sbuild (Debian sbuild) 0.91.5 (17 December 2025) on carme.larted.org.uk +==============================================================================+ | jellyfish 2.3.1-6 (amd64) Sat, 25 Apr 2026 17:51:00 +0000 | +==============================================================================+ Package: jellyfish Version: 2.3.1-6 Source Version: 2.3.1-6 Distribution: sid Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Sat, 25 Apr 2026 17:51:01 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup jellyfish_2.3.1-6 sid amd64 -------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup jellyfish_2.3.1-6 sid amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Sat, 25 Apr 2026 17:51:01 +0000 | +------------------------------------------------------------------------------+ Hit:1 http://deb.debian.org/debian unstable InRelease Hit:2 http://deb.debian.org/debian sid InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files Sat, 25 Apr 2026 17:51:04 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/jellyfish_2.3.1-6.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Sat, 25 Apr 2026 17:51:04 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), architecture-is-little-endian, architecture-is-64-bit, d-shlibs, autoconf-archive, yaggo, pkgconf, bc, time, procps, swig, python3-all-dev, libpython3-all-dev, dh-sequence-python3, python3-setuptools, perl-xs-dev, perl, chrpath, libhts-dev, dos2unix, samtools, build-essential Filtered Build-Depends: debhelper-compat (= 13), architecture-is-little-endian, architecture-is-64-bit, d-shlibs, autoconf-archive, yaggo, pkgconf, bc, time, procps, swig, python3-all-dev, libpython3-all-dev, dh-sequence-python3, python3-setuptools, perl-xs-dev, perl, chrpath, libhts-dev, dos2unix, samtools, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/jellyfish-bM2jHV/resolver-ecana5/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/jellyfish-bM2jHV/resolver-ecana5/apt_archive ./ InRelease Get:2 copy:/build/jellyfish-bM2jHV/resolver-ecana5/apt_archive ./ Release [609 B] Ign:3 copy:/build/jellyfish-bM2jHV/resolver-ecana5/apt_archive ./ Release.gpg Get:4 copy:/build/jellyfish-bM2jHV/resolver-ecana5/apt_archive ./ Sources [875 B] Get:5 copy:/build/jellyfish-bM2jHV/resolver-ecana5/apt_archive ./ Packages [900 B] Fetched 2384 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Solving dependencies... The following additional packages will be installed: architecture-properties autoconf autoconf-archive automake autopoint autotools-dev bc bsdextrautils ca-certificates chrpath comerr-dev d-shlibs debhelper dh-autoreconf dh-python dh-strip-nondeterminism dos2unix dwz file gettext gettext-base groff-base intltool-debian krb5-multidev libarchive-zip-perl libbrotli-dev libbrotli1 libbz2-dev libcom-err2 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls28-dev libgssapi-krb5-2 libgssrpc4t64 libhts-dev libhts3t64 libhtscodecs2 libidn2-dev libjs-sphinxdoc libk5crypto3 libkadm5clnt-mit12 libkadm5srv-mit12 libkdb5-10t64 libkeyutils1 libkrb5-3 libkrb5-dev libkrb5support0 libldap-dev liblzma-dev libmagic-mgc libmagic1t64 libncurses6 libnghttp2-14 libnghttp2-dev libnghttp3-9 libnghttp3-dev libngtcp2-16 libngtcp2-crypto-gnutls-dev libngtcp2-crypto-gnutls8 libngtcp2-dev libp11-kit-dev libperl-dev libpipeline1 libpkgconf7 libproc2-0 libpsl-dev libpsl5t64 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.13 libpython3.13-dev libpython3.13-minimal libpython3.13-stdlib libpython3.14 libpython3.14-dev libpython3.14-minimal libpython3.14-stdlib librtmp-dev librtmp1 libruby libruby3.3 libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libxml2-16 libyaml-0-2 libzstd-dev m4 man-db media-types netbase nettle-dev openssl pkgconf pkgconf-bin po-debconf procps python3 python3-all python3-all-dev python3-autocommand python3-dev python3-inflect python3-jaraco.context python3-jaraco.functools python3-jaraco.text python3-minimal python3-more-itertools python3-pkg-resources python3-setuptools python3-typeguard python3-typing-extensions python3-zipp python3.13 python3.13-dev python3.13-minimal python3.14 python3.14-dev python3.14-minimal rake ruby ruby-csv ruby-did-you-mean ruby-net-telnet ruby-ruby2-keywords ruby-rubygems ruby-webrick ruby-xmlrpc ruby3.3 rubygems-integration samtools sensible-utils swig time tzdata yaggo zlib1g-dev Suggested packages: gnu-standards autoconf-doc doc-base dh-make flit python3-build python3-installer python3-wheel gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff krb5-doc libcurl4-doc libidn-dev gmp-doc libgmp10-doc libmpfr-dev dns-root-data gnutls-bin gnutls-doc krb5-user liblzma-doc libnghttp2-doc p11-kit-doc libssl-doc libtool-doc gfortran | fortran95-compiler m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python-setuptools-doc python3.13-venv python3.13-doc binfmt-support python3.14-venv python3.14-doc ri ruby-dev bundler cwltool swig-doc swig-examples Recommended packages: curl | wget | lynx bzip2-doc libarchive-cpio-perl krb5-locales libgpm2 publicsuffix ruby-sdbm libtasn1-doc libltdl-dev libmail-sendmail-perl psmisc linux-sysctl-defaults zip fonts-lato libjs-jquery The following NEW packages will be installed: architecture-properties autoconf autoconf-archive automake autopoint autotools-dev bc bsdextrautils ca-certificates chrpath comerr-dev d-shlibs debhelper dh-autoreconf dh-python dh-strip-nondeterminism dos2unix dwz file gettext gettext-base groff-base intltool-debian krb5-multidev libarchive-zip-perl libbrotli-dev libbrotli1 libbz2-dev libcom-err2 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls28-dev libgssapi-krb5-2 libgssrpc4t64 libhts-dev libhts3t64 libhtscodecs2 libidn2-dev libjs-sphinxdoc libk5crypto3 libkadm5clnt-mit12 libkadm5srv-mit12 libkdb5-10t64 libkeyutils1 libkrb5-3 libkrb5-dev libkrb5support0 libldap-dev liblzma-dev libmagic-mgc libmagic1t64 libncurses6 libnghttp2-14 libnghttp2-dev libnghttp3-9 libnghttp3-dev libngtcp2-16 libngtcp2-crypto-gnutls-dev libngtcp2-crypto-gnutls8 libngtcp2-dev libp11-kit-dev libperl-dev libpipeline1 libpkgconf7 libproc2-0 libpsl-dev libpsl5t64 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.13 libpython3.13-dev libpython3.13-minimal libpython3.13-stdlib libpython3.14 libpython3.14-dev libpython3.14-minimal libpython3.14-stdlib librtmp-dev librtmp1 libruby libruby3.3 libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libxml2-16 libyaml-0-2 libzstd-dev m4 man-db media-types netbase nettle-dev openssl pkgconf pkgconf-bin po-debconf procps python3 python3-all python3-all-dev python3-autocommand python3-dev python3-inflect python3-jaraco.context python3-jaraco.functools python3-jaraco.text python3-minimal python3-more-itertools python3-pkg-resources python3-setuptools python3-typeguard python3-typing-extensions python3-zipp python3.13 python3.13-dev python3.13-minimal python3.14 python3.14-dev python3.14-minimal rake ruby ruby-csv ruby-did-you-mean ruby-net-telnet ruby-ruby2-keywords ruby-rubygems ruby-webrick ruby-xmlrpc ruby3.3 rubygems-integration samtools sbuild-build-depends-main-dummy sensible-utils swig time tzdata yaggo zlib1g-dev 0 upgraded, 154 newly installed, 0 to remove and 0 not upgraded. Need to get 74.1 MB of archives. After this operation, 293 MB of additional disk space will be used. Get:1 copy:/build/jellyfish-bM2jHV/resolver-ecana5/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [992 B] Get:2 http://deb.debian.org/debian unstable/main amd64 autoconf-archive all 20241016-3 [797 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.8.0-1 [116 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.12-1 [866 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.12-1 [2267 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.9-3 [27.6 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 media-types all 14.0.0 [30.8 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 tzdata all 2026b-1 [260 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.12-1 [1974 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.12-1 [776 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.9-3 [10.5 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.9-3 [27.6 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 libpython3.14-minimal amd64 3.14.4-2 [892 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 python3.14-minimal amd64 3.14.4-2 [2410 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-9+b2 [63.8 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-9+b2 [880 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.6.2-1 [1517 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20260223 [158 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5+b2 [337 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5+b2 [109 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5+b2 [42.6 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.2-2 [242 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b1 [68.8 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.24.1-1 [1336 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.42-4 [99.6 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-3 [49.2 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 architecture-properties amd64 0.2.6+b2 [2632 B] Get:31 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.21-1 [332 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-6 [494 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1+nmu1 [60.0 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-4 [877 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.2-2 [770 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 bc amd64 1.07.1-4 [103 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 chrpath amd64 0.18-1 [13.5 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.4-1 [19.2 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.4-1 [50.9 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 d-shlibs all 0.109 [11.1 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.31 [75.7 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-11 [539 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 22 [12.2 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get:47 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.195-1 [58.1 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-4 [108 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.2+dfsg-0.1 [641 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.2-2 [1684 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.22 [216 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.31 [932 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 dh-python all 7.20260309 [114 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 dos2unix amd64 7.5.4-1 [509 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.22.1-2+b1 [31.0 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.22.1-2+b1 [78.9 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6+b1 [9784 B] Get:59 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.22.1-2+b1 [336 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.22.1-2+b1 [137 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.22.1-2+b1 [58.1 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.22.1-2+b1 [40.2 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.22.1-2+b1 [41.2 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.22.1-2+b1 [54.0 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.22.1-2+b1 [125 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.2.0-3 [320 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.2.0-3 [324 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6+b2 [33.6 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.15.0-1 [67.2 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.22.1-1 [133 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.69.0-1 [89.0 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.22.1-1 [20.8 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.5-1 [59.9 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-2 [244 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.20.0~rc3-1 [402 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b2 [184 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.24.2-1+b1 [608 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.12-3 [475 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-4+b1 [103 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.26.2-2 [223 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.21.0-2 [99.7 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-5+b1 [330 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-5+b1 [642 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.2-1+b1 [1321 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.12-3 [1450 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.22.1-2+b1 [14.0 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.6.10+dfsg-1+b1 [313 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 libpkgconf7 amd64 2.5.1-4 [47.8 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 2.5.1-4 [35.9 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 2.5.1-4 [33.6 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.69.0-1 [128 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.15.0-1 [94.5 kB] Get:93 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.22.1-1 [20.9 kB] Get:94 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.22.1-1 [192 kB] Get:95 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.5-1 [80.5 kB] Get:96 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.6-1 [60.3 kB] Get:97 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.2-3 [918 kB] Get:98 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.6-1 [69.7 kB] Get:99 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.6.2-1 [3019 kB] Get:100 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-2 [393 kB] Get:101 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-3+b1 [375 kB] Get:102 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.20.0~rc3-1 [527 kB] Get:103 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2+b1 [49.5 kB] Get:104 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.23-2+b1 [58.1 kB] Get:105 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.8.0-1 [171 kB] Get:106 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.6-1 [101 kB] Get:107 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.22.1+ds2-1+b1 [477 kB] Get:108 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.3-1 [369 kB] Get:109 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.22.1+ds2-1+b1 [1787 kB] Get:110 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.2.3-12 [27.9 kB] Get:111 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.6+20251231-1 [106 kB] Get:112 http://deb.debian.org/debian unstable/main amd64 libperl-dev amd64 5.40.1-7+b1 [1122 kB] Get:113 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.12-1 [2187 kB] Get:114 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.12-1 [5298 kB] Get:115 