32.0 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/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/10/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/10 -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/10/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/10/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-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/5.32.0/jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0 && { 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/5.32.0 && { 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/5.32.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.32.0' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-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/dist-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++ -Werror -std=c++11 -g -O2 -fdebug-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/dist-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/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/10/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/10 -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/10/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/10/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-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/dist-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-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/dist-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/dist-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/dist-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3/dist-packages/dna_jellyfish' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-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/perl/5.32.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0' 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++ -Werror -Wno-error -std=c++11 -g -O2 -fdebug-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/5.32.0 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/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/10/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/10 -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/10/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/10/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-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/5.32.0/jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0 && { 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/5.32.0 && { 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/5.32.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.32.0' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-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/dist-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++ -Werror -std=c++11 -g -O2 -fdebug-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/dist-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/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/10/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/10 -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/10/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/10/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-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/dist-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-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/dist-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/dist-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/dist-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3/dist-packages/dna_jellyfish' /bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish' make[2]: Leaving directory '/build/jellyfish-2.3.0' dh_auto_install --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py install --root /build/jellyfish-2.3.0/debian/python3-dna-jellyfish 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/python3.9 creating /build/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib/python3.9/dist-packages copying /build/jellyfish-2.3.0/.pybuild/cpython3_3.9_dna_jellyfish/build/_dna_jellyfish.cpython-39-aarch64-linux-gnu.so -> /build/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib/python3.9/dist-packages copying /build/jellyfish-2.3.0/.pybuild/cpython3_3.9_dna_jellyfish/build/dna_jellyfish.py -> /build/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib/python3.9/dist-packages byte-compiling /build/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib/python3.9/dist-packages/dna_jellyfish.py to dna_jellyfish.cpython-39.pyc running install_egg_info Writing /build/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib/python3.9/dist-packages/dna_jellyfish-0.0.1.egg-info dh_auto_install --sourcedirectory=swig/perl5 cd swig/perl5 && make -j8 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/aarch64-linux-gnu/perl5/5.32/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 1358944 Sep 28 18:09 debian/tmp/usr/lib/aarch64-linux-gnu/perl5/5.32/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/aarch64-linux-gnu install -d -m 755 debian/libjellyfish-2.0-2/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a debian/libjellyfish-2.0-dev/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.la debian/libjellyfish-2.0-dev/usr/lib/aarch64-linux-gnu || true mv debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so debian/libjellyfish-2.0-dev/usr/lib/aarch64-linux-gnu mv /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so.2 debian/libjellyfish-2.0-2/usr/lib/aarch64-linux-gnu mv /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so.2.0.0 debian/libjellyfish-2.0-2/usr/lib/aarch64-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/aarch64-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/5.32.0 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 dpkg-gencontrol: warning: package python3-dna-jellyfish: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-dna-jellyfish: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: package python3-dna-jellyfish: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-dna-jellyfish: substitution variable ${python3:Versions} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'jellyfish' in '../jellyfish_2.3.0-10_arm64.deb'. dpkg-deb: building package 'libjellyfish-2.0-2' in '../libjellyfish-2.0-2_2.3.0-10_arm64.deb'. dpkg-deb: building package 'libjellyfish-2.0-dev' in '../libjellyfish-2.0-dev_2.3.0-10_arm64.deb'. dpkg-deb: building package 'libjellyfish-perl-dbgsym' in '../libjellyfish-perl-dbgsym_2.3.0-10_arm64.deb'. dpkg-deb: building package 'python3-dna-jellyfish-dbgsym' in '../python3-dna-jellyfish-dbgsym_2.3.0-10_arm64.deb'. dpkg-deb: building package 'libjellyfish-2.0-2-dbgsym' in '../libjellyfish-2.0-2-dbgsym_2.3.0-10_arm64.deb'. dpkg-deb: building package 'jellyfish-examples' in '../jellyfish-examples_2.3.0-10_all.deb'. dpkg-deb: building package 'libjellyfish-perl' in '../libjellyfish-perl_2.3.0-10_arm64.deb'. dpkg-deb: building package 'python3-dna-jellyfish' in '../python3-dna-jellyfish_2.3.0-10_arm64.deb'. dpkg-deb: building package 'jellyfish-dbgsym' in '../jellyfish-dbgsym_2.3.0-10_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../jellyfish_2.3.0-10_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/5875 and its subdirectories I: Current time: Wed Sep 28 18:16:18 -12 2022 I: pbuilder-time-stamp: 1664432178 Thu Aug 26 23:53:22 UTC 2021 I: 1st build successful. Starting 2nd build on remote node codethink14-arm64.debian.net. Thu Aug 26 23:53:22 UTC 2021 I: Preparing to do remote build '2' on codethink14-arm64.debian.net. Fri Aug 27 00:09:51 UTC 2021 I: Deleting $TMPDIR on codethink14-arm64.debian.net. Fri Aug 27 00:09:52 UTC 2021 I: jellyfish_2.3.0-10_arm64.changes: Format: 1.8 Date: Tue, 02 Mar 2021 12:50:29 +0100 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: arm64 all Version: 2.3.0-10 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: 976340 Changes: jellyfish (2.3.0-10) unstable; urgency=medium . [ Adrian Bunk ] * Also fix building with -l and -I in builddir in the existing -L fix Closes: #976340 Checksums-Sha1: 1a9a6bc4f79c953c36070c25af13780a907e3ee5 7759988 jellyfish-dbgsym_2.3.0-10_arm64.deb ba1162fea9ce21e8a0a002c3c53d55718fbc9eea 15288 jellyfish-examples_2.3.0-10_all.deb 20f9a8b996adfbd5049abd16c7b0d94dfb207e66 9887 jellyfish_2.3.0-10_arm64.buildinfo c995638b3745bd9dc3fab89f916bd749921e7911 705648 jellyfish_2.3.0-10_arm64.deb ea1c5a4ee2758d49385906844bde3b4ca38c3663 537748 libjellyfish-2.0-2-dbgsym_2.3.0-10_arm64.deb