sbuild (Debian sbuild) 0.91.1 (08 October 2025) on carme.larted.org.uk +==============================================================================+ | jellyfish 2.3.1-5+b2 (amd64) Wed, 03 Dec 2025 04:58:56 +0000 | +==============================================================================+ Package: jellyfish Version: 2.3.1-5+b2 Source Version: 2.3.1-5 Distribution: perl-5.42 Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: any I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Wed, 03 Dec 2025 04:58:57 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup jellyfish_2.3.1-5 perl-5.42 amd64 -------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup jellyfish_2.3.1-5 perl-5.42 amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Wed, 03 Dec 2025 04:58:58 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.42 InRelease [3042 B] Hit:2 http://deb.debian.org/debian unstable InRelease Hit:3 http://deb.debian.org/debian sid InRelease Get:1 file:/srv/reprepro perl-5.42 InRelease [3042 B] 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 Wed, 03 Dec 2025 04:59:01 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/jellyfish_2.3.1-5.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Wed, 03 Dec 2025 04:59:01 +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-YgfDsN/resolver-8ur1i5/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/jellyfish-YgfDsN/resolver-8ur1i5/apt_archive ./ InRelease Get:2 copy:/build/jellyfish-YgfDsN/resolver-8ur1i5/apt_archive ./ Release [609 B] Ign:3 copy:/build/jellyfish-YgfDsN/resolver-8ur1i5/apt_archive ./ Release.gpg Get:4 copy:/build/jellyfish-YgfDsN/resolver-8ur1i5/apt_archive ./ Sources [875 B] Get:5 copy:/build/jellyfish-YgfDsN/resolver-8ur1i5/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 libgnutls-openssl27t64 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 libpkgconf3 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 libgnutls-openssl27t64 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 libpkgconf3 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, 155 newly installed, 0 to remove and 0 not upgraded. Need to get 72.8 MB/74.2 MB of archives. After this operation, 294 MB of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.42/main amd64 libldap-dev amd64 2.6.10+dfsg-1+b1 [312 kB] Get:2 copy:/build/jellyfish-YgfDsN/resolver-8ur1i5/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [988 B] Get:3 http://deb.debian.org/debian unstable/main amd64 autoconf-archive all 20241016-3 [797 kB] Get:4 file:/srv/reprepro perl-5.42/main amd64 libperl-dev amd64 5.42.0-3 [1143 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.3-1 [112 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.9-1 [865 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.9-1 [2257 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.9-2 [27.5 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 media-types all 14.0.0 [30.8 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-5 [260 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.9-1 [1965 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.9-1 [764 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.9-2 [10.5 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.9-2 [27.5 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 libpython3.14-minimal amd64 3.14.0-5 [896 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 python3.14-minimal amd64 3.14.0-5 [2356 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.5.4-1 [1496 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20250419 [162 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.2-1 [245 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-10 [1194 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.2-4 [98.5 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-2 [42.1 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 architecture-properties amd64 0.2.6 [2336 B] Get:33 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-2 [325 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-3 [878 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.2-1 [772 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 bc amd64 1.07.1-4 [103 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 chrpath amd64 0.18-1 [13.5 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b4 [25.1 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-3+b4 [56.7 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 d-shlibs all 0.109 [11.1 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.28 [92.4 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-7 [540 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get:49 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.194-1 [185 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.1+dfsg-2+b1 [641 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.2-1 [1687 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.28 [941 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20251201 [114 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 dos2unix amd64 7.5.2-1 [518 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.22.1-2 [33.1 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.22.1-2 [81.1 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get:61 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.22.1-2 [337 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.22.1-2 [139 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.22.1-2 [60.3 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.22.1-2 [42.5 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.22.1-2 [43.4 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.22.1-2 [56.2 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.22.1-2 [127 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b9 [304 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b9 [316 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.12.0-1 [68.4 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.16.0-1 [136 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.16.0-1 [25.2 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.17.0-3 [401 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.24.2-1 [615 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.11-3 [469 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.11-3 [469 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-4 [103 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.10-1 [221 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-5 [330 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-5 [658 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.2-1 [1322 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.11-3 [1448 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.22.1-2 [16.1 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get:93 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get:94 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1.1+b1 [117 kB] Get:95 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.12.0-1 [95.5 kB] Get:96 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.16.0-1 [25.2 kB] Get:97 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.16.0-1 [193 kB] Get:98 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get:99 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get:100 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-3 [67.9 kB] Get:101 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.5.4-1 [2980 kB] Get:102 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get:103 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-2 [375 kB] Get:104 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.17.0-3 [523 kB] Get:105 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get:106 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.23-2 [55.9 kB] Get:107 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.7.3-1 [165 kB] Get:108 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get:109 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.22.1+ds2-1 [499 kB] Get:110 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.1-2 [349 kB] Get:111 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.22.1+ds2-1 [1807 kB] Get:112 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.2.3-10 [27.7 kB] Get:113 