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.9-3 [10.8 kB] Get:116 http://deb.debian.org/debian unstable/main amd64 libpython3.14-stdlib amd64 3.14.4-2 [2268 kB] Get:117 http://deb.debian.org/debian unstable/main amd64 libpython3.14 amd64 3.14.4-2 [2376 kB] Get:118 http://deb.debian.org/debian unstable/main amd64 libpython3.14-dev amd64 3.14.4-2 [5449 kB] Get:119 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.13.9-3 [1072 B] Get:120 http://deb.debian.org/debian unstable/main amd64 rubygems-integration all 1.19 [5488 B] Get:121 http://deb.debian.org/debian unstable/main amd64 ruby3.3 amd64 3.3.8-2 [834 kB] Get:122 http://deb.debian.org/debian unstable/main amd64 ruby-rubygems all 3.6.7-2 [407 kB] Get:123 http://deb.debian.org/debian unstable/main amd64 ruby amd64 1:3.3+b1 [6560 B] Get:124 http://deb.debian.org/debian unstable/main amd64 rake all 13.4.2-1 [65.4 kB] Get:125 http://deb.debian.org/debian unstable/main amd64 ruby-csv all 3.3.5-1 [42.3 kB] Get:126 http://deb.debian.org/debian unstable/main amd64 ruby-did-you-mean all 2.0.0-1 [21.0 kB] Get:127 http://deb.debian.org/debian unstable/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get:128 http://deb.debian.org/debian unstable/main amd64 ruby-ruby2-keywords all 0.0.5-1 [4300 B] Get:129 http://deb.debian.org/debian unstable/main amd64 ruby-webrick all 1.9.2-1 [59.8 kB] Get:130 http://deb.debian.org/debian unstable/main amd64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get:131 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-2+b1 [53.8 kB] Get:132 http://deb.debian.org/debian unstable/main amd64 libruby3.3 amd64 3.3.8-2 [6301 kB] Get:133 http://deb.debian.org/debian unstable/main amd64 libruby amd64 1:3.3+b1 [5440 B] Get:134 http://deb.debian.org/debian unstable/main amd64 python3.14 amd64 3.14.4-2 [837 kB] Get:135 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.13.9-3 [1048 B] Get:136 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.12-1 [504 kB] Get:137 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.9-3 [26.0 kB] Get:138 http://deb.debian.org/debian unstable/main amd64 python3.14-dev amd64 3.14.4-2 [507 kB] Get:139 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.13.9-3 [1068 B] Get:140 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-4 [13.7 kB] Get:141 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get:142 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.15.0-2 [92.5 kB] Get:143 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.4-2 [37.2 kB] Get:144 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.5.0-1 [33.0 kB] Get:145 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.1-2 [8184 B] Get:146 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get:147 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get:148 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get:149 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.23.0-1 [11.0 kB] Get:150 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get:151 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.22.1-1 [697 kB] Get:152 http://deb.debian.org/debian unstable/main amd64 swig amd64 4.4.1-2 [1508 kB] Get:153 http://deb.debian.org/debian unstable/main amd64 time amd64 1.9-0.4 [47.7 kB] Get:154 http://deb.debian.org/debian unstable/main amd64 yaggo all 1.5.11-2 [21.4 kB] Preconfiguring packages ... Fetched 74.1 MB in 1s (120 MB/s) Selecting previously unselected package autoconf-archive. (Reading database ... 23257 files and directories currently installed.) Preparing to unpack .../autoconf-archive_20241016-3_all.deb ... Unpacking autoconf-archive (20241016-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.8.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.8.0-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.12-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.12-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.12-1_amd64.deb ... Unpacking python3.13-minimal (3.13.12-1) ... Setting up libpython3.13-minimal:amd64 (3.13.12-1) ... Setting up libexpat1:amd64 (2.8.0-1) ... Setting up python3.13-minimal (3.13.12-1) ... Selecting previously unselected package python3-minimal. 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Unpacking libpython3-dev:amd64 (3.13.9-3) ... Selecting previously unselected package libpython3.14-stdlib:amd64. Preparing to unpack .../103-libpython3.14-stdlib_3.14.4-2_amd64.deb ... Unpacking libpython3.14-stdlib:amd64 (3.14.4-2) ... Selecting previously unselected package libpython3.14:amd64. Preparing to unpack .../104-libpython3.14_3.14.4-2_amd64.deb ... Unpacking libpython3.14:amd64 (3.14.4-2) ... Selecting previously unselected package libpython3.14-dev:amd64. Preparing to unpack .../105-libpython3.14-dev_3.14.4-2_amd64.deb ... Unpacking libpython3.14-dev:amd64 (3.14.4-2) ... Selecting previously unselected package libpython3-all-dev:amd64. Preparing to unpack .../106-libpython3-all-dev_3.13.9-3_amd64.deb ... Unpacking libpython3-all-dev:amd64 (3.13.9-3) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../107-rubygems-integration_1.19_all.deb ... Unpacking rubygems-integration (1.19) ... Selecting previously unselected package ruby3.3. 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Selecting previously unselected package samtools. Preparing to unpack .../138-samtools_1.22.1-1_amd64.deb ... Unpacking samtools (1.22.1-1) ... Selecting previously unselected package swig. Preparing to unpack .../139-swig_4.4.1-2_amd64.deb ... Unpacking swig (4.4.1-2) ... Selecting previously unselected package time. Preparing to unpack .../140-time_1.9-0.4_amd64.deb ... Unpacking time (1.9-0.4) ... Selecting previously unselected package yaggo. Preparing to unpack .../141-yaggo_1.5.11-2_all.deb ... Unpacking yaggo (1.5.11-2) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../142-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libhtscodecs2:amd64 (1.6.6-1) ... Setting up media-types (14.0.0) ... Setting up libpipeline1:amd64 (1.5.8-3) ... Setting up time (1.9-0.4) ... Setting up libkeyutils1:amd64 (1.6.3-6+b1) ... Setting up ruby-ruby2-keywords (0.0.5-1) ... Setting up swig (4.4.1-2) ... Setting up libzstd-dev:amd64 (1.5.7+dfsg-3+b1) ... Setting up bsdextrautils (2.42-4) ... Setting up libmagic-mgc (1:5.46-5+b2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.5-2+b1) ... Setting up architecture-properties:amd64 (0.2.6+b2) ... Setting up libxml2-16:amd64 (2.15.2+dfsg-0.1) ... Setting up libdebhelper-perl (13.31) ... Setting up libbrotli1:amd64 (1.2.0-3) ... Setting up libpython3.14-minimal:amd64 (3.14.4-2) ... Setting up libpkgconf7:amd64 (2.5.1-4) ... Setting up libmagic1t64:amd64 (1:5.46-5+b2) ... Setting up libpsl5t64:amd64 (0.21.5-1) ... Setting up libnghttp2-14:amd64 (1.69.0-1) ... Setting up libdeflate0:amd64 (1.23-2+b1) ... Setting up bc (1.07.1-4) ... Setting up gettext-base (0.23.2-2) ... Setting up m4 (1.4.21-1) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b2) ... Setting up libperl-dev:amd64 (5.40.1-7+b1) ... Setting up autoconf-archive (20241016-3) ... Setting up libcom-err2:amd64 (1.47.4-1) ... Setting up file (1:5.46-5+b2) ... Setting up libelf1t64:amd64 (0.195-1) ... Setting up libpsl-dev:amd64 (0.21.5-1) ... Setting up libkrb5support0:amd64 (1.22.1-2+b1) ... Setting up tzdata (2026b-1) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Apr 25 17:51:20 UTC 2026. Universal Time is now: Sat Apr 25 17:51:20 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1+nmu1) ... Setting up libunbound8:amd64 (1.24.2-1+b1) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-5+b1) ... Setting up libexpat1-dev:amd64 (2.8.0-1) ... Setting up libgnutls-dane0t64:amd64 (3.8.12-3) ... Setting up librtmp1:amd64 (2.6-1) ... Setting up libldap-dev:amd64 (2.6.10+dfsg-1+b1) ... Setting up libncurses6:amd64 (6.6+20251231-1) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up ruby-csv (3.3.5-1) ... Setting up libproc2-0:amd64 (2:4.0.4-9+b2) ... Setting up comerr-dev:amd64 (2.1-1.47.4-1) ... Setting up libssl-dev:amd64 (3.6.2-1) ... Setting up autopoint (0.23.2-2) ... Setting up d-shlibs (0.109) ... Setting up pkgconf-bin (2.5.1-4) ... Setting up libk5crypto3:amd64 (1.22.1-2+b1) ... Setting up libidn2-dev:amd64 (2.3.8-4+b1) ... Setting up libjs-sphinxdoc (8.2.3-12) ... Setting up autoconf (2.72-6) ... Setting up libnghttp3-9:amd64 (1.15.0-1) ... Setting up libnghttp3-dev:amd64 (1.15.0-1) ... Setting up ruby-webrick (1.9.2-1) ... Setting up liblzma-dev:amd64 (5.8.3-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.2-3) ... Setting up dwz (0.16-4) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2+b1) ... Setting up procps (2:4.0.4-9+b2) ... Setting up netbase (6.5) ... Configuration file '/etc/protocols' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Configuration file '/etc/services' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Setting up libngtcp2-16:amd64 (1.22.1-1) ... Setting up libkrb5-3:amd64 (1.22.1-2+b1) ... Setting up dos2unix (7.5.4-1) ... Setting up libssh2-1t64:amd64 (1.11.1-2) ... Setting up ruby-did-you-mean (2.0.0-1) ... Setting up libtasn1-6-dev:amd64 (4.21.0-2) ... Setting up openssl (3.6.2-1) ... Setting up libdeflate-dev:amd64 (1.23-2+b1) ... Setting up libpython3.13-stdlib:amd64 (3.13.12-1) ... Setting up ruby-xmlrpc (0.3.3-2) ... Setting up python3.14-minimal (3.14.4-2) ... Setting up libbrotli-dev:amd64 (1.2.0-3) ... Setting up chrpath (0.18-1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.22.1-1) ... Setting up libp11-kit-dev:amd64 (0.26.2-2) ... Setting up libpython3-stdlib:amd64 (3.13.9-3) ... Setting up libbz2-dev:amd64 (1.0.8-6+b2) ... Setting up libpython3.13:amd64 (3.13.12-1) ... Setting up automake (1:1.18.1-4) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.2-2) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-5+b1) ... Setting up nettle-dev:amd64 (3.10.2-1+b1) ... Setting up libtool (2.5.4-11) ... Setting up python3.13 (3.13.12-1) ... Setting up libpython3.14-stdlib:amd64 (3.14.4-2) ... Setting up python3 (3.13.9-3) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.22.1-1) ... Setting up libngtcp2-dev:amd64 (1.22.1-1) ... Setting up python3-zipp (3.23.0-1) ... Setting up python3-autocommand (2.2.2-4) ... Setting up pkgconf:amd64 (2.5.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (22) ... Setting up ca-certificates (20260223) ... Updating certificates in /etc/ssl/certs... 144 added, 0 removed; done. Setting up libpython3.13-dev:amd64 (3.13.12-1) ... Setting up libgssapi-krb5-2:amd64 (1.22.1-2+b1) ... Setting up python3-typing-extensions (4.15.0-2) ... Setting up libssh2-1-dev:amd64 (1.11.1-2) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.24.1-1) ... Setting up libpython3.14:amd64 (3.14.4-2) ... Setting up libpython3.14-dev:amd64 (3.14.4-2) ... Setting up python3.14 (3.14.4-2) ... Setting up dh-python (7.20260309) ... Setting up libgnutls28-dev:amd64 (3.8.12-3) ... Setting up python3-more-itertools (10.8.0-1) ... Setting up libnghttp2-dev:amd64 (1.69.0-1) ... Setting up libpython3-dev:amd64 (3.13.9-3) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-2) ... Setting up python3.14-dev (3.14.4-2) ... Setting up python3.13-dev (3.13.12-1) ... Setting up po-debconf (1.0.22) ... Setting up python3-typeguard (4.4.4-2) ... Setting up libcurl3t64-gnutls:amd64 (8.20.0~rc3-1) ... Setting up python3-all (3.13.9-3) ... Setting up rubygems-integration (1.19) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-inflect (7.5.0-1) ... Setting up libpython3-all-dev:amd64 (3.13.9-3) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up libgssrpc4t64:amd64 (1.22.1-2+b1) ... Setting up python3-dev (3.13.9-3) ... Setting up librtmp-dev:amd64 (2.6-1) ... Setting up libhts3t64:amd64 (1.22.1+ds2-1+b1) ... Setting up libkadm5clnt-mit12:amd64 (1.22.1-2+b1) ... Setting up python3-pkg-resources (78.1.1-0.1) ... Setting up python3-all-dev (3.13.9-3) ... Setting up python3-setuptools (78.1.1-0.1) ... Setting up libkdb5-10t64:amd64 (1.22.1-2+b1) ... Setting up debhelper (13.31) ... Setting up samtools (1.22.1-1) ... Setting up libkadm5srv-mit12:amd64 (1.22.1-2+b1) ... Setting up krb5-multidev:amd64 (1.22.1-2+b1) ... Setting up libkrb5-dev:amd64 (1.22.1-2+b1) ... Setting up libcurl4-gnutls-dev:amd64 (8.20.0~rc3-1) ... Setting up libhts-dev:amd64 (1.22.1+ds2-1+b1) ... Setting up libruby3.3:amd64 (3.3.8-2) ... Setting up ruby-rubygems (3.6.7-2) ... Setting up ruby3.3 (3.3.8-2) ... Setting up libruby:amd64 (1:3.3+b1) ... Setting up ruby (1:3.3+b1) ... Setting up rake (13.4.2-1) ... Setting up yaggo (1.5.11-2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.42-15) ... Processing triggers for ca-certificates (20260223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. +------------------------------------------------------------------------------+ | Check architectures Sat, 25 Apr 2026 17:51:33 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment Sat, 25 Apr 2026 17:51:33 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.18.5+deb14-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.18.5-1 (2026-01-16) amd64 (x86_64) Toolchain package versions: binutils_2.46-3 dpkg-dev_1.23.7 g++-13_13.4.0-10 g++-15_15.2.0-17 gcc-13_13.4.0-10 gcc-15_15.2.0-17 libc6-dev_2.42-15 libstdc++-13-dev_13.4.0-10 libstdc++-15-dev_15.2.0-17 libstdc++6_16-20260423-1 linux-libc-dev_6.19.13-1 Package versions: adduser_3.155 apt_3.2.0 architecture-properties_0.2.6+b2 autoconf_2.72-6 autoconf-archive_20241016-3 automake_1:1.18.1-4 autopoint_0.23.2-2 autotools-dev_20240727.1+nmu1 base-files_14 base-passwd_3.6.8 bash_5.3-2 bc_1.07.1-4 binutils_2.46-3 binutils-common_2.46-3 binutils-x86-64-linux-gnu_2.46-3 bsdextrautils_2.42-4 bsdutils_1:2.42-4 build-essential_12.12 bzip2_1.0.8-6+b2 ca-certificates_20260223 chrpath_0.18-1 comerr-dev_2.1-1.47.4-1 coreutils_9.10-1 cpp_4:15.2.0-5 cpp-13_13.4.0-10 cpp-13-x86-64-linux-gnu_13.4.0-10 cpp-15_15.2.0-17 cpp-15-x86-64-linux-gnu_15.2.0-17 cpp-x86-64-linux-gnu_4:15.2.0-5 d-shlibs_0.109 dash_0.5.12-12 debconf_1.5.92 debhelper_13.31 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_22 dh-python_7.20260309 dh-strip-nondeterminism_1.15.0-1 diffutils_1:3.12-1 dirmngr_2.4.9-4 dos2unix_7.5.4-1 dpkg_1.23.7 dpkg-dev_1.23.7 dwz_0.16-4 eatmydata_131-2 file_1:5.46-5+b2 findutils_4.10.0-3 g++_4:15.2.0-5 g++-13_13.4.0-10 g++-13-x86-64-linux-gnu_13.4.0-10 g++-15_15.2.0-17 g++-15-x86-64-linux-gnu_15.2.0-17 g++-x86-64-linux-gnu_4:15.2.0-5 gcc_4:15.2.0-5 gcc-13_13.4.0-10 gcc-13-base_13.4.0-10 gcc-13-x86-64-linux-gnu_13.4.0-10 gcc-14-base_14.3.0-14 gcc-15_15.2.0-17 gcc-15-base_15.2.0-17 gcc-15-x86-64-linux-gnu_15.2.0-17 gcc-16-base_16-20260423-1 gcc-x86-64-linux-gnu_4:15.2.0-5 gettext_0.23.2-2 gettext-base_0.23.2-2 gnupg_2.4.9-4 gnupg-l10n_2.4.9-4 gnupg-utils_2.4.9-4 gpg_2.4.9-4 gpg-agent_2.4.9-4 gpg-wks-client_2.4.9-4 gpgconf_2.4.9-4 gpgsm_2.4.9-4 gpgv_2.4.9-4 grep_3.12-1 groff-base_1.24.1-1 gzip_1.13-1 hostname_3.25 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 krb5-multidev_1.22.1-2+b1 libacl1_2.3.2-3 