fe6ebbd156ed2f78dca71c7a774e0fb549470d38 60956 libjellyfish-2.0-2_2.3.0-10_arm64.deb c783071fa6b0ac45d0918449919e459063c65110 135620 libjellyfish-2.0-dev_2.3.0-10_arm64.deb 538390d4d9a8e087f98f5970a3e83268b30ca30f 353164 libjellyfish-perl-dbgsym_2.3.0-10_arm64.deb 060e8da68110967c021ad09a99f16d2699760ff5 51936 libjellyfish-perl_2.3.0-10_arm64.deb c7620c4de7c17b6f255b76e2b9550ce4c6cc5afd 331168 python3-dna-jellyfish-dbgsym_2.3.0-10_arm64.deb 9023b0f069802435b1a22e40a9a82b0804d8d9e5 51820 python3-dna-jellyfish_2.3.0-10_arm64.deb Checksums-Sha256: d7258bbe681ebc265b8440eb7d456eef0e12c74d6b44cdaedc3790e29a118153 7759988 jellyfish-dbgsym_2.3.0-10_arm64.deb 6a986c991f0359569bbd55e40adb85f7d08de602e66738ab82f0629d7c7849de 15288 jellyfish-examples_2.3.0-10_all.deb 7af463c34012e20a7733d9f67e5a91d96e1a0c7e894181196775097398f9e9a3 9887 jellyfish_2.3.0-10_arm64.buildinfo ab9bb5f36a48245fa32f71455cfa6f2b813ceb3e4d00807461fcfe51b308917d 705648 jellyfish_2.3.0-10_arm64.deb da28a7a8b6bac07c53a96f8896349076bffa1bebca8ddcfb698dcdbc71f7fafd 537748 libjellyfish-2.0-2-dbgsym_2.3.0-10_arm64.deb 01fc76197139e83616f3d477559a9ca0437f5da377d5326b8313bb07074dd4ec 60956 libjellyfish-2.0-2_2.3.0-10_arm64.deb 218d9b561712c995731ab072e4c018f94d565cc1e5078beba948554803e3565d 135620 libjellyfish-2.0-dev_2.3.0-10_arm64.deb 3df651030df246aada0c347f81f8fa4af4e77f15e92b146b866b4ea1b62de0c1 353164 libjellyfish-perl-dbgsym_2.3.0-10_arm64.deb 55a92f15e22918d0908ba558b631fd86a7a800cac34a385bedc30d39bc2ea342 51936 libjellyfish-perl_2.3.0-10_arm64.deb ca51793b784f2e445bdc297502a673b2f970c9fba4e1024c864b7db37e8b9614 331168 python3-dna-jellyfish-dbgsym_2.3.0-10_arm64.deb 48c719ddd18fad739c0a256b40aaae01888d404d9148a71101a6f0e500e92734 51820 python3-dna-jellyfish_2.3.0-10_arm64.deb Files: 8bb8206acdec1b1c553b75b809eb2415 7759988 debug optional jellyfish-dbgsym_2.3.0-10_arm64.deb dd96725b16428ba6988a90a6ad14cfbc 15288 science optional jellyfish-examples_2.3.0-10_all.deb 965a9465e8e74dd531b4f0faa18fc9d0 9887 science optional jellyfish_2.3.0-10_arm64.buildinfo 89f4636eac755f635245420464aa490b 705648 science optional jellyfish_2.3.0-10_arm64.deb 2f28eb128cc3c4283465ff7900a8fe0d 537748 debug optional libjellyfish-2.0-2-dbgsym_2.3.0-10_arm64.deb 133cffe3c44feb67421f496922d5ddc7 60956 libs optional libjellyfish-2.0-2_2.3.0-10_arm64.deb f3e3bdf3988f4c17c99a482be528ef3a 135620 libdevel optional libjellyfish-2.0-dev_2.3.0-10_arm64.deb 24f880f10d22bc655f7c84adceec474e 353164 debug optional libjellyfish-perl-dbgsym_2.3.0-10_arm64.deb 2d1c8e91c56d5552a64cc297722d6651 51936 perl optional libjellyfish-perl_2.3.0-10_arm64.deb f6209d90a9e7f1caaab2fc4aac59c7ba 331168 debug optional python3-dna-jellyfish-dbgsym_2.3.0-10_arm64.deb 6247e65bba85233e42b354427cbfb08f 51820 python optional python3-dna-jellyfish_2.3.0-10_arm64.deb Fri Aug 27 00:09:53 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.9mrsrwZbHh/jellyfish_2.3.0-10.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.9mrsrwZbHh/jellyfish_2.3.0-10.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.9mrsrwZbHh/jellyfish_2.3.0-10.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.9mrsrwZbHh/b1/jellyfish_2.3.0-10_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.9mrsrwZbHh/b2/jellyfish_2.3.0-10_arm64.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: 0.349s) 0.349s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.116s) 0.115s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Fri Aug 27 00:09:54 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Fri Aug 27 00:09:54 UTC 2021 I: jellyfish from bullseye built successfully and reproducibly on arm64. Fri Aug 27 00:09:56 UTC 2021 I: Submitting .buildinfo files to external archives: Fri Aug 27 00:09:56 UTC 2021 I: Submitting 12K b1/jellyfish_2.3.0-10_arm64.buildinfo.asc Fri Aug 27 00:09:57 UTC 2021 I: Submitting 12K b2/jellyfish_2.3.0-10_arm64.buildinfo.asc Fri Aug 27 00:09:58 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Aug 27 00:09:58 UTC 2021 I: Done submitting .buildinfo files. Fri Aug 27 00:09:58 UTC 2021 I: Removing signed jellyfish_2.3.0-10_arm64.buildinfo.asc files: removed './b1/jellyfish_2.3.0-10_arm64.buildinfo.asc' removed './b2/jellyfish_2.3.0-10_arm64.buildinfo.asc'