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5+20251123-1 [107 kB] Get:114 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.9-1 [2184 kB] Get:115 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.9-1 [5311 kB] Get:116 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.9-2 [10.7 kB] Get:117 http://deb.debian.org/debian unstable/main amd64 libpython3.14-stdlib amd64 3.14.0-5 [2254 kB] Get:118 http://deb.debian.org/debian unstable/main amd64 libpython3.14 amd64 3.14.0-5 [2296 kB] Get:119 http://deb.debian.org/debian unstable/main amd64 libpython3.14-dev amd64 3.14.0-5 [5305 kB] Get:120 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.13.9-2 [1072 B] Get:121 http://deb.debian.org/debian unstable/main amd64 rubygems-integration all 1.19 [5488 B] Get:122 http://deb.debian.org/debian unstable/main amd64 ruby3.3 amd64 3.3.8-2 [834 kB] Get:123 http://deb.debian.org/debian unstable/main amd64 ruby-rubygems all 3.6.7-2 [407 kB] Get:124 http://deb.debian.org/debian unstable/main amd64 ruby amd64 1:3.3+b1 [6560 B] Get:125 http://deb.debian.org/debian unstable/main amd64 rake all 13.2.1-1 [65.2 kB] Get:126 http://deb.debian.org/debian unstable/main amd64 ruby-csv all 3.3.4-1 [42.2 kB] Get:127 http://deb.debian.org/debian unstable/main amd64 ruby-did-you-mean all 1.6.3-2 [20.9 kB] Get:128 http://deb.debian.org/debian unstable/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get:129 http://deb.debian.org/debian unstable/main amd64 ruby-ruby2-keywords all 0.0.5-1 [4300 B] Get:130 http://deb.debian.org/debian unstable/main amd64 ruby-webrick all 1.9.1-1 [59.6 kB] Get:131 http://deb.debian.org/debian unstable/main amd64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get:132 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get:133 http://deb.debian.org/debian unstable/main amd64 libruby3.3 amd64 3.3.8-2 [6301 kB] Get:134 http://deb.debian.org/debian unstable/main amd64 libruby amd64 1:3.3+b1 [5440 B] Get:135 http://deb.debian.org/debian unstable/main amd64 python3.14 amd64 3.14.0-5 [817 kB] Get:136 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.13.9-2 [1052 B] Get:137 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.9-1 [504 kB] Get:138 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.9-2 [26.0 kB] Get:139 http://deb.debian.org/debian unstable/main amd64 python3.14-dev amd64 3.14.0-5 [507 kB] Get:140 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.13.9-2 [1072 B] Get:141 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:142 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get:143 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get:144 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.4-1 [37.1 kB] Get:145 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.5.0-1 [33.0 kB] 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-pkg-resources all 78.1.1-0.1 [224 kB] Get:148 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 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 python3-jaraco.context all 6.0.1-1 [8276 B] Get:152 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.22.1-1 [697 kB] Get:153 http://deb.debian.org/debian unstable/main amd64 swig amd64 4.4.0-1 [1508 kB] Get:154 http://deb.debian.org/debian unstable/main amd64 time amd64 1.9-0.3 [48.2 kB] Get:155 http://deb.debian.org/debian unstable/main amd64 yaggo all 1.5.11-2 [21.4 kB] Preconfiguring packages ... Fetched 72.8 MB in 3s (25.1 MB/s) Selecting previously unselected package autoconf-archive. (Reading database ... 23319 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_2.7.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.3-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.9-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.9-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.9-1_amd64.deb ... Unpacking python3.13-minimal (3.13.9-1) ... Setting up libpython3.13-minimal:amd64 (3.13.9-1) ... Setting up libexpat1:amd64 (2.7.3-1) ... Setting up python3.13-minimal (3.13.9-1) ... Selecting previously unselected package python3-minimal. 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Setting up libgnutls-openssl27t64:amd64 (3.8.11-3) ... Setting up time (1.9-0.3) ... Setting up libkeyutils1:amd64 (1.6.3-6) ... Setting up ruby-ruby2-keywords (0.0.5-1) ... Setting up swig (4.4.0-1) ... Setting up libzstd-dev:amd64 (1.5.7+dfsg-2) ... Setting up bsdextrautils (2.41.2-4) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.5-2) ... Setting up architecture-properties:amd64 (0.2.6) ... Setting up libxml2-16:amd64 (2.15.1+dfsg-2+b1) ... Setting up libdebhelper-perl (13.28) ... Setting up libbrotli1:amd64 (1.1.0-2+b9) ... Setting up libpython3.14-minimal:amd64 (3.14.0-5) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Setting up libdeflate0:amd64 (1.23-2) ... Setting up bc (1.07.1-4) ... Setting up gettext-base (0.23.2-1) ... Setting up m4 (1.4.20-2) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libperl-dev:amd64 (5.42.0-3) ... Setting up autoconf-archive (20241016-3) ... Setting up libcom-err2:amd64 (1.47.2-3+b4) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.194-1) ... Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libkrb5support0:amd64 (1.22.1-2) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Dec 3 04:59:23 UTC 2025. Universal Time is now: Wed Dec 3 04:59:23 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libunbound8:amd64 (1.24.2-1) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-5) ... Setting up libexpat1-dev:amd64 (2.7.3-1) ... Setting up libgnutls-dane0t64:amd64 (3.8.11-3) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libldap-dev:amd64 (2.6.10+dfsg-1+b1) ... Setting up libncurses6:amd64 (6.5+20251123-1) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up ruby-csv (3.3.4-1) ... Setting up libproc2-0:amd64 (2:4.0.4-9) ... Setting up comerr-dev:amd64 (2.1-1.47.2-3+b4) ... Setting up libssl-dev:amd64 (3.5.4-1) ... Setting up autopoint (0.23.2-1) ... Setting up d-shlibs (0.109) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.22.1-2) ... Setting up libidn2-dev:amd64 (2.3.8-4) ... Setting up libjs-sphinxdoc (8.2.3-10) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:amd64 (1.12.0-1) ... Setting up libnghttp3-dev:amd64 (1.12.0-1) ... Setting up ruby-webrick (1.9.1-1) ... Setting up liblzma-dev:amd64 (5.8.1-2) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up procps (2:4.0.4-9) ... 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 (1.16.0-1) ... Setting up libkrb5-3:amd64 (1.22.1-2) ... Setting up dos2unix (7.5.2-1) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up ruby-did-you-mean (1.6.3-2) ... Setting up libtasn1-6-dev:amd64 (4.20.0-2) ... Setting up openssl (3.5.4-1) ... Setting up libdeflate-dev:amd64 (1.23-2) ... Setting up libpython3.13-stdlib:amd64 (3.13.9-1) ... Setting up ruby-xmlrpc (0.3.3-2) ... Setting up python3.14-minimal (3.14.0-5) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b9) ... Setting up chrpath (0.18-1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.16.0-1) ... Setting up libp11-kit-dev:amd64 (0.25.10-1) ... Setting up libpython3-stdlib:amd64 (3.13.9-2) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up libpython3.13:amd64 (3.13.9-1) ... Setting up automake (1:1.18.1-3) ... 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 (0.23.2-1) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-5) ... Setting up nettle-dev:amd64 (3.10.2-1) ... Setting up libtool (2.5.4-7) ... Setting up python3.13 (3.13.9-1) ... Setting up libpython3.14-stdlib:amd64 (3.14.0-5) ... Setting up python3 (3.13.9-2) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.16.0-1) ... Setting up libngtcp2-dev:amd64 (1.16.0-1) ... Setting up python3-zipp (3.23.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 150 added, 0 removed; done. Setting up libpython3.13-dev:amd64 (3.13.9-1) ... Setting up libgssapi-krb5-2:amd64 (1.22.1-2) ... Setting up python3-typing-extensions (4.15.0-1) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-10) ... Setting up libpython3.14:amd64 (3.14.0-5) ... Setting up libpython3.14-dev:amd64 (3.14.0-5) ... Setting up python3.14 (3.14.0-5) ... Setting up dh-python (6.20251201) ... Setting up libgnutls28-dev:amd64 (3.8.11-3) ... Setting up python3-more-itertools (10.8.0-1) ... Setting up libnghttp2-dev:amd64 (1.64.0-1.1+b1) ... Setting up libpython3-dev:amd64 (3.13.9-2) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3.14-dev (3.14.0-5) ... Setting up python3.13-dev (3.13.9-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3-typeguard (4.4.4-1) ... Setting up libcurl3t64-gnutls:amd64 (8.17.0-3) ... Setting up python3-all (3.13.9-2) ... 