libapt-pkg6.0t64_2.9.29 libapt-pkg7.0_3.2.0 libarchive-zip-perl_1.68-1 libasan8_16-20260423-1 libassuan0_2.5.6-1+b1 libassuan9_3.0.2-2+b1 libatomic1_16-20260423-1 libattr1_1:2.5.2-4 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libbinutils_2.46-3 libblkid1_2.42-4 libbrotli-dev_1.2.0-3 libbrotli1_1.2.0-3 libbsd0_0.12.2-2+b1 libbz2-1.0_1.0.8-6+b2 libbz2-dev_1.0.8-6+b2 libc-bin_2.42-15 libc-dev-bin_2.42-15 libc-gconv-modules-extra_2.42-15 libc-l10n_2.42-15 libc6_2.42-15 libc6-dev_2.42-15 libcap-ng0_0.9.3-1 libcap2_1:2.78-1 libcc1-0_16-20260423-1 libcom-err2_1.47.4-1 libcrypt-dev_1:4.5.1-1+b1 libcrypt1_1:4.5.1-1+b1 libctf-nobfd0_2.46-3 libctf0_2.46-3 libcurl3t64-gnutls_8.20.0~rc3-1 libcurl4-gnutls-dev_8.20.0~rc3-1 libdb5.3t64_5.3.28+dfsg2-11+b1 libdebconfclient0_0.282+b3 libdebhelper-perl_13.31 libdeflate-dev_1.23-2+b1 libdeflate0_1.23-2+b1 libdpkg-perl_1.23.7 libeatmydata1_131-2+b2 libelf1t64_0.195-1 libevent-2.1-7t64_2.1.12-stable-10+b2 libexpat1_2.8.0-1 libexpat1-dev_2.8.0-1 libffi8_3.5.2-4 libfile-stripnondeterminism-perl_1.15.0-1 libgcc-13-dev_13.4.0-10 libgcc-15-dev_15.2.0-17 libgcc-s1_16-20260423-1 libgcrypt20_1.12.2-1 libgdbm-compat4t64_1.26-1+b1 libgdbm6t64_1.26-1+b1 libgmp-dev_2:6.3.0+dfsg-5+b1 libgmp10_2:6.3.0+dfsg-5+b1 libgmpxx4ldbl_2:6.3.0+dfsg-5+b1 libgnutls-dane0t64_3.8.12-3 libgnutls28-dev_3.8.12-3 libgnutls30t64_3.8.12-3 libgomp1_16-20260423-1 libgpg-error0_1.59-4 libgprofng0_2.46-3 libgssapi-krb5-2_1.22.1-2+b1 libgssrpc4t64_1.22.1-2+b1 libhogweed6t64_3.10.2-1+b1 libhts-dev_1.22.1+ds2-1+b1 libhts3t64_1.22.1+ds2-1+b1 libhtscodecs2_1.6.6-1 libhwasan0_16-20260423-1 libidn2-0_2.3.8-4+b1 libidn2-dev_2.3.8-4+b1 libisl23_0.27-2 libitm1_16-20260423-1 libjansson4_2.14-2+b4 libjs-sphinxdoc_8.2.3-12 libk5crypto3_1.22.1-2+b1 libkadm5clnt-mit12_1.22.1-2+b1 libkadm5srv-mit12_1.22.1-2+b1 libkdb5-10t64_1.22.1-2+b1 libkeyutils1_1.6.3-6+b1 libkrb5-3_1.22.1-2+b1 libkrb5-dev_1.22.1-2+b1 libkrb5support0_1.22.1-2+b1 libksba8_1.6.8-2 libldap-2.5-0_2.5.19+dfsg-1 libldap-dev_2.6.10+dfsg-1+b1 libldap2_2.6.10+dfsg-1+b1 liblsan0_16-20260423-1 liblz4-1_1.10.0-10 liblzma-dev_5.8.3-1 liblzma5_5.8.3-1 libmagic-mgc_1:5.46-5+b2 libmagic1t64_1:5.46-5+b2 libmd0_1.1.0-2+b2 libmount1_2.42-4 libmpc3_1.3.1-3 libmpfr6_4.2.2-3 libncurses6_6.6+20251231-1 libncursesw6_6.6+20251231-1 libnettle8t64_3.10.2-1+b1 libnghttp2-14_1.69.0-1 libnghttp2-dev_1.69.0-1 libnghttp3-9_1.15.0-1 libnghttp3-dev_1.15.0-1 libngtcp2-16_1.22.1-1 libngtcp2-crypto-gnutls-dev_1.22.1-1 libngtcp2-crypto-gnutls8_1.22.1-1 libngtcp2-dev_1.22.1-1 libnpth0t64_1.8-3+b1 libp11-kit-dev_0.26.2-2 libp11-kit0_0.26.2-2 libpam-modules_1.7.0-5+b1 libpam-modules-bin_1.7.0-5+b1 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5+b1 libpcre2-8-0_10.46-1+b1 libperl-dev_5.40.1-7+b1 libperl5.38t64_5.38.2-5 libperl5.40_5.40.1-7+b1 libpipeline1_1.5.8-3 libpkgconf7_2.5.1-4 libproc2-0_2:4.0.4-9+b2 libpsl-dev_0.21.5-1 libpsl5t64_0.21.5-1 libpython3-all-dev_3.13.9-3 libpython3-dev_3.13.9-3 libpython3-stdlib_3.13.9-3 libpython3.13_3.13.12-1 libpython3.13-dev_3.13.12-1 libpython3.13-minimal_3.13.12-1 libpython3.13-stdlib_3.13.12-1 libpython3.14_3.14.4-2 libpython3.14-dev_3.14.4-2 libpython3.14-minimal_3.14.4-2 libpython3.14-stdlib_3.14.4-2 libquadmath0_16-20260423-1 libreadline8t64_8.3-4 librtmp-dev_2.6-1 librtmp1_2.6-1 libruby_1:3.3+b1 libruby3.3_3.3.8-2 libsasl2-2_2.1.28+dfsg1-11 libsasl2-modules-db_2.1.28+dfsg1-11 libseccomp2_2.6.0-2+b1 libselinux1_3.10-1 libsemanage-common_3.10-1 libsemanage2_3.10-1 libsepol2_3.10-1 libsframe1_2.44-3 libsframe3_2.46-3 libsmartcols1_2.42-4 libsqlite3-0_3.46.1-9+b1 libssh2-1-dev_1.11.1-2 libssh2-1t64_1.11.1-2 libssl-dev_3.6.2-1 libssl3t64_3.6.2-1 libstdc++-13-dev_13.4.0-10 libstdc++-15-dev_15.2.0-17 libstdc++6_16-20260423-1 libsystemd0_260.1-1 libtasn1-6_4.21.0-2 libtasn1-6-dev_4.21.0-2 libtinfo6_6.6+20251231-1 libtool_2.5.4-11 libtsan2_16-20260423-1 libubsan1_16-20260423-1 libuchardet0_0.0.8-2+b1 libudev1_260.1-1 libunbound8_1.24.2-1+b1 libunistring5_1.4.2-1 libuuid1_2.42-4 libxml2-16_2.15.2+dfsg-0.1 libxxhash0_0.8.3-2+b1 libyaml-0-2_0.2.5-2+b1 libzstd-dev_1.5.7+dfsg-3+b1 libzstd1_1.5.7+dfsg-3+b1 linux-libc-dev_6.19.13-1 locales-all_2.42-15 login_1:4.16.0-2+really2.42-4 login.defs_1:4.19.3-2 m4_1.4.21-1 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20260302-1 media-types_14.0.0 ncurses-base_6.6+20251231-1 ncurses-bin_6.6+20251231-1 netbase_6.5 nettle-dev_3.10.2-1+b1 openssl_3.6.2-1 openssl-provider-legacy_3.6.2-1 passwd_1:4.19.3-2 patch_2.8-2 perl_5.40.1-7+b1 perl-base_5.40.1-7+b1 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.1-7 pinentry-curses_1.3.2-4 pkgconf_2.5.1-4 pkgconf-bin_2.5.1-4 po-debconf_1.0.22 procps_2:4.0.4-9+b2 python3_3.13.9-3 python3-all_3.13.9-3 python3-all-dev_3.13.9-3 python3-autocommand_2.2.2-4 python3-dev_3.13.9-3 python3-inflect_7.5.0-1 python3-jaraco.context_6.0.1-2 python3-jaraco.functools_4.1.0-1 python3-jaraco.text_4.0.0-1 python3-minimal_3.13.9-3 python3-more-itertools_10.8.0-1 python3-pkg-resources_78.1.1-0.1 python3-setuptools_78.1.1-0.1 python3-typeguard_4.4.4-2 python3-typing-extensions_4.15.0-2 python3-zipp_3.23.0-1 python3.13_3.13.12-1 python3.13-dev_3.13.12-1 python3.13-minimal_3.13.12-1 python3.14_3.14.4-2 python3.14-dev_3.14.4-2 python3.14-minimal_3.14.4-2 rake_13.4.2-1 readline-common_8.3-4 rpcsvc-proto_1.4.3-1 ruby_1:3.3+b1 ruby-csv_3.3.5-1 ruby-did-you-mean_2.0.0-1 ruby-net-telnet_0.2.0-1 ruby-ruby2-keywords_0.0.5-1 ruby-rubygems_3.6.7-2 ruby-webrick_1.9.2-1 ruby-xmlrpc_0.3.3-2 ruby3.3_3.3.8-2 rubygems-integration_1.19 samtools_1.22.1-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-3 sensible-utils_0.0.26 sqv_1.3.0-5+b1 swig_4.4.1-2 sysvinit-utils_3.18-1 tar_1.35+dfsg-4 time_1.9-0.4 tzdata_2026b-1 usr-is-merged_39+nmu2 util-linux_2.42-4 xz-utils_5.8.3-1 yaggo_1.5.11-2 zlib1g_1:1.3.dfsg+really1.3.2-3 zlib1g-dev_1:1.3.dfsg+really1.3.2-3 +------------------------------------------------------------------------------+ | Build Sat, 25 Apr 2026 17:51:33 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----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: any all Version: 2.3.1-6 Maintainer: Debian Med Packaging Team Uploaders: Shaun Jackman , Andreas Tille , Michael R. Crusoe , Étienne Mollier Homepage: https://www.genome.umd.edu/jellyfish.html Standards-Version: 4.7.2 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), architecture-is-little-endian, architecture-is-64-bit, d-shlibs, autoconf-archive, yaggo, pkgconf, bc, time, procps, swig, python3-all-dev:native, libpython3-all-dev, dh-sequence-python3, python3-setuptools, perl-xs-dev, perl:native, chrpath, libhts-dev, dos2unix, samtools Package-List: jellyfish deb science optional arch=any jellyfish-examples deb science optional arch=all libjellyfish-2.0-2 deb libs optional arch=any libjellyfish-2.0-dev deb libdevel optional arch=any libjellyfish-perl deb perl optional arch=any python3-dna-jellyfish deb python optional arch=any Checksums-Sha1: 9aaf5f07cecf638544d27ca3de7cb7057184c92c 681990 jellyfish_2.3.1.orig.tar.gz f9f0554c337d61a96abeef3dcb4ed3e62c299c87 13600 jellyfish_2.3.1-6.debian.tar.xz Checksums-Sha256: 540d09457fb4e14b98c7f1428cf885c333e2d6ef4f6a3735aa06be13eb523d69 681990 jellyfish_2.3.1.orig.tar.gz 1d42fd4fcb0a81634e1e7de6bedee282ecc2f772583c0ac9793d0ec98aacb221 13600 jellyfish_2.3.1-6.debian.tar.xz Files: 27fb29ad3edfe25d776cfbf98dcc8c0e 681990 jellyfish_2.3.1.orig.tar.gz 60e49df49d7175420b31ea2c407468bd 13600 jellyfish_2.3.1-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEI3pUsQKHKL8A7zH00Ot2KGX8XjYFAmnnvm4UHHNlcmdpb2Rq QGRlYmlhbi5vcmcACgkQ0Ot2KGX8XjZvww/9EVyaYP324GnYRSezasbkjMVeVXvl 7eK1TRr1tX+f60FExDCfGs3pnpIqSby9z3pUd68VJGkPNac+7bxjQMcQs1pc29QU kpufKHsDrCfgjPGNoivMckIfthigZTo0UFJxpS3YO+JfY/ZM0ziBWDsfLNUiPx5n ZT5luF+kHN4vguqUDk1N+qt6aJYySPGCNKTXWMicmegMqNcjUzFuOFIRNPfpPMiY kK0nZorkYDnYGJGms6ofncb4g/08oEV2JkIhId1LX5ZhDq5J4vDEJlJMiOW+J/+R 6inwagQCQYEOenEDNyCA8uH55AoAWfm/r4Iz/MAPELNDthHjUNxPAPho4qgzGL5g elJMOOiTK4nRXUQAyWlg1G8DUCZ2RwzyxIg+6ZvhKuLmBi/Gh5E5XV9t8IKLxM/H DN9bTvqPruMGwid3sU8LsbTWj99GQYYmu2RJxSJDwiXCAWUBrXOXVQcidOSyD+UE ZiiTr462epwRB8oO83gJwIRaBK0ARQzUy8slawxMlPlLaw2LHpP7x2tgv18v9I6j 6s/PGQHnJIhnh/41yxKmiqdgUi3yF+7NkDXb/kaTj8n/ZpLd205b3hCFxf/L7vyA Ebetsk9z1rEzlhIu0m0GUh/MfBr2xfTBTI6G4Mo7A41tn+frACCqifGvNZI7r9Zh L0N0goYyg8pErZI= =qZJn -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./jellyfish_2.3.1-6.dsc: missing OpenPGP keyrings dpkg-source: info: verifying ./jellyfish_2.3.1-6.dsc dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-keyring.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-tag2upload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting jellyfish in /build/jellyfish-bM2jHV/jellyfish-2.3.1 dpkg-source: info: unpacking jellyfish_2.3.1.orig.tar.gz dpkg-source: info: unpacking jellyfish_2.3.1-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying drop_distutils dpkg-source: info: applying manpage_whatis_entry.patch dpkg-source: info: applying portability.patch dpkg-source: info: applying test_needs_bash dpkg-source: info: applying python3 clean up apt cache ------------------ Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands Sat, 25 Apr 2026 17:51:34 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network jellyfish_2.3.1-6 sid amd64 -------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network jellyfish_2.3.1-6 sid amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/jellyfish-bM2jHV/jellyfish-2.3.1 SCHROOT_ALIAS_NAME=sid-amd64-debomatic SCHROOT_CHROOT_NAME=sid-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=sid-amd64-debomatic-3dbf649a-69f5-49ef-9b64-83620d0ee5e8 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -Zxz dpkg-buildpackage: info: source package jellyfish dpkg-buildpackage: info: source version 2.3.1-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sergio Durigan Junior dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules execute_after_dh_clean make[1]: Entering directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' if [ -d debian/tmp_save_tests ] ; then \ mv debian/tmp_save_tests/* tests ; \ rmdir debian/tmp_save_tests ; \ fi make[1]: Leaving directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building jellyfish using existing ../jellyfish_2.3.1.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: warning: ignoring deletion of file swig/python/jellyfish.py, use --include-removal to override dpkg-source: info: building jellyfish in ../jellyfish_2.3.1-6.debian.tar.xz dpkg-source: info: building jellyfish in ../jellyfish_2.3.1-6.dsc debian/rules binary dh binary debian/rules override_dh_update_autotools_config make[1]: Entering directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' # use python configuration from autoconf-archive mv m4/m4-ax_python_devel.m4 /tmp dh_update_autotools_config make[1]: Leaving directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' dh_autoreconf autoreconf: export WARNINGS= autoreconf: Entering directory '.' autoreconf: configure.ac: not using Gettext autoreconf: running: aclocal --force -I m4 autoreconf: configure.ac: tracing autoreconf: running: libtoolize --copy --force 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' autoreconf: configure.ac: not using Intltool autoreconf: configure.ac: not using Gtkdoc autoreconf: running: aclocal --force -I m4 autoreconf: running: /usr/bin/autoconf --force autoreconf: running: /usr/bin/autoheader --force autoreconf: running: automake --add-missing --copy --force-missing 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' autoreconf: Leaving directory '.' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' dh_auto_configure -- --enable-swig --enable-perl-binding --enable-htslib --enable-python-binding PYTHON=/usr/bin/python3 ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-swig --enable-perl-binding --enable-htslib --enable-python-binding PYTHON=/usr/bin/python3 checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/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 xargs -n works... yes checking whether UID '1002' is supported by ustar format... yes checking whether GID '110' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/x86_64-linux-gnu-ld checking if the linker (/usr/bin/x86_64-linux-gnu-ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/x86_64-linux-gnu-ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ranlib... ranlib checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/x86_64-linux-gnu-ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for ld... /usr/bin/x86_64-linux-gnu-ld -m elf_x86_64 checking if the linker (/usr/bin/x86_64-linux-gnu-ld -m elf_x86_64) is GNU ld... yes checking for shared library run path origin... done checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/x86_64-linux-gnu-ld -m elf_x86_64 checking if the linker (/usr/bin/x86_64-linux-gnu-ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/x86_64-linux-gnu-ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/x86_64-linux-gnu-ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking 32-bit host C ABI... no checking for egrep -e... (cached) /usr/bin/grep -E checking for ELF binary format... yes checking for the common suffixes of directories in the library search path... lib,lib,lib64 checking for htslib... yes checking for samtools... /usr/bin/samtools checking for unix2dos... /usr/bin/unix2dos checking for md5sum... md5sum checking for yaggo... /usr/bin/yaggo checking for x86 cpuid output... unknown checking for x86-AVX xgetbv output... unknown checking for x86 cpuid 0x00000000 output... 12:756e6547:6c65746e:49656e69 checking for x86 cpuid 0x80000000 output... 80000008:756e6547:6c65746e:49656e69 checking for x86 cpuid 0x00000001 output... 506e3:800:fffa3223:f8bfbff checking for x86 cpuid 0x00000007 output... 0:9c07af:4:ac000400 checking for x86 cpuid 0x80000001 output... 506e3:0:121:2c100800 checking for x86-AVX xgetbv 0x00000000 output... 