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 (3.13.9-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up libgssrpc4t64:amd64 (1.22.1-2) ... Setting up python3-dev (3.13.9-2) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libhts3t64:amd64 (1.22.1+ds2-1) ... Setting up libkadm5clnt-mit12:amd64 (1.22.1-2) ... Setting up python3-pkg-resources (78.1.1-0.1) ... Setting up python3-all-dev (3.13.9-2) ... Setting up python3-setuptools (78.1.1-0.1) ... Setting up libkdb5-10t64:amd64 (1.22.1-2) ... Setting up debhelper (13.28) ... Setting up samtools (1.22.1-1) ... Setting up libkadm5srv-mit12:amd64 (1.22.1-2) ... Setting up krb5-multidev:amd64 (1.22.1-2) ... Setting up libkrb5-dev:amd64 (1.22.1-2) ... Setting up libcurl4-gnutls-dev:amd64 (8.17.0-3) ... Setting up libhts-dev:amd64 (1.22.1+ds2-1) ... 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 (13.2.1-1) ... Setting up yaggo (1.5.11-2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.41-12) ... Processing triggers for ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. +------------------------------------------------------------------------------+ | Check architectures Wed, 03 Dec 2025 04:59:41 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment Wed, 03 Dec 2025 04:59:42 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.16.5+deb14-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.16.5-1 (2025-09-05) amd64 (x86_64) Toolchain package versions: binutils_2.45.50.20251201-1 dpkg-dev_1.22.21 g++-14_14.3.0-10 g++-15_15.2.0-9 gcc-14_14.3.0-10 gcc-15_15.2.0-9 libc6-dev_2.41-12 libstdc++-14-dev_14.3.0-10 libstdc++-15-dev_15.2.0-9 libstdc++6_15.2.0-9 linux-libc-dev_6.17.9-1 Package versions: adduser_3.153 apt_3.1.12 architecture-properties_0.2.6 autoconf_2.72-3.1 autoconf-archive_20241016-3 automake_1:1.18.1-3 autopoint_0.23.2-1 autotools-dev_20240727.1 base-files_14 base-passwd_3.6.8 bash_5.3-1 bc_1.07.1-4 binutils_2.45.50.20251201-1 binutils-common_2.45.50.20251201-1 binutils-gold_2.44-3 binutils-gold-x86-64-linux-gnu_2.44-3 binutils-x86-64-linux-gnu_2.45.50.20251201-1 bsdextrautils_2.41.2-4 bsdutils_1:2.41.2-4 build-essential_12.12 bzip2_1.0.8-6 ca-certificates_20250419 chrpath_0.18-1 comerr-dev_2.1-1.47.2-3+b4 coreutils_9.7-3 cpp_4:15.2.0-4 cpp-14_14.3.0-10 cpp-14-x86-64-linux-gnu_14.3.0-10 cpp-15_15.2.0-9 cpp-15-x86-64-linux-gnu_15.2.0-9 cpp-x86-64-linux-gnu_4:15.2.0-4 d-shlibs_0.109 dash_0.5.12-12 debconf_1.5.91 debhelper_13.28 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_21 dh-python_6.20251201 dh-strip-nondeterminism_1.15.0-1 diffutils_1:3.12-1 dirmngr_2.4.8-4+b1 dos2unix_7.5.2-1 dpkg_1.22.21 dpkg-dev_1.22.21 dwz_0.16-2 eatmydata_131-2 file_1:5.46-5 findutils_4.10.0-3 g++_4:15.2.0-4 g++-14_14.3.0-10 g++-14-x86-64-linux-gnu_14.3.0-10 g++-15_15.2.0-9 g++-15-x86-64-linux-gnu_15.2.0-9 g++-x86-64-linux-gnu_4:15.2.0-4 gcc_4:15.2.0-4 gcc-14_14.3.0-10 gcc-14-base_14.3.0-10 gcc-14-x86-64-linux-gnu_14.3.0-10 gcc-15_15.2.0-9 gcc-15-base_15.2.0-9 gcc-15-x86-64-linux-gnu_15.2.0-9 gcc-x86-64-linux-gnu_4:15.2.0-4 gettext_0.23.2-1 gettext-base_0.23.2-1 gnupg_2.4.8-4 gnupg-l10n_2.4.8-4 gpg_2.4.8-4+b1 gpg-agent_2.4.8-4+b1 gpgconf_2.4.8-4+b1 gpgsm_2.4.8-4+b1 grep_3.12-1 groff-base_1.23.0-10 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 libacl1_2.3.2-2+b1 libapt-pkg7.0_3.1.12 libarchive-zip-perl_1.68-1 libasan8_15.2.0-9 libassuan9_3.0.2-2 libatomic1_15.2.0-9 libattr1_1:2.5.2-3 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1 libbinutils_2.45.50.20251201-1 libblkid1_2.41.2-4 libbrotli-dev_1.1.0-2+b9 libbrotli1_1.1.0-2+b9 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libbz2-dev_1.0.8-6 libc-bin_2.41-12 libc-dev-bin_2.41-12 libc-l10n_2.41-12 libc6_2.41-12 libc6-dev_2.41-12 libcap-ng0_0.8.5-4+b2 libcap2_1:2.75-10+b2 libcc1-0_15.2.0-9 libcom-err2_1.47.2-3+b4 libcrypt-dev_1:4.5.1-1 libcrypt1_1:4.5.1-1 libctf-nobfd0_2.45.50.20251201-1 libctf0_2.45.50.20251201-1 libcurl3t64-gnutls_8.17.0-3 libcurl4-gnutls-dev_8.17.0-3 libdb5.3t64_5.3.28+dfsg2-10 libdebconfclient0_0.282 libdebhelper-perl_13.28 libdeflate-dev_1.23-2 libdeflate0_1.23-2 libdpkg-perl_1.22.21 libeatmydata1_131-2+b1 libelf1t64_0.194-1 libevent-2.1-7t64_2.1.12-stable-10+b1 libexpat1_2.7.3-1 libexpat1-dev_2.7.3-1 libffi8_3.5.2-2 libfile-stripnondeterminism-perl_1.15.0-1 libgcc-14-dev_14.3.0-10 libgcc-15-dev_15.2.0-9 libgcc-s1_15.2.0-9 libgcrypt20_1.11.2-3 libgdbm-compat4t64_1.26-1 libgdbm6t64_1.26-1 libgmp-dev_2:6.3.0+dfsg-5 libgmp10_2:6.3.0+dfsg-5 libgmpxx4ldbl_2:6.3.0+dfsg-5 libgnutls-dane0t64_3.8.11-3 libgnutls-openssl27t64_3.8.11-3 libgnutls28-dev_3.8.11-3 libgnutls30t64_3.8.11-3 libgomp1_15.2.0-9 libgpg-error0_1.56-2 libgprofng0_2.45.50.20251201-1 libgssapi-krb5-2_1.22.1-2 libgssrpc4t64_1.22.1-2 libhogweed6t64_3.10.2-1 libhts-dev_1.22.1+ds2-1 libhts3t64_1.22.1+ds2-1 libhtscodecs2_1.6.1-2 libhwasan0_15.2.0-9 libidn2-0_2.3.8-4 libidn2-dev_2.3.8-4 libisl23_0.27-1 libitm1_15.2.0-9 libjansson4_2.14-2+b3 libjs-sphinxdoc_8.2.3-10 libk5crypto3_1.22.1-2 libkadm5clnt-mit12_1.22.1-2 libkadm5srv-mit12_1.22.1-2 libkdb5-10t64_1.22.1-2 libkeyutils1_1.6.3-6 libkrb5-3_1.22.1-2 libkrb5-dev_1.22.1-2 libkrb5support0_1.22.1-2 libksba8_1.6.7-2+b1 liblastlog2-2_2.41.2-4 libldap-dev_2.6.10+dfsg-1+b1 libldap2_2.6.10+dfsg-1+b1 liblsan0_15.2.0-9 liblz4-1_1.10.0-6 liblzma-dev_5.8.1-2 liblzma5_5.8.1-2 libmagic-mgc_1:5.46-5 libmagic1t64_1:5.46-5 libmd0_1.1.0-2+b1 libmount1_2.41.2-4 libmpc3_1.3.1-2 libmpfr6_4.2.2-2 libncurses6_6.5+20251123-1 libncursesw6_6.5+20251123-1 libnettle8t64_3.10.2-1 libnghttp2-14_1.64.0-1.1+b1 libnghttp2-dev_1.64.0-1.1+b1 libnghttp3-9_1.12.0-1 libnghttp3-dev_1.12.0-1 libngtcp2-16_1.16.0-1 libngtcp2-crypto-gnutls-dev_1.16.0-1 libngtcp2-crypto-gnutls8_1.16.0-1 libngtcp2-dev_1.16.0-1 libnpth0t64_1.8-3 libp11-kit-dev_0.25.10-1 libp11-kit0_0.25.10-1 libpam-modules_1.7.0-5 libpam-modules-bin_1.7.0-5 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5 libpcre2-8-0_10.46-1 libperl-dev_5.42.0-3 libperl5.40_5.40.1-7 libperl5.42_5.42.0-3 libpipeline1_1.5.8-2 libpkgconf3_1.8.1-4 libproc2-0_2:4.0.4-9 libpsl-dev_0.21.2-1.1+b1 libpsl5t64_0.21.2-1.1+b1 libpython3-all-dev_3.13.9-2 libpython3-dev_3.13.9-2 libpython3-stdlib_3.13.9-2 libpython3.13_3.13.9-1 libpython3.13-dev_3.13.9-1 libpython3.13-minimal_3.13.9-1 libpython3.13-stdlib_3.13.9-1 libpython3.14_3.14.0-5 libpython3.14-dev_3.14.0-5 libpython3.14-minimal_3.14.0-5 libpython3.14-stdlib_3.14.0-5 libquadmath0_15.2.0-9 libreadline8t64_8.3-3 librtmp-dev_2.4+20151223.gitfa8646d.1-3 librtmp1_2.4+20151223.gitfa8646d.1-3 libruby_1:3.3+b1 libruby3.3_3.3.8-2 libsasl2-2_2.1.28+dfsg1-10 libsasl2-modules-db_2.1.28+dfsg1-10 libseccomp2_2.6.0-2+b1 libselinux1_3.9-4+b1 libsemanage-common_3.9-1 libsemanage2_3.9-1 libsepol2_3.9-2 libsframe2_2.45.50.20251201-1 libsmartcols1_2.41.2-4 libsqlite3-0_3.46.1-8 libssh2-1-dev_1.11.1-1 libssh2-1t64_1.11.1-1 libssl-dev_3.5.4-1 libssl3t64_3.5.4-1 libstdc++-14-dev_14.3.0-10 libstdc++-15-dev_15.2.0-9 libstdc++6_15.2.0-9 libsystemd0_259~rc2-1 libtasn1-6_4.20.0-2 libtasn1-6-dev_4.20.0-2 libtinfo6_6.5+20251123-1 libtool_2.5.4-7 libtsan2_15.2.0-9 libubsan1_15.2.0-9 libuchardet0_0.0.8-2 libudev1_259~rc2-1 libunbound8_1.24.2-1 libunistring5_1.3-2 libuuid1_2.41.2-4 libxml2-16_2.15.1+dfsg-2+b1 libxxhash0_0.8.3-2 libyaml-0-2_0.2.5-2 libzstd-dev_1.5.7+dfsg-2 libzstd1_1.5.7+dfsg-2 linux-libc-dev_6.17.9-1 locales-all_2.41-12 login.defs_1:4.18.0-2 m4_1.4.20-2 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20250131-1 media-types_14.0.0 ncurses-base_6.5+20251123-1 ncurses-bin_6.5+20251123-1 netbase_6.5 nettle-dev_3.10.2-1 openssl_3.5.4-1 openssl-provider-legacy_3.5.4-1 passwd_1:4.18.0-2 patch_2.8-2 perl_5.42.0-3 perl-base_5.42.0-3 perl-modules-5.40_5.40.1-7 perl-modules-5.42_5.42.0-3 pinentry-curses_1.3.2-3 pkgconf_1.8.1-4 pkgconf-bin_1.8.1-4 po-debconf_1.0.21+nmu1 procps_2:4.0.4-9 python3_3.13.9-2 python3-all_3.13.9-2 python3-all-dev_3.13.9-2 python3-autocommand_2.2.2-3 