7:0 checking whether RDRND is supported by the processor... yes checking whether RDRND is supported by the processor and OS... yes checking whether C++ compiler accepts -mrdrnd... yes checking whether BMI1 is supported by the processor... yes checking whether BMI1 is supported by the processor and OS... yes checking whether C++ compiler accepts -mbmi... yes checking whether BMI2 is supported by the processor... yes checking whether BMI2 is supported by the processor and OS... yes checking whether C++ compiler accepts -mbmi2... yes checking whether ADX is supported by the processor... yes checking whether ADX is supported by the processor and OS... yes checking whether C++ compiler accepts -madx... yes checking whether MPX is supported by the processor... no checking whether PREFETCHWT1 is supported by the processor... no checking whether ABM is supported by the processor... yes checking whether ABM is supported by the processor and OS... yes checking whether C++ compiler accepts -mabm... yes checking whether MMX is supported by the processor... yes checking whether MMX is supported by the processor and OS... yes checking whether C++ compiler accepts -mmmx... yes checking whether SSE is supported by the processor... yes checking whether SSE is supported by the processor and OS... yes checking whether C++ compiler accepts -msse... yes checking whether SSE2 is supported by the processor... yes checking whether SSE2 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse2... yes checking whether SSE3 is supported by the processor... yes checking whether SSE3 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse3... yes checking whether SSSE3 is supported by the processor... yes checking whether SSSE3 is supported by the processor and OS... yes checking whether C++ compiler accepts -mssse3... yes checking whether SSE4.1 is supported by the processor... yes checking whether SSE4.1 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse4.1... yes checking whether SSE4.2 is supported by the processor... yes checking whether SSE4.2 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse4.2... yes checking whether SSE4a is supported by the processor... no checking whether SHA is supported by the processor... no checking whether AES is supported by the processor... yes checking whether AES is supported by the processor and OS... yes checking whether C++ compiler accepts -maes... yes checking whether AVX is supported by the processor... yes checking whether AVX is supported by the processor and OS... yes checking whether C++ compiler accepts -mavx... yes checking whether FMA3 is supported by the processor... yes checking whether FMA3 is supported by the processor and OS... yes checking whether C++ compiler accepts -mfma... yes checking whether FMA4 is supported by the processor... no checking whether XOP is supported by the processor... no checking whether AVX2 is supported by the processor... yes checking whether AVX2 is supported by the processor and OS... yes checking whether C++ compiler accepts -mavx2... yes checking whether AVX512-F is supported by the processor... no checking whether AVX512-CD is supported by the processor... no checking whether AVX512-PF is supported by the processor... no checking whether AVX512-ER is supported by the processor... no checking whether AVX512-VL is supported by the processor... no checking whether AVX512-BW is supported by the processor... no checking whether AVX512-DQ is supported by the processor... no checking whether AVX512-IFMA is supported by the processor... no checking whether AVX512-VBMI is supported by the processor... no checking for __int128... yes checking for std::numeric_limits<__int128>... yes checking for _NSGetExecutablePath... no checking for execinfo.h... yes checking for ext/stdio_filebuf.h... yes checking for sys/syscall.h... yes checking for sys/prctl.h... yes checking for siginfo_t.si_int... yes checking for swig... /usr/bin/swig checking SWIG version... 4.4.1 checking for SWIG library... /usr/share/swig/4.4.1 checking for python... /usr/bin/python3 checking for a version of Python >= '2.1.0'... yes checking for the sysconfig Python package... yes checking for Python include path... -I/usr/include/python3.13 checking for Python library path... -L/usr/lib/x86_64-linux-gnu -lpython3.13 checking for Python site-packages path... /usr/lib/python3.13/site-packages checking for Python platform specific site-packages path... /usr/lib/python3.13/site-packages checking python extra libraries... -ldl -lm checking python extra linking flags... -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions checking consistency of all components of python development environment... yes checking for perl... /usr/bin/perl checking for Perl prefix... /usr checking for Perl extension include path... /usr/lib/x86_64-linux-gnu/perl/5.40/CORE checking for Perl extension target directory... /usr/lib/perl/5.40.0 checking for Perl extensions C preprocessor flags... -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include checking for Perl extensions linker flags... -shared -L/usr/local/lib -fstack-protector-strong checking for posix_memalign... yes checking for aligned_alloc... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating compat.sh config.status: creating jellyfish-2.0.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_configure --sourcedirectory=swig/perl5 cd swig/perl5 && /usr/bin/perl Makefile.PL INSTALLDIRS=vendor OPTIMIZE="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" LD="x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -lpthread" -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1 -L/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -lpthread -L/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu Warning (mostly harmless): No library found for -ljellyfish-2.0 Generating a Unix-style Makefile Writing Makefile for jellyfish Writing MYMETA.yml and MYMETA.json dh_auto_configure --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:385: python3.14 setup.py config running config I: pybuild base:385: python3.13 setup.py config running config mv /tmp/m4-ax_python_devel.m4 m4 make[1]: Leaving directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' debian/rules override_dh_auto_build make[1]: Entering directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' 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-bM2jHV/jellyfish-2.3.1' /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-bM2jHV/jellyfish-2.3.1' g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o sub_commands/jellyfish.o sub_commands/jellyfish.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o sub_commands/count_main.o sub_commands/count_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o sub_commands/info_main.o sub_commands/info_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o sub_commands/dump_main.o sub_commands/dump_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time 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-fno-strict-aliasing -pipe -I/usr/local/include -I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo `test -f 'swig/perl5/swig_wrap.cpp' || echo './'`swig/perl5/swig_wrap.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection 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-I/usr/include/python3.13 -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c swig/python/swig_wrap.cpp -o swig/python/swig_python__dna_jellyfish_la-swig_wrap.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3.13/site-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o jellyfish/backtrace.o jellyfish/backtrace.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o jellyfish/dbg.o jellyfish/dbg.cc /bin/bash ./libtool --tag=CXX --mode=link g++ -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -pthread -L/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -lhts -R/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o bin/generate_sequence jellyfish/generate_sequence.o jellyfish/mersenne.o jellyfish/backtrace.o jellyfish/dbg.o libjellyfish-2.0.la libtool: link: g++ -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/generate_sequence jellyfish/generate_sequence.o jellyfish/mersenne.o jellyfish/backtrace.o jellyfish/dbg.o -L/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o unit_tests/bin_test_all-test_main.o `test -f 'unit_tests/test_main.cc' || echo './'`unit_tests/test_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o unit_tests/bin_test_all-test_misc.o `test -f 'unit_tests/test_misc.cc' || echo './'`unit_tests/test_misc.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o unit_tests/bin_test_all-test_offsets_key_value.o `test -f 'unit_tests/test_offsets_key_value.cc' || echo './'`unit_tests/test_offsets_key_value.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o unit_tests/bin_test_all-test_simple_circular_buffer.o `test -f 'unit_tests/test_simple_circular_buffer.cc' || echo './'`unit_tests/test_simple_circular_buffer.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o unit_tests/bin_test_all-test_rectangular_binary_matrix.o `test -f 'unit_tests/test_rectangular_binary_matrix.cc' || echo './'`unit_tests/test_rectangular_binary_matrix.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o unit_tests/bin_test_all-test_mer_dna.o `test -f 'unit_tests/test_mer_dna.cc' || echo './'`unit_tests/test_mer_dna.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o unit_tests/bin_test_all-test_large_hash_array.o `test -f 'unit_tests/test_large_hash_array.cc' || echo './'`unit_tests/test_large_hash_array.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o unit_tests/bin_test_all-test_mer_overlap_sequence_parser.o `test -f 'unit_tests/test_mer_overlap_sequence_parser.cc' || echo './'`unit_tests/test_mer_overlap_sequence_parser.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o unit_tests/bin_test_all-test_file_header.o `test -f 'unit_tests/test_file_header.cc' || echo './'`unit_tests/test_file_header.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o unit_tests/bin_test_all-test_mer_iterator.o `test -f 'unit_tests/test_mer_iterator.cc' || echo './'`unit_tests/test_mer_iterator.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o unit_tests/bin_test_all-test_hash_counter.o `test -f 'unit_tests/test_hash_counter.cc' || echo './'`unit_tests/test_hash_counter.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o unit_tests/bin_test_all-test_mer_heap.o `test -f 'unit_tests/test_mer_heap.cc' || echo './'`unit_tests/test_mer_heap.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o unit_tests/bin_test_all-test_stream_iterator.o `test -f 'unit_tests/test_stream_iterator.cc' || echo './'`unit_tests/test_stream_iterator.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o unit_tests/bin_test_all-test_token_ring.o `test -f 'unit_tests/test_token_ring.cc' || echo './'`unit_tests/test_token_ring.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o unit_tests/bin_test_all-test_text_dumper.o `test -f 'unit_tests/test_text_dumper.cc' || echo './'`unit_tests/test_text_dumper.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o unit_tests/bin_test_all-test_dumpers.o `test -f 'unit_tests/test_dumpers.cc' || echo './'`unit_tests/test_dumpers.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o unit_tests/bin_test_all-test_mapped_file.o `test -f 'unit_tests/test_mapped_file.cc' || echo './'`unit_tests/test_mapped_file.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o unit_tests/bin_test_all-test_int128.o `test -f 'unit_tests/test_int128.cc' || echo './'`unit_tests/test_int128.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o unit_tests/bin_test_all-test_mer_dna_bloom_counter.o `test -f 'unit_tests/test_mer_dna_bloom_counter.cc' || echo './'`unit_tests/test_mer_dna_bloom_counter.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o unit_tests/bin_test_all-test_whole_sequence_parser.o `test -f 'unit_tests/test_whole_sequence_parser.cc' || echo './'`unit_tests/test_whole_sequence_parser.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o unit_tests/bin_test_all-test_allocators_mmap.o `test -f 'unit_tests/test_allocators_mmap.cc' || echo './'`unit_tests/test_allocators_mmap.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o unit_tests/bin_test_all-test_cooperative_pool2.o `test -f 'unit_tests/test_cooperative_pool2.cc' || echo './'`unit_tests/test_cooperative_pool2.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o unit_tests/bin_test_all-test_generator_manager.o `test -f 'unit_tests/test_generator_manager.cc' || echo './'`unit_tests/test_generator_manager.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o unit_tests/bin_test_all-test_atomic_bits_array.o `test -f 'unit_tests/test_atomic_bits_array.cc' || echo './'`unit_tests/test_atomic_bits_array.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o unit_tests/bin_test_all-test_stdio_filebuf.o `test -f 'unit_tests/test_stdio_filebuf.cc' || echo './'`unit_tests/test_stdio_filebuf.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o jellyfish/bin_test_all-backtrace.o `test -f 'jellyfish/backtrace.cc' || echo './'`jellyfish/backtrace.cc /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -I./unit_tests/gtest -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o unit_tests/gtest/src/libgtest_la-gtest-all.lo `test -f 'unit_tests/gtest/src/gtest-all.cc' || echo './'`unit_tests/gtest/src/gtest-all.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -I./unit_tests/gtest -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c unit_tests/gtest/src/gtest-all.cc -fPIC -DPIC -o unit_tests/gtest/src/.libs/libgtest_la-gtest-all.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -I./unit_tests/gtest -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c unit_tests/gtest/src/gtest-all.cc -o unit_tests/gtest/src/libgtest_la-gtest-all.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -I./unit_tests -I./unit_tests/gtest -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -pthread -L/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -lhts -R/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o libgtest.la unit_tests/gtest/src/libgtest_la-gtest-all.lo libtool: link: ar cr .libs/libgtest.a unit_tests/gtest/src/.libs/libgtest_la-gtest-all.o libtool: link: ranlib .libs/libgtest.a libtool: link: ( cd ".libs" && rm -f "libgtest.la" && ln -s "../libgtest.la" "libgtest.la" ) /bin/bash ./libtool --tag=CXX --mode=link g++ -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -pthread -L/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -lhts -R/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o bin/test_all unit_tests/bin_test_all-test_main.o unit_tests/bin_test_all-test_misc.o unit_tests/bin_test_all-test_offsets_key_value.o unit_tests/bin_test_all-test_simple_circular_buffer.o unit_tests/bin_test_all-test_rectangular_binary_matrix.o unit_tests/bin_test_all-test_mer_dna.o unit_tests/bin_test_all-test_large_hash_array.o unit_tests/bin_test_all-test_mer_overlap_sequence_parser.o unit_tests/bin_test_all-test_file_header.o unit_tests/bin_test_all-test_mer_iterator.o unit_tests/bin_test_all-test_hash_counter.o unit_tests/bin_test_all-test_mer_heap.o unit_tests/bin_test_all-test_stream_iterator.o unit_tests/bin_test_all-test_token_ring.o unit_tests/bin_test_all-test_text_dumper.o unit_tests/bin_test_all-test_dumpers.o unit_tests/bin_test_all-test_mapped_file.o unit_tests/bin_test_all-test_int128.o unit_tests/bin_test_all-test_mer_dna_bloom_counter.o unit_tests/bin_test_all-test_whole_sequence_parser.o unit_tests/bin_test_all-test_allocators_mmap.o unit_tests/bin_test_all-test_cooperative_pool2.o unit_tests/bin_test_all-test_generator_manager.o unit_tests/bin_test_all-test_atomic_bits_array.o unit_tests/bin_test_all-test_stdio_filebuf.o jellyfish/bin_test_all-backtrace.o libgtest.la libjellyfish-2.0.la libtool: link: g++ -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -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-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu ./.libs/libgtest.a -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o jellyfish/fastq2sam.o jellyfish/fastq2sam.cc /bin/bash ./libtool --tag=CXX --mode=link g++ -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -pthread -L/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -lhts -R/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o bin/fastq2sam jellyfish/fastq2sam.o libjellyfish-2.0.la libtool: link: g++ -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/fastq2sam jellyfish/fastq2sam.o -L/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu make[2]: Leaving directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' dh_auto_install -- install-data make -j1 install DESTDIR=/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp AM_UPDATE_INFO_DIR=no install-data make[2]: Entering directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' make install-am make[3]: Entering directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' make[4]: Entering directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; }) libtool: install: (cd /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/bin' /bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/bin' libtool: warning: 'libjellyfish-2.0.