python3-dev_3.13.9-2 python3-inflect_7.5.0-1 python3-jaraco.context_6.0.1-1 python3-jaraco.functools_4.1.0-1 python3-jaraco.text_4.0.0-1 python3-minimal_3.13.9-2 python3-more-itertools_10.8.0-1 python3-pkg-resources_78.1.1-0.1 python3-setuptools_78.1.1-0.1 python3-typeguard_4.4.4-1 python3-typing-extensions_4.15.0-1 python3-zipp_3.23.0-1 python3.13_3.13.9-1 python3.13-dev_3.13.9-1 python3.13-minimal_3.13.9-1 python3.14_3.14.0-5 python3.14-dev_3.14.0-5 python3.14-minimal_3.14.0-5 rake_13.2.1-1 readline-common_8.3-3 rpcsvc-proto_1.4.3-1 ruby_1:3.3+b1 ruby-csv_3.3.4-1 ruby-did-you-mean_1.6.3-2 ruby-net-telnet_0.2.0-1 ruby-ruby2-keywords_0.0.5-1 ruby-rubygems_3.6.7-2 ruby-webrick_1.9.1-1 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_4.9-2 sensible-utils_0.0.26 sqv_1.3.0-3+b1 swig_4.4.0-1 sysvinit-utils_3.15-6 tar_1.35+dfsg-3.1 time_1.9-0.3 tzdata_2025b-5 util-linux_2.41.2-4 xz-utils_5.8.1-2 yaggo_1.5.11-2 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Wed, 03 Dec 2025 04:59:42 +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: 2.3.1-5 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 22b99f7072c7bd71e947271fe42e4f5d2a333805 13504 jellyfish_2.3.1-5.debian.tar.xz Checksums-Sha256: 540d09457fb4e14b98c7f1428cf885c333e2d6ef4f6a3735aa06be13eb523d69 681990 jellyfish_2.3.1.orig.tar.gz 8f6c81d3cbfcc71073a2e5b500e447de1c63beb2d98aea446f2d444e535f265b 13504 jellyfish_2.3.1-5.debian.tar.xz Files: 27fb29ad3edfe25d776cfbf98dcc8c0e 681990 jellyfish_2.3.1.orig.tar.gz 0b803d7adb5f68e86c130823b6bdd9c2 13504 jellyfish_2.3.1-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmkWM7MUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdrtmRAAvCmGnYIrLiFK0jhDwJPNaj8ya8lw 4YTVFIMYfQ/Eoi/EojbJ/2l1mrn9sewkvXiWX5l0VHso5LsWpitr0ft6EakY42iz 28PTKOZuwKFNxdWPjABn87SjxcXx7UrLSjpu9j7RWhe6ldU+1TPW0lGWiREMAZJt qlgyavDz5Em5uZ+5bfV+xJbMtCFm3JlirwpQzWGnhfYt0xNiAFfgEI+apPqEVCmi TltSF3WkRqvTvnH840cbKtHBfRpLor2/dLkFNcK9QWoQS8MCWxBbtZZATrnt9GBt 0N7CDZt49B8tQWeU5955Jt52P3i0oW80vDevF1APCl8XQ0agPHMnMgSRlEW1tPKL DlEJ/7o4DDoGMmnG8dDkwrLTOlvvz98KNqJ4g3VIN9ZHR2r7pjOyK8b/2IBR/zmw KQspR+MmmD3Uo6aTq0+cOo/ZdKn8g0nqGazZu6vgSrtybEPTtwsKcqKLl4pYTdiJ ZRCRsjPeNwfqdXcA4qjAN1vA7I2dmA/D4zncNC0iyz2JBddsGvsgtRVXz6g2Sr0H aV8pJNF1DMmalHZ11328VE3iIHln0/VZkTewXMukrx3Z2QVBHnIgwliIlRRXcyES xTzjoBPHJC5Ex3sPynGYmlWg01d+zJL+LI/ZiT9+r8cf92gNO1flEHqfSe3K3F7u MAN1diM3wdWqojc= =sAcT -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./jellyfish_2.3.1-5.dsc: no acceptable signature found dpkg-source: info: extracting jellyfish in /build/jellyfish-YgfDsN/jellyfish-2.3.1 dpkg-source: info: unpacking jellyfish_2.3.1.orig.tar.gz dpkg-source: info: unpacking jellyfish_2.3.1-5.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 Check disk space ---------------- Sufficient free space for build Hack binNMU version ------------------- Created changelog entry for binNMU version 2.3.1-5+b2 +------------------------------------------------------------------------------+ | Starting Timed Build Commands Wed, 03 Dec 2025 04:59:42 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network jellyfish_2.3.1-5 perl-5.42 amd64 -------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network jellyfish_2.3.1-5 perl-5.42 amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent 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-YgfDsN/jellyfish-2.3.1 SCHROOT_ALIAS_NAME=perl-5.42-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.42-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.42-amd64-debomatic-e3f924f3-020c-48ef-96e6-0e4915f7f9c5 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -mDebian Perl autobuilder -B -Zxz dpkg-buildpackage: info: source package jellyfish dpkg-buildpackage: info: source version 2.3.1-5+b2 dpkg-buildpackage: info: source distribution perl-5.42 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-YgfDsN/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-YgfDsN/jellyfish-2.3.1' debian/rules binary-arch dh binary-arch debian/rules override_dh_update_autotools_config make[1]: Entering directory '/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1' dh_autoreconf -a libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:8: installing './compile' configure.ac:2: installing './config.guess' configure.ac:2: installing './config.sub' configure.ac:4: installing './install-sh' configure.ac:4: installing './missing' Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/jellyfish-YgfDsN/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... 506e3:1000800: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... 4.4.0 checking for SWIG library... /usr/share/swig/4.4.0 checking for python... /usr/bin/python3 checking for a version of Python >= '2.1.0'... yes checking for the sysconfig Python package... yes checking for Python include path... -I/usr/include/python3.13 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/5.42/CORE checking for Perl extension target directory... /usr/lib/perl/5.42.0 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-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1 -L/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -lpthread -L/build/jellyfish-YgfDsN/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:317: python3.14 setup.py config running config I: pybuild base:317: python3.13 setup.py config running config mv /tmp/m4-ax_python_devel.m4 m4 make[1]: Leaving directory '/build/jellyfish-YgfDsN/jellyfish-2.3.1' debian/rules override_dh_auto_build make[1]: Entering directory '/build/jellyfish-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o sub_commands/jellyfish.o sub_commands/jellyfish.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o sub_commands/count_main.o sub_commands/count_main.cc g++ -DHAVE_CONFIG_H -I. -Wall 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-f "jellyfish.so.0" && ln -s "jellyfish.so.0.0.0" "jellyfish.so.0") libtool: link: (cd "swig/perl5/.libs" && rm -f "jellyfish.so" && ln -s "jellyfish.so.0.0.0" "jellyfish.so") libtool: link: ar cr swig/perl5/.libs/jellyfish.a swig/perl5/swig_perl5_jellyfish_la-swig_wrap.o libtool: link: ranlib swig/perl5/.libs/jellyfish.a libtool: link: ( cd "swig/perl5/.libs" && rm -f "jellyfish.la" && ln -s "../jellyfish.la" "jellyfish.la" ) /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I/usr/include/python3.13 -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo `test -f 'swig/python/swig_wrap.cpp' || echo './'`swig/python/swig_wrap.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/include/python3.13 -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c swig/python/swig_wrap.cpp -fPIC -DPIC -o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/include/python3.13 -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c swig/python/swig_wrap.cpp -o swig/python/swig_python__dna_jellyfish_la-swig_wrap.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -I/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -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 libtool: link: 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 -Wl,-rpath -Wl,/build/jellyfish-YgfDsN/jellyfish-2.3.1/.libs -lpthread ./.libs/libjellyfish-2.0.so -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/x86_64-linux-gnu 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/usr/bin/python3 -c 'import py_compile, sys; py_compile.compile(sys.argv[1], sys.argv[2])' swig/python/dna_jellyfish.py swig/python/__init__.pyc make[3]: Leaving directory '/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o jellyfish/generate_sequence.o jellyfish/generate_sequence.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o jellyfish/mersenne.o jellyfish/mersenne.cpp g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o jellyfish/backtrace.o jellyfish/backtrace.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o jellyfish/dbg.o jellyfish/dbg.cc /bin/bash ./libtool --tag=CXX --mode=link g++ -I/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 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-L/build/jellyfish-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_main.o `test -f 'unit_tests/test_main.cc' || echo './'`unit_tests/test_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_misc.o `test -f 'unit_tests/test_misc.cc' || echo './'`unit_tests/test_misc.