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c bin/.libs/jellyfish /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/bin/jellyfish /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/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-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/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-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/jellyfish-bM2jHV/jellyfish-2.3.1; /bin/bash "/build/jellyfish-bM2jHV/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.40.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/15/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/15/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/15 -L/usr/lib/gcc/x86_64-linux-gnu/15/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/15/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/15/../../.. -L/lib -L/usr/lib -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/15/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/15/../../../x86_64-linux-gnu/crtn.o -Werror -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -Werror=format-security -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-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0 && { 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-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0 && { 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-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: chmod 644 /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: ranlib /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.40.0' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' libtool: warning: relinking 'swig/python/_dna_jellyfish.la' libtool: install: (cd /build/jellyfish-bM2jHV/jellyfish-2.3.1; /bin/bash "/build/jellyfish-bM2jHV/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3.13/site-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/15/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/15/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/15 -L/usr/lib/gcc/x86_64-linux-gnu/15/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/15/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/15/../../.. -L/lib -L/usr/lib -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/15/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/15/../../../x86_64-linux-gnu/crtn.o -Werror -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -Werror=format-security -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-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0 || { rm -f _dna_jellyfish.so.0 && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0; }; }) libtool: install: (cd /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so || { rm -f _dna_jellyfish.so && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.lai /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.la libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3.13/site-packages/dna_jellyfish' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' make[4]: Leaving directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' make[3]: Leaving directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/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-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/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-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; }) libtool: install: (cd /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/jellyfish-bM2jHV/jellyfish-2.3.1; /bin/bash "/build/jellyfish-bM2jHV/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.40.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/15/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/15/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/15 -L/usr/lib/gcc/x86_64-linux-gnu/15/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/15/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/15/../../.. -L/lib -L/usr/lib -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/15/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/15/../../../x86_64-linux-gnu/crtn.o -Werror -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -Werror=format-security -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-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0 && { 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-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0 && { 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-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: chmod 644 /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: ranlib /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.40.0' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' libtool: warning: relinking 'swig/python/_dna_jellyfish.la' libtool: install: (cd /build/jellyfish-bM2jHV/jellyfish-2.3.1; /bin/bash "/build/jellyfish-bM2jHV/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3.13/site-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/15/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/15/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/15 -L/usr/lib/gcc/x86_64-linux-gnu/15/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/15/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/15/../../.. -L/lib -L/usr/lib -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/15/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/15/../../../x86_64-linux-gnu/crtn.o -Werror -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -Werror=format-security -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-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0 || { rm -f _dna_jellyfish.so.0 && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0; }; }) libtool: install: (cd /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so || { rm -f _dna_jellyfish.so && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.lai /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.la libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3.13/site-packages/dna_jellyfish' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' make[2]: Leaving directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' dh_auto_build --sourcedirectory=swig/perl5 cd swig/perl5 && make -j2 make[2]: Entering directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1/swig/perl5' Running Mkbootstrap for jellyfish () g++ -c -std=c++0x -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.0.1\" -DXS_VERSION=\"0.0.1\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" swig_wrap.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ chmod 644 "jellyfish.bs" "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- jellyfish.bs blib/arch/auto/jellyfish/jellyfish.bs 644 rm -f blib/arch/auto/jellyfish/jellyfish.so x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-bM2jHV/jellyfish-2.3.1/swig/perl5' dh_auto_build --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:385: /usr/bin/python3.14 setup.py build build_ext -L/build/jellyfish-bM2jHV/jellyfish-2.3.1/.libs running build running build_py copying dna_jellyfish.py -> /build/jellyfish-bM2jHV/jellyfish-2.3.1/.pybuild/cpython3_3.14_dna_jellyfish/build running build_ext building '_dna_jellyfish' extension creating build/temp.linux-x86_64-cpython-314 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1 -I/usr/include/python3.14 -c swig_wrap.cpp -o build/temp.linux-x86_64-cpython-314/swig_wrap.o -std=c++0x x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -lpthread -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-314/swig_wrap.o -L-L/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -L/build/jellyfish-bM2jHV/jellyfish-2.3.1/.libs -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -lpthread -o /build/jellyfish-bM2jHV/jellyfish-2.3.1/.pybuild/cpython3_3.14_dna_jellyfish/build/_dna_jellyfish.cpython-314-x86_64-linux-gnu.so -Wl,-rpath,-L/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu I: pybuild base:385: /usr/bin/python3 setup.py build build_ext -L/build/jellyfish-bM2jHV/jellyfish-2.3.1/.libs running build running build_py copying dna_jellyfish.py -> /build/jellyfish-bM2jHV/jellyfish-2.3.1/.pybuild/cpython3_3.13_dna_jellyfish/build running build_ext building '_dna_jellyfish' extension creating build/temp.linux-x86_64-cpython-313 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1 -I/usr/include/python3.13 -c swig_wrap.cpp -o build/temp.linux-x86_64-cpython-313/swig_wrap.o -std=c++0x x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -lpthread -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/swig_wrap.o -L-L/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -L/build/jellyfish-bM2jHV/jellyfish-2.3.1/.libs -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -lpthread -o /build/jellyfish-bM2jHV/jellyfish-2.3.1/.pybuild/cpython3_3.13_dna_jellyfish/build/_dna_jellyfish.cpython-313-x86_64-linux-gnu.so -Wl,-rpath,-L/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu make[1]: Leaving directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' debian/rules override_dh_auto_test make[1]: Entering directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' if ! dh_auto_test \ ; then echo "E: tests failed, ./test-suite.log follows:" \ ; cat ./test-suite.log \ ; echo "E: end of ./test-suite.log after test failure." \ ; exit 1 \ ; fi make -j2 check TESTSUITEFLAGS="-j2 --verbose" VERBOSE=1 make[2]: Entering directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' make check-am make[3]: Entering directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' make bin/generate_sequence bin/fastq2sam bin/test_all libgtest.la libgtest_main.la make[4]: Entering directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' make[4]: 'bin/generate_sequence' is up to date. make[4]: 'bin/fastq2sam' is up to date. make[4]: 'bin/test_all' is up to date. make[4]: 'libgtest.la' is up to date. /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c -o unit_tests/gtest/src/libgtest_main_la-gtest_main.lo `test -f 'unit_tests/gtest/src/gtest_main.cc' || echo './'`unit_tests/gtest/src/gtest_main.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c unit_tests/gtest/src/gtest_main.cc -fPIC -DPIC -o unit_tests/gtest/src/.libs/libgtest_main_la-gtest_main.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -c unit_tests/gtest/src/gtest_main.cc -o unit_tests/gtest/src/libgtest_main_la-gtest_main.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -pthread -L/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -lhts -R/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o libgtest_main.la unit_tests/gtest/src/libgtest_main_la-gtest_main.lo libgtest.la libtool: link: (cd .libs/libgtest_main.lax/libgtest.a && ar x "/build/jellyfish-bM2jHV/jellyfish-2.3.1/./.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-bM2jHV/jellyfish-2.3.1' make check-TESTS make[4]: Entering directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' make[5]: Entering directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' SKIP: tests/big.sh PASS: tests/generate_sequence.sh PASS: tests/parallel_hashing.sh PASS: tests/merge.sh PASS: unit_tests/unit_tests.sh PASS: tests/subset_hashing.sh PASS: tests/bloom_filter.sh PASS: tests/bloom_counter.sh PASS: tests/large_key.sh PASS: tests/multi_file.sh PASS: tests/sam.sh PASS: tests/small_mers.sh SKIP: tests/swig_ruby.sh PASS: tests/swig_perl.sh PASS: tests/swig_python.sh ============================================================================ Testsuite summary for jellyfish 2.3.1 ============================================================================ # TOTAL: 15 # PASS: 13 # SKIP: 2 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' make[4]: Leaving directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' make[3]: Leaving directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' make[2]: Leaving directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' make[1]: Leaving directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' chrpath --delete bin/.libs/* dh_auto_install -- install-data make -j1 install DESTDIR=/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp AM_UPDATE_INFO_DIR=no install-data make[2]: Entering directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' make install-am make[3]: Entering directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' make[4]: Entering directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; }) libtool: install: (cd /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/bin' /bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/bin' libtool: warning: 'libjellyfish-2.0.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c bin/.libs/jellyfish /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/bin/jellyfish /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/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-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/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-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/jellyfish-bM2jHV/jellyfish-2.3.1; /bin/bash "/build/jellyfish-bM2jHV/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.40.