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_offsets_key_value.o `test -f 'unit_tests/test_offsets_key_value.cc' || echo './'`unit_tests/test_offsets_key_value.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_simple_circular_buffer.o `test -f 'unit_tests/test_simple_circular_buffer.cc' || echo './'`unit_tests/test_simple_circular_buffer.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_rectangular_binary_matrix.o `test -f 'unit_tests/test_rectangular_binary_matrix.cc' || echo './'`unit_tests/test_rectangular_binary_matrix.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_mer_dna.o `test -f 'unit_tests/test_mer_dna.cc' || echo './'`unit_tests/test_mer_dna.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_large_hash_array.o `test -f 'unit_tests/test_large_hash_array.cc' || echo './'`unit_tests/test_large_hash_array.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_mer_overlap_sequence_parser.o `test -f 'unit_tests/test_mer_overlap_sequence_parser.cc' || echo './'`unit_tests/test_mer_overlap_sequence_parser.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_file_header.o `test -f 'unit_tests/test_file_header.cc' || echo './'`unit_tests/test_file_header.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_mer_iterator.o `test -f 'unit_tests/test_mer_iterator.cc' || echo './'`unit_tests/test_mer_iterator.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_hash_counter.o `test -f 'unit_tests/test_hash_counter.cc' || echo './'`unit_tests/test_hash_counter.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_mer_heap.o `test -f 'unit_tests/test_mer_heap.cc' || echo './'`unit_tests/test_mer_heap.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_stream_iterator.o `test -f 'unit_tests/test_stream_iterator.cc' || echo './'`unit_tests/test_stream_iterator.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_token_ring.o `test -f 'unit_tests/test_token_ring.cc' || echo './'`unit_tests/test_token_ring.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_text_dumper.o `test -f 'unit_tests/test_text_dumper.cc' || echo './'`unit_tests/test_text_dumper.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_dumpers.o `test -f 'unit_tests/test_dumpers.cc' || echo './'`unit_tests/test_dumpers.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_mapped_file.o `test -f 'unit_tests/test_mapped_file.cc' || echo './'`unit_tests/test_mapped_file.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_whole_sequence_parser.o `test -f 'unit_tests/test_whole_sequence_parser.cc' || echo './'`unit_tests/test_whole_sequence_parser.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_allocators_mmap.o `test -f 'unit_tests/test_allocators_mmap.cc' || echo './'`unit_tests/test_allocators_mmap.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_cooperative_pool2.o `test -f 'unit_tests/test_cooperative_pool2.cc' || echo './'`unit_tests/test_cooperative_pool2.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-YgfDsN/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 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-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-YgfDsN/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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -pthread -L/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -lhts -R/build/jellyfish-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/test_all unit_tests/bin_test_all-test_main.o unit_tests/bin_test_all-test_misc.o unit_tests/bin_test_all-test_offsets_key_value.o unit_tests/bin_test_all-test_simple_circular_buffer.o unit_tests/bin_test_all-test_rectangular_binary_matrix.o unit_tests/bin_test_all-test_mer_dna.o unit_tests/bin_test_all-test_large_hash_array.o unit_tests/bin_test_all-test_mer_overlap_sequence_parser.o unit_tests/bin_test_all-test_file_header.o unit_tests/bin_test_all-test_mer_iterator.o unit_tests/bin_test_all-test_hash_counter.o unit_tests/bin_test_all-test_mer_heap.o unit_tests/bin_test_all-test_stream_iterator.o unit_tests/bin_test_all-test_token_ring.o unit_tests/bin_test_all-test_text_dumper.o unit_tests/bin_test_all-test_dumpers.o unit_tests/bin_test_all-test_mapped_file.o unit_tests/bin_test_all-test_int128.o unit_tests/bin_test_all-test_mer_dna_bloom_counter.o unit_tests/bin_test_all-test_whole_sequence_parser.o unit_tests/bin_test_all-test_allocators_mmap.o unit_tests/bin_test_all-test_cooperative_pool2.o unit_tests/bin_test_all-test_generator_manager.o unit_tests/bin_test_all-test_atomic_bits_array.o unit_tests/bin_test_all-test_stdio_filebuf.o jellyfish/bin_test_all-backtrace.o -L/build/jellyfish-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o jellyfish/fastq2sam.o jellyfish/fastq2sam.cc /bin/bash ./libtool --tag=CXX --mode=link g++ -I/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -pthread -L/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -lhts -R/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/fastq2sam jellyfish/fastq2sam.o -L/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu make[2]: Leaving directory '/build/jellyfish-YgfDsN/jellyfish-2.3.1' dh_auto_install -- install-data make -j1 install DESTDIR=/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp AM_UPDATE_INFO_DIR=no install-data make[2]: Entering directory '/build/jellyfish-YgfDsN/jellyfish-2.3.1' make install-am make[3]: Entering directory '/build/jellyfish-YgfDsN/jellyfish-2.3.1' make[4]: Entering directory '/build/jellyfish-YgfDsN/jellyfish-2.3.1' /usr/bin/mkdir -p '/build/jellyfish-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/jellyfish-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/bin' /bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/bin/jellyfish /usr/bin/mkdir -p '/build/jellyfish-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/mkdir -p '/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/jellyfish-YgfDsN/jellyfish-2.3.1; /bin/bash "/build/jellyfish-YgfDsN/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.42.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0/jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0 && { 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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0 && { 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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0/jellyfish.a libtool: install: chmod 644 /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0/jellyfish.a libtool: install: ranlib /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.42.0' /usr/bin/mkdir -p '/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0' /usr/bin/mkdir -p '/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/mkdir -p '/build/jellyfish-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1; /bin/bash "/build/jellyfish-YgfDsN/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -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-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' make[4]: Leaving directory '/build/jellyfish-YgfDsN/jellyfish-2.3.1' make[3]: Leaving directory '/build/jellyfish-YgfDsN/jellyfish-2.3.1' /usr/bin/mkdir -p '/build/jellyfish-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/mkdir -p '/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/build/jellyfish-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/jellyfish-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/jellyfish-YgfDsN/jellyfish-2.3.1; /bin/bash "/build/jellyfish-YgfDsN/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.42.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0/jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0 && { 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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0 && { 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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0/jellyfish.a libtool: install: chmod 644 /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0/jellyfish.a libtool: install: ranlib /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.42.0' /usr/bin/mkdir -p '/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0' /usr/bin/mkdir -p '/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/mkdir -p '/build/jellyfish-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1; /bin/bash "/build/jellyfish-YgfDsN/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -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-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' make[2]: Leaving directory '/build/jellyfish-YgfDsN/jellyfish-2.3.1' dh_auto_build --sourcedirectory=swig/perl5 cd swig/perl5 && make -j2 make[2]: Entering directory '/build/jellyfish-YgfDsN/jellyfish-2.3.1/swig/perl5' Running Mkbootstrap for jellyfish () g++ -c -std=c++0x -I/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/jellyfish-YgfDsN/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/5.42/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1/swig/perl5' dh_auto_build --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:317: /usr/bin/python3.14 setup.py build build_ext -L/build/jellyfish-YgfDsN/jellyfish-2.3.1/.libs running build running build_py copying dna_jellyfish.py -> /build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-314/swig_wrap.o -L-L/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -L/build/jellyfish-YgfDsN/jellyfish-2.3.1/.libs -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -lpthread -o /build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu I: pybuild base:317: /usr/bin/python3 setup.py build build_ext -L/build/jellyfish-YgfDsN/jellyfish-2.3.1/.libs running build running build_py copying dna_jellyfish.py -> /build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/swig_wrap.o -L-L/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -L/build/jellyfish-YgfDsN/jellyfish-2.3.1/.libs -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -lpthread -o /build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu make[1]: Leaving directory '/build/jellyfish-YgfDsN/jellyfish-2.3.1' debian/rules override_dh_auto_test make[1]: Entering directory '/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1' make check-am make[3]: Entering directory '/build/jellyfish-YgfDsN/jellyfish-2.3.1' make bin/generate_sequence bin/fastq2sam bin/test_all libgtest.la libgtest_main.la make[4]: Entering directory '/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/gtest/src/libgtest_main_la-gtest_main.lo `test -f 'unit_tests/gtest/src/gtest_main.cc' || echo './'`unit_tests/gtest/src/gtest_main.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c unit_tests/gtest/src/gtest_main.cc -fPIC -DPIC -o unit_tests/gtest/src/.libs/libgtest_main_la-gtest_main.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c unit_tests/gtest/src/gtest_main.cc -o unit_tests/gtest/src/libgtest_main_la-gtest_main.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -pthread -L/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -lhts -R/build/jellyfish-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1' make check-TESTS make[4]: Entering directory '/build/jellyfish-YgfDsN/jellyfish-2.3.1' make[5]: Entering directory '/build/jellyfish-YgfDsN/jellyfish-2.3.1' SKIP: tests/big.sh PASS: tests/generate_sequence.sh PASS: tests/parallel_hashing.sh PASS: tests/merge.sh PASS: tests/bloom_filter.sh PASS: unit_tests/unit_tests.sh PASS: tests/subset_hashing.sh PASS: tests/bloom_counter.sh PASS: tests/large_key.sh PASS: tests/multi_file.sh PASS: tests/sam.sh PASS: tests/swig_python.sh SKIP: tests/swig_ruby.sh PASS: tests/small_mers.sh PASS: tests/swig_perl.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-YgfDsN/jellyfish-2.3.1' make[4]: Leaving directory '/build/jellyfish-YgfDsN/jellyfish-2.3.1' make[3]: Leaving directory '/build/jellyfish-YgfDsN/jellyfish-2.3.1' make[2]: Leaving directory '/build/jellyfish-YgfDsN/jellyfish-2.3.1' make[1]: Leaving directory '/build/jellyfish-YgfDsN/jellyfish-2.3.1' create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/jellyfish-YgfDsN/jellyfish-2.3.1' chrpath --delete bin/.libs/* dh_auto_install -- install-data make -j1 install DESTDIR=/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp AM_UPDATE_INFO_DIR=no install-data make[2]: Entering directory '/build/jellyfish-YgfDsN/jellyfish-2.3.1' make install-am make[3]: Entering directory '/build/jellyfish-YgfDsN/jellyfish-2.3.1' make[4]: Entering directory '/build/jellyfish-YgfDsN/jellyfish-2.3.1' /usr/bin/mkdir -p '/build/jellyfish-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/jellyfish-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/bin' /bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/bin/jellyfish /usr/bin/mkdir -p '/build/jellyfish-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/mkdir -p '/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/jellyfish-YgfDsN/jellyfish-2.3.1; /bin/bash "/build/jellyfish-YgfDsN/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.42.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0/jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0 && { 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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0 && { 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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0/jellyfish.a libtool: install: chmod 644 /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0/jellyfish.a libtool: install: ranlib /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.42.0' /usr/bin/mkdir -p '/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0' /usr/bin/mkdir -p '/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/mkdir -p '/build/jellyfish-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1; /bin/bash "/build/jellyfish-YgfDsN/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -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-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' make[4]: Leaving directory '/build/jellyfish-YgfDsN/jellyfish-2.3.1' make[3]: Leaving directory '/build/jellyfish-YgfDsN/jellyfish-2.3.1' /usr/bin/mkdir -p '/build/jellyfish-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/mkdir -p '/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/build/jellyfish-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/jellyfish-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/jellyfish-YgfDsN/jellyfish-2.3.1; /bin/bash "/build/jellyfish-YgfDsN/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.42.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0/jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0 && { 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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0 && { 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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0/jellyfish.a libtool: install: chmod 644 /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0/jellyfish.a libtool: install: ranlib /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.42.0' /usr/bin/mkdir -p '/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.42.0' /usr/bin/mkdir -p '/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/mkdir -p '/build/jellyfish-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1; /bin/bash "/build/jellyfish-YgfDsN/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-YgfDsN/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -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-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' make[2]: Leaving directory '/build/jellyfish-YgfDsN/jellyfish-2.3.1' dh_auto_install --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:317: /usr/bin/python3.14 setup.py install --root /build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1/.pybuild/cpython3_3.14_dna_jellyfish/build running build_ext running install_lib creating /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.14/dist-packages copying /build/jellyfish-YgfDsN/jellyfish-2.3.1/.pybuild/cpython3_3.14_dna_jellyfish/build/dna_jellyfish.py -> /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.14/dist-packages copying /build/jellyfish-YgfDsN/jellyfish-2.3.1/.pybuild/cpython3_3.14_dna_jellyfish/build/_dna_jellyfish.cpython-314-x86_64-linux-gnu.so -> /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.14/dist-packages byte-compiling /build/jellyfish-YgfDsN/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-YgfDsN/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:317: /usr/bin/python3 setup.py install --root /build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1/.pybuild/cpython3_3.13_dna_jellyfish/build