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/15/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/15/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/15 -L/usr/lib/gcc/x86_64-linux-gnu/15/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/15/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/15/../../.. -L/lib -L/usr/lib -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/15/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/15/../../../x86_64-linux-gnu/crtn.o -Werror -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -Werror=format-security -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-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0 && { 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-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0 && { 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-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: chmod 644 /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: ranlib /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.40.0' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' libtool: warning: relinking 'swig/python/_dna_jellyfish.la' libtool: install: (cd /build/jellyfish-bM2jHV/jellyfish-2.3.1; /bin/bash "/build/jellyfish-bM2jHV/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3.13/site-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/15/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/15/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/15 -L/usr/lib/gcc/x86_64-linux-gnu/15/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/15/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/15/../../.. -L/lib -L/usr/lib -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/15/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/15/../../../x86_64-linux-gnu/crtn.o -Werror -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -Werror=format-security -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-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0 || { rm -f _dna_jellyfish.so.0 && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0; }; }) libtool: install: (cd /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so || { rm -f _dna_jellyfish.so && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.lai /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.la libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3.13/site-packages/dna_jellyfish' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' make[4]: Leaving directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' make[3]: Leaving directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/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-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/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-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; }) libtool: install: (cd /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/jellyfish-bM2jHV/jellyfish-2.3.1; /bin/bash "/build/jellyfish-bM2jHV/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.40.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/15/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/15/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/15 -L/usr/lib/gcc/x86_64-linux-gnu/15/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/15/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/15/../../.. -L/lib -L/usr/lib -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/15/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/15/../../../x86_64-linux-gnu/crtn.o -Werror -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -Werror=format-security -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-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0 && { 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-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0 && { 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-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: chmod 644 /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: ranlib /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.40.0' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' libtool: warning: relinking 'swig/python/_dna_jellyfish.la' libtool: install: (cd /build/jellyfish-bM2jHV/jellyfish-2.3.1; /bin/bash "/build/jellyfish-bM2jHV/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wno-unused-but-set-variable -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3.13/site-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/15/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/15/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/15 -L/usr/lib/gcc/x86_64-linux-gnu/15/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/15/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/15/../../.. -L/lib -L/usr/lib -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/15/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/15/../../../x86_64-linux-gnu/crtn.o -Werror -g -O2 -ffile-prefix-map=/build/jellyfish-bM2jHV/jellyfish-2.3.1=. -fstack-protector-strong -Werror=format-security -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-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0 || { rm -f _dna_jellyfish.so.0 && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0; }; }) libtool: install: (cd /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so || { rm -f _dna_jellyfish.so && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.lai /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.la libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3.13/site-packages/dna_jellyfish' /usr/bin/mkdir -p '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' make[2]: Leaving directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' dh_auto_install --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:385: /usr/bin/python3.14 setup.py install --root /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/python3-dna-jellyfish running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py copying dna_jellyfish.py -> /build/jellyfish-bM2jHV/jellyfish-2.3.1/.pybuild/cpython3_3.14_dna_jellyfish/build running build_ext running install_lib creating /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.14/dist-packages copying /build/jellyfish-bM2jHV/jellyfish-2.3.1/.pybuild/cpython3_3.14_dna_jellyfish/build/dna_jellyfish.py -> /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.14/dist-packages copying /build/jellyfish-bM2jHV/jellyfish-2.3.1/.pybuild/cpython3_3.14_dna_jellyfish/build/_dna_jellyfish.cpython-314-x86_64-linux-gnu.so -> /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.14/dist-packages byte-compiling /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.14/dist-packages/dna_jellyfish.py to dna_jellyfish.cpython-314.pyc running install_egg_info running egg_info creating dna_jellyfish.egg-info writing dna_jellyfish.egg-info/PKG-INFO writing dependency_links to dna_jellyfish.egg-info/dependency_links.txt writing top-level names to dna_jellyfish.egg-info/top_level.txt writing manifest file 'dna_jellyfish.egg-info/SOURCES.txt' reading manifest file 'dna_jellyfish.egg-info/SOURCES.txt' writing manifest file 'dna_jellyfish.egg-info/SOURCES.txt' Copying dna_jellyfish.egg-info to /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.14/dist-packages/dna_jellyfish-0.0.1.egg-info Skipping SOURCES.txt running install_scripts I: pybuild base:385: /usr/bin/python3 setup.py install --root /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/python3-dna-jellyfish running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py copying dna_jellyfish.py -> /build/jellyfish-bM2jHV/jellyfish-2.3.1/.pybuild/cpython3_3.13_dna_jellyfish/build running build_ext running install_lib creating /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.13/dist-packages copying /build/jellyfish-bM2jHV/jellyfish-2.3.1/.pybuild/cpython3_3.13_dna_jellyfish/build/_dna_jellyfish.cpython-313-x86_64-linux-gnu.so -> /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.13/dist-packages copying /build/jellyfish-bM2jHV/jellyfish-2.3.1/.pybuild/cpython3_3.13_dna_jellyfish/build/dna_jellyfish.py -> /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.13/dist-packages byte-compiling /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.13/dist-packages/dna_jellyfish.py to dna_jellyfish.cpython-313.pyc running install_egg_info running egg_info writing dna_jellyfish.egg-info/PKG-INFO writing dependency_links to dna_jellyfish.egg-info/dependency_links.txt writing top-level names to dna_jellyfish.egg-info/top_level.txt reading manifest file 'dna_jellyfish.egg-info/SOURCES.txt' writing manifest file 'dna_jellyfish.egg-info/SOURCES.txt' Copying dna_jellyfish.egg-info to /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.13/dist-packages/dna_jellyfish-0.0.1.egg-info Skipping SOURCES.txt running install_scripts dh_auto_install --sourcedirectory=swig/perl5 cd swig/perl5 && make -j2 install DESTDIR=/build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr make[2]: Entering directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1/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-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/jellyfish/jellyfish.so make[2]: Leaving directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1/swig/perl5' ls -l debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so -r-xr-xr-x 1 debomatic sbuild 1125672 Apr 25 17:54 debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/jellyfish/jellyfish.so if [ ! -e debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so ] ; then sleep 1; fi chmod +w debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so chrpath --delete debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so dh_install d-shlibmove --commit \ --multiarch \ --devunversioned \ --movedev "debian/tmp/usr/include/jellyfish*/jellyfish/*.hpp" usr/include/jellyfish \ --movedev "debian/tmp/usr/include/jellyfish*/jellyfish/*.h" usr/include/jellyfish \ --movedev config.h usr/include/jellyfish \ debian/tmp/usr/lib/*/libjellyfish-*.so Library package automatic movement utility set -e install -d -m 755 debian/libjellyfish-2.0-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/libjellyfish-2.0-2/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a debian/libjellyfish-2.0-dev/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.la debian/libjellyfish-2.0-dev/usr/lib/x86_64-linux-gnu || true mv debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so debian/libjellyfish-2.0-dev/usr/lib/x86_64-linux-gnu mv /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2 debian/libjellyfish-2.0-2/usr/lib/x86_64-linux-gnu mv /build/jellyfish-bM2jHV/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 debian/libjellyfish-2.0-2/usr/lib/x86_64-linux-gnu PKGDEV=libjellyfish-2.0-dev PKGSHL=libjellyfish-2.0-2 install -d -m 755 debian/libjellyfish-2.0-dev/usr/include/jellyfish mv debian/tmp/usr/include/jellyfish*/jellyfish/*.hpp debian/libjellyfish-2.0-dev/usr/include/jellyfish install -d -m 755 debian/libjellyfish-2.0-dev/usr/include/jellyfish mv debian/tmp/usr/include/jellyfish*/jellyfish/*.h debian/libjellyfish-2.0-dev/usr/include/jellyfish install -d -m 755 debian/libjellyfish-2.0-dev/usr/include/jellyfish mv config.h debian/libjellyfish-2.0-dev/usr/include/jellyfish sed -i "/dependency_libs/ s/'.*'/''/" ./debian/libjellyfish-2.0-dev/usr/lib/x86_64-linux-gnu/*.la chrpath --delete debian/*/usr/lib/python*/dist-packages/_dna_jellyfish*.so make[1]: Leaving directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' dh_install debian/rules execute_after_dh_install make[1]: Entering directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' # Fix PACKAGE_NAME defined in config.h colliding with potential reverse # dependencies autotools invocations, per lintian warning. rm -vf debian/libjellyfish-2.0-dev/usr/include/jellyfish/config.h removed 'debian/libjellyfish-2.0-dev/usr/include/jellyfish/config.h' make[1]: Leaving directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' 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-bM2jHV/jellyfish-2.3.1' # Python files are just installed rm -rf debian/tmp/usr/lib/python3/dist-packages # Necessary Perl files are just installed rm -rf debian/tmp/usr/lib/perl/5.* dh_missing make[1]: Leaving directory '/build/jellyfish-bM2jHV/jellyfish-2.3.1' dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package jellyfish-examples: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'jellyfish' in '../jellyfish_2.3.1-6_amd64.deb'. dpkg-deb: building package 'python3-dna-jellyfish' in '../python3-dna-jellyfish_2.3.1-6_amd64.deb'. dpkg-deb: building package 'python3-dna-jellyfish-dbgsym' in '../python3-dna-jellyfish-dbgsym_2.3.1-6_amd64.deb'. dpkg-deb: building package 'libjellyfish-perl' in '../libjellyfish-perl_2.3.1-6_amd64.deb'. dpkg-deb: building package 'libjellyfish-perl-dbgsym' in '../libjellyfish-perl-dbgsym_2.3.1-6_amd64.deb'. dpkg-deb: building package 'jellyfish-examples' in '../jellyfish-examples_2.3.1-6_all.deb'. dpkg-deb: building package 'jellyfish-dbgsym' in '../jellyfish-dbgsym_2.3.1-6_amd64.deb'. dpkg-deb: building package 'libjellyfish-2.0-2' in '../libjellyfish-2.0-2_2.3.1-6_amd64.deb'. dpkg-deb: building package 'libjellyfish-2.0-2-dbgsym' in '../libjellyfish-2.0-2-dbgsym_2.3.1-6_amd64.deb'. dpkg-deb: building package 'libjellyfish-2.0-dev' in '../libjellyfish-2.0-dev_2.3.1-6_amd64.deb'. dpkg-genbuildinfo -O../jellyfish_2.3.1-6_amd64.buildinfo dpkg-genchanges -O../jellyfish_2.3.1-6_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2026-04-25T17:57:20Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Sat, 25 Apr 2026 17:57:21 +0000 | +------------------------------------------------------------------------------+ jellyfish_2.3.1-6_amd64.changes: -------------------------------- Format: 1.8 Date: Tue, 21 Apr 2026 14:08:05 -0400 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: source amd64 all Version: 2.3.1-6 Distribution: sid Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sergio Durigan Junior 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: 1133507 Changes: jellyfish (2.3.1-6) unstable; urgency=medium . * Team upload. * d/rules: Disable -Wunused-but-set-variable. Some of the occurrences the flag complains about are actually good code (test) that shouldn't be changed. (Closes: #1133507) Checksums-Sha1: 3aeaa933b9f1cd340eaa22fa00d8e20e4768905e 1851 jellyfish_2.3.1-6.dsc f9f0554c337d61a96abeef3dcb4ed3e62c299c87 13600 jellyfish_2.3.1-6.debian.tar.xz 80ca34e8071663a5f6dac97c8cfcdf15943daf49 7688632 jellyfish-dbgsym_2.3.1-6_amd64.deb c1a131be20d67cf61770dbb0815256fd5f1e7c4c 12892 jellyfish-examples_2.3.1-6_all.deb 8e0939b79d92848ba78ef34079708ea50fa8df9d 12319 jellyfish_2.3.1-6_amd64.buildinfo 60192fc58b30ab58eb763eade4b2e4744a01132e 809548 jellyfish_2.3.1-6_amd64.deb f415a5f00358a12909c3fd7f5657139cc9256093 539688 libjellyfish-2.0-2-dbgsym_2.3.1-6_amd64.deb 82a69123dc579ec9275adf4e6e9e56b5089e1be1 66232 libjellyfish-2.0-2_2.3.1-6_amd64.deb bc8496f8fbafa9e6375abf8506bcf61b76beb76a 137108 libjellyfish-2.0-dev_2.3.1-6_amd64.deb f882634a46ff81e3623ba5e1e3d2b6a5ff9525bb 350592 libjellyfish-perl-dbgsym_2.3.1-6_amd64.deb 2f5161f0bd7988d0dddd45e9320c62e89b1e3c43 56660 libjellyfish-perl_2.3.1-6_amd64.deb 216c75ffcc436ae2d2393a842dd12d878d68b0b1 639304 python3-dna-jellyfish-dbgsym_2.3.1-6_amd64.deb 64c5b803b8fb0670ef5a63dec323caf4a9edc431 65760 python3-dna-jellyfish_2.3.1-6_amd64.deb Checksums-Sha256: 803204f1c29546813b2d806c21ed2d8b6bffef85b3969b909dd23ccf3cb0d020 1851 jellyfish_2.3.1-6.dsc 1d42fd4fcb0a81634e1e7de6bedee282ecc2f772583c0ac9793d0ec98aacb221 13600 jellyfish_2.3.1-6.debian.tar.xz ac5866cc484739a690aafa230406b77d75d7fc71198a055b33a3d673851eaea0 7688632 jellyfish-dbgsym_2.3.1-6_amd64.deb f1f1a45a492cf8a837ba1054377d4eb14e7e5cd562e93b2c2c2c9cef72cfa5ee 12892 jellyfish-examples_2.3.1-6_all.deb 45e7be7882bba7dfc0ea3373066e6f3956ec5fecb3e9136cb3a5b6632ee87066 12319 jellyfish_2.3.1-6_amd64.buildinfo e4bf8b87cd28f988b0643c4206dc8da534b752194180776b6b18ceab34e686e9 809548 jellyfish_2.3.1-6_amd64.deb 66b2c23567f915f11f01cfac39d951269d69f377ff155afad8601d6ccfce9479 539688 libjellyfish-2.0-2-dbgsym_2.3.1-6_amd64.deb b722ff1c4f5dce9114bc30b5aaf52accbe12b813d2fc25a7532be7b7ebf221da 66232 libjellyfish-2.0-2_2.3.1-6_amd64.deb be0395091756506cfc6ce86f720c564251980690286545799f513408035a1270 137108 libjellyfish-2.0-dev_2.3.1-6_amd64.deb c0c3a6a29c7a10897cb3c59e07b76c500b71af3d897383e01b30b9dae450b98d 350592 libjellyfish-perl-dbgsym_2.3.1-6_amd64.deb e0823e424e0e6da04a9a9c5bd7de5bebaacda611acb3d47de581a1ba61f62cf1 56660 libjellyfish-perl_2.3.1-6_amd64.deb 427299be5fdc7de30fe01b3ec2c593639e0fcd47b428b3a5f481f751e9814740 639304 python3-dna-jellyfish-dbgsym_2.3.1-6_amd64.deb dd36bc3c0fb65e57506a93c47081db29f3d97abe08dfe793be83df25219bb3ee 65760 python3-dna-jellyfish_2.3.1-6_amd64.deb Files: 9e31638dacd822fa16c36cc1bfa09cd6 1851 science optional jellyfish_2.3.1-6.dsc 60e49df49d7175420b31ea2c407468bd 13600 science optional jellyfish_2.3.1-6.debian.tar.xz 42489c275468ce4af9cb559c035add2f 7688632 debug optional jellyfish-dbgsym_2.3.1-6_amd64.deb ee92ed64979fd976e1d9b8d7826c6bd7 12892 science optional jellyfish-examples_2.3.1-6_all.deb ea194ce6a5923b1a5334c8d7a58a7927 12319 science optional jellyfish_2.3.1-6_amd64.buildinfo 3d78e73bd9d0131564af0f28b05c5146 809548 science optional jellyfish_2.3.1-6_amd64.deb 534650f4096ad5db350c9c6a34136213 539688 debug optional libjellyfish-2.0-2-dbgsym_2.3.1-6_amd64.deb d8d80c3190f2af001ba7943c42932174 66232 libs optional libjellyfish-2.0-2_2.3.1-6_amd64.deb 122af7f0d2f53c4c1b631604c8f26126 137108 libdevel optional libjellyfish-2.0-dev_2.3.1-6_amd64.deb ea7b03de8cf0ba5932d313c30c09c119 350592 debug optional libjellyfish-perl-dbgsym_2.3.1-6_amd64.deb 936fc6d7aca2c4c35815344ac9b2df70 56660 perl optional libjellyfish-perl_2.3.1-6_amd64.deb e662560b402047b2ab5f0d1292416175 639304 debug optional python3-dna-jellyfish-dbgsym_2.3.1-6_amd64.deb d33c235ecc5d818fd8045ebcfcd6c33c 65760 python optional python3-dna-jellyfish_2.3.1-6_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Sat, 25 Apr 2026 17:57:21 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 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: all amd64 source Version: 2.3.1-6 Checksums-Md5: 9e31638dacd822fa16c36cc1bfa09cd6 1851 jellyfish_2.3.1-6.dsc 42489c275468ce4af9cb559c035add2f 7688632 jellyfish-dbgsym_2.3.1-6_amd64.deb ee92ed64979fd976e1d9b8d7826c6bd7 12892 jellyfish-examples_2.3.1-6_all.deb 3d78e73bd9d0131564af0f28b05c5146 809548 jellyfish_2.3.1-6_amd64.deb 534650f4096ad5db350c9c6a34136213 539688 libjellyfish-2.0-2-dbgsym_2.3.1-6_amd64.deb d8d80c3190f2af001ba7943c42932174 66232 libjellyfish-2.0-2_2.3.1-6_amd64.deb 122af7f0d2f53c4c1b631604c8f26126 137108 libjellyfish-2.0-dev_2.3.1-6_amd64.deb ea7b03de8cf0ba5932d313c30c09c119 350592 libjellyfish-perl-dbgsym_2.3.1-6_amd64.deb 936fc6d7aca2c4c35815344ac9b2df70 56660 libjellyfish-perl_2.3.1-6_amd64.deb 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build-essential (= 12.12), bzip2 (= 1.0.8-6+b2), ca-certificates (= 20260223), chrpath (= 0.18-1), comerr-dev (= 2.1-1.47.4-1), coreutils (= 9.10-1), cpp (= 4:15.2.0-5), cpp-13 (= 13.4.0-10), cpp-13-x86-64-linux-gnu (= 13.4.0-10), cpp-15 (= 15.2.0-17), cpp-15-x86-64-linux-gnu (= 15.2.0-17), cpp-x86-64-linux-gnu (= 4:15.2.0-5), d-shlibs (= 0.109), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 13.31), debian-archive-keyring (= 2025.1), debianutils (= 5.23.2), dh-autoreconf (= 22), dh-python (= 7.20260309), dh-strip-nondeterminism (= 1.15.0-1), diffutils (= 1:3.12-1), dos2unix (= 7.5.4-1), dpkg (= 1.23.7), dpkg-dev (= 1.23.7), dwz (= 0.16-4), file (= 1:5.46-5+b2), findutils (= 4.10.0-3), g++ (= 4:15.2.0-5), g++-15 (= 15.2.0-17), g++-15-x86-64-linux-gnu (= 15.2.0-17), g++-x86-64-linux-gnu (= 4:15.2.0-5), gcc (= 4:15.2.0-5), gcc-13 (= 13.4.0-10), gcc-13-base (= 13.4.0-10), gcc-13-x86-64-linux-gnu (= 13.4.0-10), gcc-15 (= 15.2.0-17), gcc-15-base (= 15.2.0-17), gcc-15-x86-64-linux-gnu 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libruby (= 1:3.3+b1), libruby3.3 (= 3.3.8-2), libsasl2-2 (= 2.1.28+dfsg1-11), libsasl2-modules-db (= 2.1.28+dfsg1-11), libseccomp2 (= 2.6.0-2+b1), libselinux1 (= 3.10-1), libsemanage-common (= 3.10-1), libsemanage2 (= 3.10-1), libsepol2 (= 3.10-1), libsframe3 (= 2.46-3), libsmartcols1 (= 2.42-4), libsqlite3-0 (= 3.46.1-9+b1), libssh2-1-dev (= 1.11.1-2), libssh2-1t64 (= 1.11.1-2), libssl-dev (= 3.6.2-1), libssl3t64 (= 3.6.2-1), libstdc++-15-dev (= 15.2.0-17), libstdc++6 (= 16-20260423-1), libsystemd0 (= 260.1-1), libtasn1-6 (= 4.21.0-2), libtasn1-6-dev (= 4.21.0-2), libtinfo6 (= 6.6+20251231-1), libtool (= 2.5.4-11), libtsan2 (= 16-20260423-1), libubsan1 (= 16-20260423-1), libuchardet0 (= 0.0.8-2+b1), libudev1 (= 260.1-1), libunbound8 (= 1.24.2-1+b1), libunistring5 (= 1.4.2-1), libuuid1 (= 2.42-4), libxml2-16 (= 2.15.2+dfsg-0.1), libxxhash0 (= 0.8.3-2+b1), libyaml-0-2 (= 0.2.5-2+b1), libzstd-dev (= 1.5.7+dfsg-3+b1), libzstd1 (= 1.5.7+dfsg-3+b1), linux-libc-dev (= 6.19.13-1), login.defs (= 1:4.19.3-2), m4 (= 1.4.21-1), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20260302-1), media-types (= 14.0.0), ncurses-base (= 6.6+20251231-1), ncurses-bin (= 6.6+20251231-1), netbase (= 6.5), nettle-dev (= 3.10.2-1+b1), openssl (= 3.6.2-1), openssl-provider-legacy (= 3.6.2-1), passwd (= 1:4.19.3-2), patch (= 2.8-2), perl (= 5.40.1-7+b1), perl-base (= 5.40.1-7+b1), perl-modules-5.40 (= 5.40.1-7), pkgconf (= 2.5.1-4), pkgconf-bin (= 2.5.1-4), po-debconf (= 1.0.22), procps (= 2:4.0.4-9+b2), python3 (= 3.13.9-3), python3-all (= 3.13.9-3), python3-all-dev (= 3.13.9-3), python3-autocommand (= 2.2.2-4), python3-dev (= 3.13.9-3), python3-inflect (= 7.5.0-1), python3-jaraco.context (= 6.0.1-2), python3-jaraco.functools (= 4.1.0-1), python3-jaraco.text (= 4.0.0-1), python3-minimal (= 3.13.9-3), python3-more-itertools (= 10.8.0-1), python3-pkg-resources (= 78.1.1-0.1), python3-setuptools (= 78.1.1-0.1), python3-typeguard (= 4.4.4-2), python3-typing-extensions (= 4.15.0-2), python3-zipp (= 3.23.0-1), python3.13 (= 3.13.12-1), python3.13-dev (= 3.13.12-1), python3.13-minimal (= 3.13.12-1), python3.14 (= 3.14.4-2), python3.14-dev (= 3.14.4-2), python3.14-minimal (= 3.14.4-2), rake (= 13.4.2-1), readline-common (= 8.3-4), rpcsvc-proto (= 1.4.3-1), ruby (= 1:3.3+b1), ruby-csv (= 3.3.5-1), ruby-did-you-mean (= 2.0.0-1), ruby-net-telnet (= 0.2.0-1), ruby-ruby2-keywords (= 0.0.5-1), ruby-rubygems (= 3.6.7-2), ruby-webrick (= 1.9.2-1), ruby-xmlrpc (= 0.3.3-2), ruby3.3 (= 3.3.8-2), rubygems-integration (= 1.19), samtools (= 1.22.1-1), sed (= 4.9-3), sensible-utils (= 0.0.26), sqv (= 1.3.0-5+b1), swig (= 4.4.1-2), sysvinit-utils (= 3.18-1), tar (= 1.35+dfsg-4), time (= 1.9-0.4), tzdata (= 2026b-1), util-linux (= 2.42-4), xz-utils (= 5.8.3-1), yaggo (= 1.5.11-2), zlib1g (= 1:1.3.dfsg+really1.3.2-3), zlib1g-dev (= 1:1.3.dfsg+really1.3.2-3) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LANGUAGE="en_GB:en" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" LD_PRELOAD="libeatmydata.so" SOURCE_DATE_EPOCH="1776794885" +------------------------------------------------------------------------------+ | Package contents Sat, 25 Apr 2026 17:57:21 +0000 | +------------------------------------------------------------------------------+ jellyfish-dbgsym_2.3.1-6_amd64.deb ---------------------------------- new Debian package, version 2.0. size 7688632 bytes: control archive=744 bytes. 502 bytes, 12 lines control 510 bytes, 5 lines md5sums Package: jellyfish-dbgsym Source: jellyfish Version: 2.3.1-6 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 8851 Depends: jellyfish (= 2.3.1-6) Section: debug Priority: optional Description: debug symbols for jellyfish Build-Ids: 92e5572894950907e2fe44a1d3d02f625623bad5 a6604f4af06fca06509334df248f2181b5e85a75 a917c48da87a23a115ac9ab38561167fb1bc5600 e0f313a80a4d9c99a555973ae5d36d5eea579cbe drwxr-xr-x root/root 0 2026-04-21 18:08 ./ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/debug/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/debug/.build-id/92/ -rw-r--r-- root/root 7291000 2026-04-21 18:08 ./usr/lib/debug/.build-id/92/e5572894950907e2fe44a1d3d02f625623bad5.debug drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/debug/.build-id/a6/ -rw-r--r-- root/root 66024 2026-04-21 18:08 ./usr/lib/debug/.build-id/a6/604f4af06fca06509334df248f2181b5e85a75.debug drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/debug/.build-id/a9/ -rw-r--r-- root/root 1524320 2026-04-21 18:08 ./usr/lib/debug/.build-id/a9/17c48da87a23a115ac9ab38561167fb1bc5600.debug drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/debug/.build-id/e0/ -rw-r--r-- root/root 84928 2026-04-21 18:08 ./usr/lib/debug/.build-id/e0/f313a80a4d9c99a555973ae5d36d5eea579cbe.debug drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 79120 2026-04-21 18:08 ./usr/lib/debug/.dwz/x86_64-linux-gnu/jellyfish.debug drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/doc/ lrwxrwxrwx root/root 0 2026-04-21 18:08 ./usr/share/doc/jellyfish-dbgsym -> jellyfish jellyfish-examples_2.3.1-6_all.deb ---------------------------------- new Debian package, version 2.0. size 12892 bytes: control archive=1844 bytes. 1173 bytes, 27 lines control 3133 bytes, 34 lines md5sums Package: jellyfish-examples Source: jellyfish Version: 2.3.1-6 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 59 Recommends: jellyfish Section: science Priority: optional Multi-Arch: foreign Homepage: https://www.genome.umd.edu/jellyfish.html Description: count k-mers in DNA sequences (examples for testing) JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. . JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish dump" command. . This package contains examples to test the package drwxr-xr-x root/root 0 2026-04-21 18:08 ./ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/jellyfish/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/jellyfish/bin/ lrwxrwxrwx root/root 0 2026-04-21 18:08 ./usr/lib/jellyfish/bin/jellyfish -> ../../../bin/jellyfish drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/doc/jellyfish-examples/ -rw-r--r-- root/root 1816 2026-04-21 18:08 ./usr/share/doc/jellyfish-examples/changelog.Debian.gz -rw-r--r-- root/root 284 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/changelog.gz -rw-r--r-- root/root 6395 2026-04-21 17:56 ./usr/share/doc/jellyfish-examples/copyright drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/doc/jellyfish-examples/examples/ -rw-r--r-- root/root 809 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/big.sh -rw-r--r-- root/root 1535 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/bloom_counter.sh -rw-r--r-- root/root 931 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/bloom_filter.sh -rw-r--r-- root/root 695 2026-04-21 18:08 ./usr/share/doc/jellyfish-examples/examples/compat.sh -rw-r--r-- root/root 755 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/from_stream.sh -rw-r--r-- root/root 567 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/from_stream_fastq.sh -rw-r--r-- root/root 227 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/generate_fastq_sequence.sh -rwxr-xr-x root/root 620 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/generate_sequence.sh -rw-r--r-- root/root 837 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/large_key.sh -rw-r--r-- root/root 1954 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/merge.sh -rw-r--r-- root/root 454 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/min_qual.sh -rw-r--r-- root/root 1286 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/multi_file.sh -rw-r--r-- root/root 544 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/multi_file_fastq.sh -rwxr-xr-x root/root 891 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/parallel_direct_indexing.sh -rw-r--r-- root/root 798 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/parallel_fastq_direct_indexing.sh -rw-r--r-- root/root 629 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/parallel_fastq_hashing.sh -rw-r--r-- root/root 541 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/parallel_fastq_sequence_hashing.sh -rwxr-xr-x root/root 3795 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/parallel_hashing.sh -rw-r--r-- root/root 309 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/parsers.sh -rw-r--r-- root/root 881 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/quality_filter.sh -rw-r--r-- root/root 863 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/raw_hash.sh -rw-r--r-- root/root 1242 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/sam.sh -rwxr-xr-x root/root 427 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/serial_direct_indexing.sh -rwxr-xr-x root/root 541 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/serial_hashing.sh -rwxr-xr-x root/root 540 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/small.sh -rw-r--r-- root/root 455 2026-04-21 18:08 ./usr/share/doc/jellyfish-examples/examples/small_mers.sh -rw-r--r-- root/root 696 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/subset_hashing.sh -rw-r--r-- root/root 536 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/swig_perl.sh -rw-r--r-- root/root 595 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/swig_python.sh -rw-r--r-- root/root 490 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/swig_ruby.sh -rw-r--r-- root/root 132 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/unit_tests.sh jellyfish_2.3.1-6_amd64.deb --------------------------- new Debian package, version 2.0. size 809548 bytes: control archive=1324 bytes. 