running build_ext running install_lib creating /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.13/dist-packages copying /build/jellyfish-YgfDsN/jellyfish-2.3.1/.pybuild/cpython3_3.13_dna_jellyfish/build/_dna_jellyfish.cpython-313-x86_64-linux-gnu.so -> /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.13/dist-packages copying /build/jellyfish-YgfDsN/jellyfish-2.3.1/.pybuild/cpython3_3.13_dna_jellyfish/build/dna_jellyfish.py -> /build/jellyfish-YgfDsN/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.13/dist-packages byte-compiling /build/jellyfish-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr make[2]: Entering directory '/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.42/auto/jellyfish/jellyfish.so make[2]: Leaving directory '/build/jellyfish-YgfDsN/jellyfish-2.3.1/swig/perl5' ls -l debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so -r-xr-xr-x 1 debomatic sbuild 1126968 Dec 3 05:03 debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.42/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-YgfDsN/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-YgfDsN/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-YgfDsN/jellyfish-2.3.1' dh_install -a debian/rules execute_after_dh_install make[1]: Entering directory '/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1' dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_python3 -a dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a debian/rules override_dh_missing make[1]: Entering directory '/build/jellyfish-YgfDsN/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-YgfDsN/jellyfish-2.3.1' dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'jellyfish' in '../jellyfish_2.3.1-5+b2_amd64.deb'. dpkg-deb: building package 'python3-dna-jellyfish' in '../python3-dna-jellyfish_2.3.1-5+b2_amd64.deb'. dpkg-deb: building package 'python3-dna-jellyfish-dbgsym' in '../python3-dna-jellyfish-dbgsym_2.3.1-5+b2_amd64.deb'. dpkg-deb: building package 'libjellyfish-perl' in '../libjellyfish-perl_2.3.1-5+b2_amd64.deb'. dpkg-deb: building package 'libjellyfish-perl-dbgsym' in '../libjellyfish-perl-dbgsym_2.3.1-5+b2_amd64.deb'. dpkg-deb: building package 'jellyfish-dbgsym' in '../jellyfish-dbgsym_2.3.1-5+b2_amd64.deb'. dpkg-deb: building package 'libjellyfish-2.0-2' in '../libjellyfish-2.0-2_2.3.1-5+b2_amd64.deb'. dpkg-deb: building package 'libjellyfish-2.0-2-dbgsym' in '../libjellyfish-2.0-2-dbgsym_2.3.1-5+b2_amd64.deb'. dpkg-deb: building package 'libjellyfish-2.0-dev' in '../libjellyfish-2.0-dev_2.3.1-5+b2_amd64.deb'. dpkg-genbuildinfo --build=any -O../jellyfish_2.3.1-5+b2_amd64.buildinfo dpkg-genchanges --build=any -mDebian Perl autobuilder -O../jellyfish_2.3.1-5+b2_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2025-12-03T05:05:57Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Wed, 03 Dec 2025 05:05:58 +0000 | +------------------------------------------------------------------------------+ jellyfish_2.3.1-5+b2_amd64.changes: ----------------------------------- Format: 1.8 Date: Wed, 03 Dec 2025 04:58:56 +0000 Source: jellyfish (2.3.1-5) Binary: jellyfish jellyfish-dbgsym 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 Binary-Only: yes Architecture: amd64 Version: 2.3.1-5+b2 Distribution: perl-5.42 Urgency: low Maintainer: Debian Perl autobuilder Changed-By: Debian Perl autobuilder Description: jellyfish - count k-mers in DNA sequences 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) Changes: jellyfish (2.3.1-5+b2) perl-5.42; urgency=low, binary-only=yes . * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild for Perl 5.42 Checksums-Sha1: 8564d51fdc47b8c02709325551ebc93f9d82cb95 7689536 jellyfish-dbgsym_2.3.1-5+b2_amd64.deb dade2d7a21822531a1d949853036b8b8759b55a5 12071 jellyfish_2.3.1-5+b2_amd64.buildinfo 5135a6c12add49e457b2622e60cf0323bd1cf3ca 811248 jellyfish_2.3.1-5+b2_amd64.deb 1195bb87e7ea147e09d226d57d432c943daf9237 545276 libjellyfish-2.0-2-dbgsym_2.3.1-5+b2_amd64.deb 82665a63d6f610804f83bf8770b5be2e9d068804 68300 libjellyfish-2.0-2_2.3.1-5+b2_amd64.deb a2a55d55345c9aed4c67ab83c5f70b16277584e5 139168 libjellyfish-2.0-dev_2.3.1-5+b2_amd64.deb 27ea96c0e90ec4aebc37fa926c75265e746987e8 351136 libjellyfish-perl-dbgsym_2.3.1-5+b2_amd64.deb 939e38f8a43dc1e17c5a23fa297c5c1a656a24db 58420 libjellyfish-perl_2.3.1-5+b2_amd64.deb a876ad5569f927d2146d45f7295c44d8da8c9413 637208 python3-dna-jellyfish-dbgsym_2.3.1-5+b2_amd64.deb 4c6082615e759d06c1809897ae165d6bc23b0c4f 67160 python3-dna-jellyfish_2.3.1-5+b2_amd64.deb Checksums-Sha256: f246de74c49986291afaa4cfa794b6b1392420518cc93ea46a4a38a12cb2d2f5 7689536 jellyfish-dbgsym_2.3.1-5+b2_amd64.deb 7e36699f5bec94c8c67670f0f230a22085f6e06756cf65174b00de4d57f4465e 12071 jellyfish_2.3.1-5+b2_amd64.buildinfo 8efeb45096efe88d11eb50fed4d76989327c1846c4995ced683e198104555023 811248 jellyfish_2.3.1-5+b2_amd64.deb f523e740120d23ee4cd76869a6c4f97c3eb90d865ec96782d197867f49e12849 545276 libjellyfish-2.0-2-dbgsym_2.3.1-5+b2_amd64.deb 60b3c36dfe6d8cd02574904c8cb46cab751ed0eaf3a7ffe2778d5ac81d930806 68300 libjellyfish-2.0-2_2.3.1-5+b2_amd64.deb bbf41f2833e5fa091ecdf62a373bafc628ad56e10ef46598d91c92abc33534e1 139168 libjellyfish-2.0-dev_2.3.1-5+b2_amd64.deb f9b50387d1bec49f3cdf9ceb4738467ddb619add4c4efd2227ae91ff41a8c802 351136 libjellyfish-perl-dbgsym_2.3.1-5+b2_amd64.deb 7785516554840fe8013f1ef07864319e9c8dd91a8008fa7eff1438ba19e58fdd 58420 libjellyfish-perl_2.3.1-5+b2_amd64.deb 71b47bbdd3c6e5dfc2fd109d5e7ff4bdf72b82bf743310defcc61c1a2813d89f 637208 python3-dna-jellyfish-dbgsym_2.3.1-5+b2_amd64.deb 46603abee70a5e3204a5903cc9810991251274fb8894665defd4a8d8094fe87a 67160 python3-dna-jellyfish_2.3.1-5+b2_amd64.deb Files: 0d110625cc5ca07c4581a5bf390d9735 7689536 debug optional jellyfish-dbgsym_2.3.1-5+b2_amd64.deb 832de7a466954a686271897f683564fc 12071 science optional jellyfish_2.3.1-5+b2_amd64.buildinfo faaf93b2d317d6507afcab05618eab27 811248 science optional jellyfish_2.3.1-5+b2_amd64.deb 22e4b4012b16181b2f9467da1b2a8cae 545276 debug optional libjellyfish-2.0-2-dbgsym_2.3.1-5+b2_amd64.deb 8655140a9d729ca252747775fb0ef324 68300 libs optional libjellyfish-2.0-2_2.3.1-5+b2_amd64.deb 1e9fbb492c64ec91a6adbf494e26e33f 139168 libdevel optional libjellyfish-2.0-dev_2.3.1-5+b2_amd64.deb 58fc188a982641ce2c717bb647c10dbb 351136 debug optional libjellyfish-perl-dbgsym_2.3.1-5+b2_amd64.deb 7bb8e478d7c2a11680c6cf6aa3f0ffbe 58420 perl optional libjellyfish-perl_2.3.1-5+b2_amd64.deb 2502e7c18504775e6cdff0e7999ed570 637208 debug optional python3-dna-jellyfish-dbgsym_2.3.1-5+b2_amd64.deb 4712b729bf5fff1bc6bea89f11a4f22c 67160 python optional python3-dna-jellyfish_2.3.1-5+b2_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Wed, 03 Dec 2025 05:05:58 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: jellyfish (2.3.1-5) Binary: jellyfish jellyfish-dbgsym libjellyfish-2.0-2 libjellyfish-2.0-2-dbgsym libjellyfish-2.0-dev libjellyfish-perl libjellyfish-perl-dbgsym python3-dna-jellyfish python3-dna-jellyfish-dbgsym Architecture: amd64 Version: 2.3.1-5+b2 Binary-Only-Changes: jellyfish (2.3.1-5+b2) perl-5.42; urgency=low, binary-only=yes . * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild for Perl 5.42 . -- Debian Perl autobuilder Wed, 03 Dec 2025 04:58:56 +0000 Checksums-Md5: 0d110625cc5ca07c4581a5bf390d9735 7689536 jellyfish-dbgsym_2.3.1-5+b2_amd64.deb faaf93b2d317d6507afcab05618eab27 811248 jellyfish_2.3.1-5+b2_amd64.deb 22e4b4012b16181b2f9467da1b2a8cae 545276 libjellyfish-2.0-2-dbgsym_2.3.1-5+b2_amd64.deb 8655140a9d729ca252747775fb0ef324 68300 libjellyfish-2.0-2_2.3.1-5+b2_amd64.deb 1e9fbb492c64ec91a6adbf494e26e33f 139168 libjellyfish-2.0-dev_2.3.1-5+b2_amd64.deb 58fc188a982641ce2c717bb647c10dbb 351136 libjellyfish-perl-dbgsym_2.3.1-5+b2_amd64.deb 7bb8e478d7c2a11680c6cf6aa3f0ffbe 58420 libjellyfish-perl_2.3.1-5+b2_amd64.deb 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Checksums-Sha256: f246de74c49986291afaa4cfa794b6b1392420518cc93ea46a4a38a12cb2d2f5 7689536 jellyfish-dbgsym_2.3.1-5+b2_amd64.deb 8efeb45096efe88d11eb50fed4d76989327c1846c4995ced683e198104555023 811248 jellyfish_2.3.1-5+b2_amd64.deb f523e740120d23ee4cd76869a6c4f97c3eb90d865ec96782d197867f49e12849 545276 libjellyfish-2.0-2-dbgsym_2.3.1-5+b2_amd64.deb 