1149 bytes, 23 lines control 904 bytes, 13 lines md5sums Package: jellyfish Version: 2.3.1-6 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 2557 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libhts3t64 (>= 1.17), libjellyfish-2.0-2 (= 2.3.1-6), libstdc++6 (>= 14) Section: science Priority: optional Homepage: https://www.genome.umd.edu/jellyfish.html Description: count k-mers in DNA sequences JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. . JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish dump" command. drwxr-xr-x root/root 0 2026-04-21 18:08 ./ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/bin/ -rwxr-xr-x root/root 351736 2026-04-21 18:08 ./usr/bin/jellyfish drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/jellyfish/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/jellyfish/bin/ -rwxr-xr-x root/root 27168 2026-04-21 18:08 ./usr/lib/jellyfish/bin/fastq2sam -rwxr-xr-x root/root 39656 2026-04-21 18:08 ./usr/lib/jellyfish/bin/generate_sequence -rwxr-xr-x root/root 1940160 2026-04-21 18:08 ./usr/lib/jellyfish/bin/test_all drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/doc-base/ -rw-r--r-- root/root 987 2026-04-21 17:56 ./usr/share/doc-base/jellyfish.jellyfish drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/doc/jellyfish/ -rw-r--r-- root/root 321 2026-04-21 17:56 ./usr/share/doc/jellyfish/README.test -rw-r--r-- root/root 1815 2026-04-21 18:08 ./usr/share/doc/jellyfish/changelog.Debian.gz -rw-r--r-- root/root 284 2023-12-06 21:50 ./usr/share/doc/jellyfish/changelog.gz -rw-r--r-- root/root 6395 2026-04-21 17:56 ./usr/share/doc/jellyfish/copyright -rw-r--r-- root/root 221453 2023-12-06 21:50 ./usr/share/doc/jellyfish/jellyfish.pdf.gz -rw-r--r-- root/root 1665 2026-04-21 17:56 ./usr/share/doc/jellyfish/run-unit-test drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/lintian/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 144 2026-04-21 17:56 ./usr/share/lintian/overrides/jellyfish drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/man/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/man/man1/ -rw-r--r-- root/root 4554 2026-04-21 18:08 ./usr/share/man/man1/jellyfish.1.gz libjellyfish-2.0-2-dbgsym_2.3.1-6_amd64.deb ------------------------------------------- new Debian package, version 2.0. size 539688 bytes: control archive=564 bytes. 422 bytes, 13 lines control 106 bytes, 1 lines md5sums Package: libjellyfish-2.0-2-dbgsym Source: jellyfish Version: 2.3.1-6 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 573 Depends: libjellyfish-2.0-2 (= 2.3.1-6) Section: debug Priority: optional Multi-Arch: same Description: debug symbols for libjellyfish-2.0-2 Build-Ids: b737064ea06f3dff18a2f4cf1f7334af3b7e9896 drwxr-xr-x root/root 0 2026-04-21 18:08 ./ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/debug/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/debug/.build-id/b7/ -rw-r--r-- root/root 576184 2026-04-21 18:08 ./usr/lib/debug/.build-id/b7/37064ea06f3dff18a2f4cf1f7334af3b7e9896.debug drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/doc/ lrwxrwxrwx root/root 0 2026-04-21 18:08 ./usr/share/doc/libjellyfish-2.0-2-dbgsym -> libjellyfish-2.0-2 libjellyfish-2.0-2_2.3.1-6_amd64.deb ------------------------------------ new Debian package, version 2.0. size 66232 bytes: control archive=1292 bytes. 1370 bytes, 31 lines control 410 bytes, 5 lines md5sums 49 bytes, 1 lines shlibs 66 bytes, 2 lines triggers Package: libjellyfish-2.0-2 Source: jellyfish Version: 2.3.1-6 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 203 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libstdc++6 (>= 13.1) Conflicts: libjellyfish-2.0-2t64 Replaces: libjellyfish-2.0-2t64 Provides: libjellfish-2.0-2t64 (= 2.3.1-6) Section: libs Priority: optional Multi-Arch: same Homepage: https://www.genome.umd.edu/jellyfish.html Description: count k-mers in DNA sequences (dynamic library of jellyfish) JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. . JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish dump" command. . This package contains the dynamic library the main executable of jellyfish is linked to. drwxr-xr-x root/root 0 2026-04-21 18:08 ./ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/x86_64-linux-gnu/ lrwxrwxrwx root/root 0 2026-04-21 18:08 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2 -> libjellyfish-2.0.so.2.0.0 -rw-r--r-- root/root 182296 2026-04-21 18:08 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/doc/libjellyfish-2.0-2/ -rw-r--r-- root/root 1816 2026-04-21 18:08 ./usr/share/doc/libjellyfish-2.0-2/changelog.Debian.gz -rw-r--r-- root/root 284 2023-12-06 21:50 ./usr/share/doc/libjellyfish-2.0-2/changelog.gz -rw-r--r-- root/root 6395 2026-04-21 17:56 ./usr/share/doc/libjellyfish-2.0-2/copyright drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/lintian/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 178 2026-04-21 17:56 ./usr/share/lintian/overrides/libjellyfish-2.0-2 libjellyfish-2.0-dev_2.3.1-6_amd64.deb -------------------------------------- new Debian package, version 2.0. size 137108 bytes: control archive=2516 bytes. 1215 bytes, 27 lines control 4183 bytes, 56 lines md5sums Package: libjellyfish-2.0-dev Source: jellyfish Version: 2.3.1-6 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 690 Depends: libjellyfish-2.0-2 (= 2.3.1-6) Section: libdevel Priority: optional Homepage: https://www.genome.umd.edu/jellyfish.html Description: count k-mers in DNA sequences (development files of jellyfish) JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. . JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish dump" command. . This package contains the development files (static library and header files) drwxr-xr-x root/root 0 2026-04-21 18:08 ./ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/include/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/include/jellyfish/ -rw-r--r-- root/root 1596 2026-04-21 18:08 ./usr/include/jellyfish/allocators_mmap.hpp -rw-r--r-- root/root 5898 2026-04-21 18:08 ./usr/include/jellyfish/atomic_bits_array.hpp -rw-r--r-- root/root 4770 2026-04-21 18:08 ./usr/include/jellyfish/atomic_field.hpp -rw-r--r-- root/root 1392 2026-04-21 18:08 ./usr/include/jellyfish/atomic_gcc.hpp -rw-r--r-- root/root 272 2026-04-21 18:08 ./usr/include/jellyfish/backtrace.hpp -rw-r--r-- root/root 6829 2026-04-21 18:08 ./usr/include/jellyfish/binary_dumper.hpp -rw-r--r-- root/root 3480 2026-04-21 18:08 ./usr/include/jellyfish/bloom_common.hpp -rw-r--r-- root/root 6778 2026-04-21 18:08 ./usr/include/jellyfish/bloom_counter2.hpp -rw-r--r-- root/root 5447 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root/root 8326 2026-04-21 18:08 ./usr/include/jellyfish/hash_counter.hpp -rw-r--r-- root/root 7025 2026-04-21 18:08 ./usr/include/jellyfish/int128.hpp -rw-r--r-- root/root 1118 2026-04-21 18:08 ./usr/include/jellyfish/jellyfish.hpp -rw-r--r-- root/root 61697 2026-04-21 18:08 ./usr/include/jellyfish/json.h -rw-r--r-- root/root 40578 2026-04-21 18:08 ./usr/include/jellyfish/large_hash_array.hpp -rw-r--r-- root/root 7564 2026-04-21 18:08 ./usr/include/jellyfish/large_hash_iterator.hpp -rw-r--r-- root/root 4328 2026-04-21 18:08 ./usr/include/jellyfish/locks_pthread.hpp -rw-r--r-- root/root 5181 2026-04-21 18:08 ./usr/include/jellyfish/mapped_file.hpp -rw-r--r-- root/root 23839 2026-04-21 18:08 ./usr/include/jellyfish/mer_dna.hpp -rw-r--r-- root/root 1296 2026-04-21 18:08 ./usr/include/jellyfish/mer_dna_bloom_counter.hpp -rw-r--r-- root/root 3076 2026-04-21 18:08 ./usr/include/jellyfish/mer_heap.hpp -rw-r--r-- root/root 2588 2026-04-21 18:08 ./usr/include/jellyfish/mer_iterator.hpp 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18:08 ./usr/include/jellyfish/stream_iterator.hpp -rw-r--r-- root/root 6318 2026-04-21 18:08 ./usr/include/jellyfish/stream_manager.hpp -rw-r--r-- root/root 2063 2026-04-21 18:08 ./usr/include/jellyfish/text_dumper.hpp -rw-r--r-- root/root 994 2026-04-21 18:08 ./usr/include/jellyfish/thread_exec.hpp -rw-r--r-- root/root 1884 2026-04-21 18:08 ./usr/include/jellyfish/time.hpp -rw-r--r-- root/root 1599 2026-04-21 18:08 ./usr/include/jellyfish/token_ring.hpp -rw-r--r-- root/root 6761 2026-04-21 18:08 ./usr/include/jellyfish/whole_sequence_parser.hpp drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/x86_64-linux-gnu/ -rw-r--r-- root/root 319310 2026-04-21 18:08 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a -rw-r--r-- root/root 1006 2026-04-21 18:08 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.la lrwxrwxrwx root/root 0 2026-04-21 18:08 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so -> libjellyfish-2.0.so.2.0.0 drwxr-xr-x root/root 0 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Team Installed-Size: 370 Depends: libjellyfish-perl (= 2.3.1-6) Section: debug Priority: optional Multi-Arch: same Description: debug symbols for libjellyfish-perl Build-Ids: 246799fe6bd4c8c89641f762a5ee9b329f031696 drwxr-xr-x root/root 0 2026-04-21 18:08 ./ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/debug/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/debug/.build-id/24/ -rw-r--r-- root/root 368264 2026-04-21 18:08 ./usr/lib/debug/.build-id/24/6799fe6bd4c8c89641f762a5ee9b329f031696.debug drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/doc/ lrwxrwxrwx root/root 0 2026-04-21 18:08 ./usr/share/doc/libjellyfish-perl-dbgsym -> libjellyfish-perl libjellyfish-perl_2.3.1-6_amd64.deb ----------------------------------- new Debian package, version 2.0. size 56660 bytes: control archive=1136 bytes. 1240 bytes, 27 lines control 402 bytes, 5 lines md5sums Package: libjellyfish-perl Source: jellyfish Version: 2.3.1-6 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 175 Depends: perl (>= 5.40.1-7+b1), perlapi-5.40.1, libc6 (>= 2.38), libgcc-s1 (>= 3.0) Section: perl Priority: optional Multi-Arch: same Homepage: https://www.genome.umd.edu/jellyfish.html Description: count k-mers in DNA sequences (Perl bindings of jellyfish) JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. . JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish dump" command. . This package contains the Perl bindings of jellyfish. drwxr-xr-x root/root 0 2026-04-21 18:08 ./ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/x86_64-linux-gnu/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/x86_64-linux-gnu/perl5/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/x86_64-linux-gnu/perl5/5.40/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/x86_64-linux-gnu/perl5/5.40/auto/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/x86_64-linux-gnu/perl5/5.40/auto/jellyfish/ -rw-r--r-- root/root 146664 2026-04-21 18:08 ./usr/lib/x86_64-linux-gnu/perl5/5.40/auto/jellyfish/jellyfish.so drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/doc/libjellyfish-perl/ -rw-r--r-- root/root 1817 2026-04-21 18:08 ./usr/share/doc/libjellyfish-perl/changelog.Debian.gz -rw-r--r-- root/root 284 2023-12-06 21:50 ./usr/share/doc/libjellyfish-perl/changelog.gz -rw-r--r-- root/root 6395 2026-04-21 17:56 ./usr/share/doc/libjellyfish-perl/copyright drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/perl5/ -rw-r--r-- root/root 7414 2026-04-21 18:08 ./usr/share/perl5/jellyfish.pm python3-dna-jellyfish-dbgsym_2.3.1-6_amd64.deb ---------------------------------------------- new Debian package, version 2.0. size 639304 bytes: control archive=656 bytes. 455 bytes, 12 lines control 310 bytes, 3 lines md5sums Package: python3-dna-jellyfish-dbgsym Source: jellyfish Version: 2.3.1-6 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 691 Depends: python3-dna-jellyfish (= 2.3.1-6) Section: debug Priority: optional Description: debug symbols for python3-dna-jellyfish Build-Ids: 1597ebd458d68ca90db8007695feab4e6ac88115 ad138d8b3bd99327d40f1d3f77856dd756f1ff2f drwxr-xr-x root/root 0 2026-04-21 18:08 ./ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/debug/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/debug/.build-id/15/ -rw-r--r-- root/root 289680 2026-04-21 18:08 ./usr/lib/debug/.build-id/15/97ebd458d68ca90db8007695feab4e6ac88115.debug drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/debug/.build-id/ad/ -rw-r--r-- root/root 288904 2026-04-21 18:08 ./usr/lib/debug/.build-id/ad/138d8b3bd99327d40f1d3f77856dd756f1ff2f.debug drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 114352 2026-04-21 18:08 ./usr/lib/debug/.dwz/x86_64-linux-gnu/python3-dna-jellyfish.debug drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/doc/ lrwxrwxrwx root/root 0 2026-04-21 18:08 ./usr/share/doc/python3-dna-jellyfish-dbgsym -> python3-dna-jellyfish python3-dna-jellyfish_2.3.1-6_amd64.deb --------------------------------------- new Debian package, version 2.0. size 65760 bytes: control archive=1608 bytes. 1299 bytes, 26 lines control 879 bytes, 9 lines md5sums 297 bytes, 12 lines * postinst #!/bin/sh 435 bytes, 12 lines * prerm #!/bin/sh Package: python3-dna-jellyfish Source: jellyfish Version: 2.3.1-6 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 332 Depends: python3 (<< 3.15), python3 (>= 3.13~), python3:any, libc6 (>= 2.38), libgcc-s1 (>= 3.0), libjellyfish-2.0-2 (>= 2.3.1), libstdc++6 (>= 13.1) Section: python Priority: optional Homepage: https://www.genome.umd.edu/jellyfish.html Description: count k-mers in DNA sequences (Python bindings of jellyfish) JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. . JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish dump" command. . This package contains the Python bindings of jellyfish. drwxr-xr-x root/root 0 2026-04-21 18:08 ./ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/python3/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/python3/dist-packages/ -rw-r--r-- root/root 149856 2026-04-21 18:08 ./usr/lib/python3/dist-packages/_dna_jellyfish.cpython-313-x86_64-linux-gnu.so -rw-r--r-- root/root 149856 2026-04-21 18:08 ./usr/lib/python3/dist-packages/_dna_jellyfish.cpython-314-x86_64-linux-gnu.so drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/lib/python3/dist-packages/dna_jellyfish-0.0.1.egg-info/ -rw-r--r-- root/root 160 2026-04-21 18:08 ./usr/lib/python3/dist-packages/dna_jellyfish-0.0.1.egg-info/PKG-INFO -rw-r--r-- root/root 1 2026-04-21 18:08 ./usr/lib/python3/dist-packages/dna_jellyfish-0.0.1.egg-info/dependency_links.txt -rw-r--r-- root/root 29 2026-04-21 18:08 ./usr/lib/python3/dist-packages/dna_jellyfish-0.0.1.egg-info/top_level.txt -rw-r--r-- root/root 12643 2026-04-21 18:08 ./usr/lib/python3/dist-packages/dna_jellyfish.py drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-04-21 18:08 ./usr/share/doc/python3-dna-jellyfish/ -rw-r--r-- root/root 1821 2026-04-21 18:08 ./usr/share/doc/python3-dna-jellyfish/changelog.Debian.gz -rw-r--r-- root/root 284 2023-12-06 21:50 ./usr/share/doc/python3-dna-jellyfish/changelog.gz -rw-r--r-- root/root 6395 2026-04-21 17:56 ./usr/share/doc/python3-dna-jellyfish/copyright +------------------------------------------------------------------------------+ | Post Build Sat, 25 Apr 2026 17:57:24 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Sat, 25 Apr 2026 17:57:24 +0000 | +------------------------------------------------------------------------------+ Purging /build/jellyfish-bM2jHV Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Sat, 25 Apr 2026 17:57:25 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 1800868 Build-Time: 346 Distribution: sid Host Architecture: amd64 Install-Time: 29 Job: /srv/debomatic/incoming/jellyfish_2.3.1-6.dsc Machine Architecture: amd64 Package: jellyfish Package-Time: 380 Source-Version: 2.3.1-6 Space: 1800868 Status: successful Version: 2.3.1-6 -------------------------------------------------------------------------------- Finished at 2026-04-25T17:57:20Z Build needed 00:06:20, 1800868k disk space