60b3c36dfe6d8cd02574904c8cb46cab751ed0eaf3a7ffe2778d5ac81d930806 68300 libjellyfish-2.0-2_2.3.1-5+b2_amd64.deb bbf41f2833e5fa091ecdf62a373bafc628ad56e10ef46598d91c92abc33534e1 139168 libjellyfish-2.0-dev_2.3.1-5+b2_amd64.deb f9b50387d1bec49f3cdf9ceb4738467ddb619add4c4efd2227ae91ff41a8c802 351136 libjellyfish-perl-dbgsym_2.3.1-5+b2_amd64.deb 7785516554840fe8013f1ef07864319e9c8dd91a8008fa7eff1438ba19e58fdd 58420 libjellyfish-perl_2.3.1-5+b2_amd64.deb 71b47bbdd3c6e5dfc2fd109d5e7ff4bdf72b82bf743310defcc61c1a2813d89f 637208 python3-dna-jellyfish-dbgsym_2.3.1-5+b2_amd64.deb 46603abee70a5e3204a5903cc9810991251274fb8894665defd4a8d8094fe87a 67160 python3-dna-jellyfish_2.3.1-5+b2_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Wed, 03 Dec 2025 05:05:57 +0000 Build-Path: /build/jellyfish-YgfDsN/jellyfish-2.3.1 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: adduser (= 3.153), apt (= 3.1.12), architecture-properties (= 0.2.6), autoconf (= 2.72-3.1), autoconf-archive (= 20241016-3), automake (= 1:1.18.1-3), autopoint (= 0.23.2-1), autotools-dev (= 20240727.1), base-files (= 14), base-passwd (= 3.6.8), bash (= 5.3-1), bc (= 1.07.1-4), binutils (= 2.45.50.20251201-1), binutils-common (= 2.45.50.20251201-1), binutils-x86-64-linux-gnu (= 2.45.50.20251201-1), bsdextrautils (= 2.41.2-4), build-essential (= 12.12), bzip2 (= 1.0.8-6), ca-certificates (= 20250419), chrpath (= 0.18-1), comerr-dev (= 2.1-1.47.2-3+b4), coreutils (= 9.7-3), cpp (= 4:15.2.0-4), cpp-14 (= 14.3.0-10), cpp-14-x86-64-linux-gnu (= 14.3.0-10), cpp-15 (= 15.2.0-9), cpp-15-x86-64-linux-gnu (= 15.2.0-9), cpp-x86-64-linux-gnu (= 4:15.2.0-4), d-shlibs (= 0.109), dash (= 0.5.12-12), debconf (= 1.5.91), debhelper (= 13.28), debian-archive-keyring (= 2025.1), debianutils (= 5.23.2), dh-autoreconf (= 21), dh-python (= 6.20251201), dh-strip-nondeterminism (= 1.15.0-1), diffutils (= 1:3.12-1), dos2unix (= 7.5.2-1), dpkg (= 1.22.21), dpkg-dev (= 1.22.21), dwz (= 0.16-2), file (= 1:5.46-5), findutils (= 4.10.0-3), g++ (= 4:15.2.0-4), g++-15 (= 15.2.0-9), g++-15-x86-64-linux-gnu (= 15.2.0-9), g++-x86-64-linux-gnu (= 4:15.2.0-4), gcc (= 4:15.2.0-4), gcc-14 (= 14.3.0-10), gcc-14-base (= 14.3.0-10), gcc-14-x86-64-linux-gnu (= 14.3.0-10), gcc-15 (= 15.2.0-9), gcc-15-base (= 15.2.0-9), gcc-15-x86-64-linux-gnu (= 15.2.0-9), gcc-x86-64-linux-gnu (= 4:15.2.0-4), gettext (= 0.23.2-1), gettext-base (= 0.23.2-1), grep (= 3.12-1), groff-base (= 1.23.0-10), 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), libacl1 (= 2.3.2-2+b1), libapt-pkg7.0 (= 3.1.12), libarchive-zip-perl (= 1.68-1), libasan8 (= 15.2.0-9), libatomic1 (= 15.2.0-9), libattr1 (= 1:2.5.2-3), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1), libbinutils (= 2.45.50.20251201-1), libblkid1 (= 2.41.2-4), libbrotli-dev (= 1.1.0-2+b9), libbrotli1 (= 1.1.0-2+b9), libbsd0 (= 0.12.2-2), libbz2-1.0 (= 1.0.8-6), libbz2-dev (= 1.0.8-6), libc-bin (= 2.41-12), libc-dev-bin (= 2.41-12), libc6 (= 2.41-12), libc6-dev (= 2.41-12), libcap-ng0 (= 0.8.5-4+b2), libcap2 (= 1:2.75-10+b2), libcc1-0 (= 15.2.0-9), libcom-err2 (= 1.47.2-3+b4), libcrypt-dev (= 1:4.5.1-1), libcrypt1 (= 1:4.5.1-1), libctf-nobfd0 (= 2.45.50.20251201-1), libctf0 (= 2.45.50.20251201-1), libcurl3t64-gnutls (= 8.17.0-3), libcurl4-gnutls-dev (= 8.17.0-3), libdb5.3t64 (= 5.3.28+dfsg2-10), libdebconfclient0 (= 0.282), libdebhelper-perl (= 13.28), libdeflate-dev (= 1.23-2), libdeflate0 (= 1.23-2), libdpkg-perl (= 1.22.21), libelf1t64 (= 0.194-1), libevent-2.1-7t64 (= 2.1.12-stable-10+b1), libexpat1 (= 2.7.3-1), libexpat1-dev (= 2.7.3-1), libffi8 (= 3.5.2-2), libfile-stripnondeterminism-perl (= 1.15.0-1), libgcc-14-dev (= 14.3.0-10), libgcc-15-dev (= 15.2.0-9), libgcc-s1 (= 15.2.0-9), libgdbm-compat4t64 (= 1.26-1), libgdbm6t64 (= 1.26-1), libgmp-dev (= 2:6.3.0+dfsg-5), libgmp10 (= 2:6.3.0+dfsg-5), libgmpxx4ldbl (= 2:6.3.0+dfsg-5), libgnutls-dane0t64 (= 3.8.11-3), libgnutls-openssl27t64 (= 3.8.11-3), libgnutls28-dev (= 3.8.11-3), libgnutls30t64 (= 3.8.11-3), libgomp1 (= 15.2.0-9), libgprofng0 (= 2.45.50.20251201-1), libgssapi-krb5-2 (= 1.22.1-2), libgssrpc4t64 (= 1.22.1-2), libhogweed6t64 (= 3.10.2-1), libhts-dev (= 1.22.1+ds2-1), libhts3t64 (= 1.22.1+ds2-1), libhtscodecs2 (= 1.6.1-2), libhwasan0 (= 15.2.0-9), libidn2-0 (= 2.3.8-4), libidn2-dev (= 2.3.8-4), libisl23 (= 0.27-1), libitm1 (= 15.2.0-9), libjansson4 (= 2.14-2+b3), libjs-sphinxdoc (= 8.2.3-10), libk5crypto3 (= 1.22.1-2), libkadm5clnt-mit12 (= 1.22.1-2), libkadm5srv-mit12 (= 1.22.1-2), libkdb5-10t64 (= 1.22.1-2), libkeyutils1 (= 1.6.3-6), libkrb5-3 (= 1.22.1-2), libkrb5-dev (= 1.22.1-2), libkrb5support0 (= 1.22.1-2), libldap-dev (= 2.6.10+dfsg-1+b1), libldap2 (= 2.6.10+dfsg-1+b1), liblsan0 (= 15.2.0-9), liblz4-1 (= 1.10.0-6), liblzma-dev (= 5.8.1-2), liblzma5 (= 5.8.1-2), libmagic-mgc (= 1:5.46-5), libmagic1t64 (= 1:5.46-5), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.41.2-4), libmpc3 (= 1.3.1-2), libmpfr6 (= 4.2.2-2), libncurses6 (= 6.5+20251123-1), libncursesw6 (= 6.5+20251123-1), libnettle8t64 (= 3.10.2-1), libnghttp2-14 (= 1.64.0-1.1+b1), libnghttp2-dev (= 1.64.0-1.1+b1), libnghttp3-9 (= 1.12.0-1), libnghttp3-dev (= 1.12.0-1), libngtcp2-16 (= 1.16.0-1), libngtcp2-crypto-gnutls-dev (= 1.16.0-1), libngtcp2-crypto-gnutls8 (= 1.16.0-1), libngtcp2-dev (= 1.16.0-1), libp11-kit-dev (= 0.25.10-1), libp11-kit0 (= 0.25.10-1), libpam-modules (= 1.7.0-5), libpam-modules-bin (= 1.7.0-5), libpam-runtime (= 1.7.0-5), libpam0g (= 1.7.0-5), libpcre2-8-0 (= 10.46-1), libperl-dev (= 5.42.0-3), libperl5.42 (= 5.42.0-3), libpipeline1 (= 1.5.8-2), libpkgconf3 (= 1.8.1-4), libproc2-0 (= 2:4.0.4-9), libpsl-dev (= 0.21.2-1.1+b1), libpsl5t64 (= 0.21.2-1.1+b1), libpython3-all-dev (= 3.13.9-2), libpython3-dev (= 3.13.9-2), libpython3-stdlib (= 3.13.9-2), libpython3.13 (= 3.13.9-1), libpython3.13-dev (= 3.13.9-1), libpython3.13-minimal (= 3.13.9-1), libpython3.13-stdlib (= 3.13.9-1), libpython3.14 (= 3.14.0-5), libpython3.14-dev (= 3.14.0-5), libpython3.14-minimal (= 3.14.0-5), libpython3.14-stdlib (= 3.14.0-5), libquadmath0 (= 15.2.0-9), libreadline8t64 (= 8.3-3), librtmp-dev (= 2.4+20151223.gitfa8646d.1-3), librtmp1 (= 2.4+20151223.gitfa8646d.1-3), libruby (= 1:3.3+b1), libruby3.3 (= 3.3.8-2), libsasl2-2 (= 2.1.28+dfsg1-10), libsasl2-modules-db (= 2.1.28+dfsg1-10), libseccomp2 (= 2.6.0-2+b1), libselinux1 (= 3.9-4+b1), libsemanage-common (= 3.9-1), libsemanage2 (= 3.9-1), libsepol2 (= 3.9-2), libsframe2 (= 2.45.50.20251201-1), libsmartcols1 (= 2.41.2-4), libsqlite3-0 (= 3.46.1-8), libssh2-1-dev (= 1.11.1-1), libssh2-1t64 (= 1.11.1-1), libssl-dev (= 3.5.4-1), libssl3t64 (= 3.5.4-1), libstdc++-15-dev (= 15.2.0-9), libstdc++6 (= 15.2.0-9), libsystemd0 (= 259~rc2-1), libtasn1-6 (= 4.20.0-2), libtasn1-6-dev (= 4.20.0-2), libtinfo6 (= 6.5+20251123-1), libtool (= 2.5.4-7), libtsan2 (= 15.2.0-9), libubsan1 (= 15.2.0-9), libuchardet0 (= 0.0.8-2), libudev1 (= 259~rc2-1), libunbound8 (= 1.24.2-1), libunistring5 (= 1.3-2), libuuid1 (= 2.41.2-4), libxml2-16 (= 2.15.1+dfsg-2+b1), libxxhash0 (= 0.8.3-2), libyaml-0-2 (= 0.2.5-2), libzstd-dev (= 1.5.7+dfsg-2), libzstd1 (= 1.5.7+dfsg-2), linux-libc-dev (= 6.17.9-1), login.defs (= 1:4.18.0-2), m4 (= 1.4.20-2), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20250131-1), media-types (= 14.0.0), ncurses-base (= 6.5+20251123-1), ncurses-bin (= 6.5+20251123-1), netbase (= 6.5), nettle-dev (= 3.10.2-1), openssl (= 3.5.4-1), openssl-provider-legacy (= 3.5.4-1), passwd (= 1:4.18.0-2), patch (= 2.8-2), perl (= 5.42.0-3), perl-base (= 5.42.0-3), perl-modules-5.42 (= 5.42.0-3), pkgconf (= 1.8.1-4), pkgconf-bin (= 1.8.1-4), po-debconf (= 1.0.21+nmu1), procps (= 2:4.0.4-9), python3 (= 3.13.9-2), python3-all (= 3.13.9-2), python3-all-dev (= 3.13.9-2), python3-autocommand (= 2.2.2-3), python3-dev (= 3.13.9-2), python3-inflect (= 7.5.0-1), python3-jaraco.context (= 6.0.1-1), python3-jaraco.functools (= 4.1.0-1), python3-jaraco.text (= 4.0.0-1), python3-minimal (= 3.13.9-2), python3-more-itertools (= 10.8.0-1), python3-pkg-resources (= 78.1.1-0.1), python3-setuptools (= 78.1.1-0.1), python3-typeguard (= 4.4.4-1), python3-typing-extensions (= 4.15.0-1), python3-zipp (= 3.23.0-1), python3.13 (= 3.13.9-1), python3.13-dev (= 3.13.9-1), python3.13-minimal (= 3.13.9-1), python3.14 (= 3.14.0-5), python3.14-dev (= 3.14.0-5), python3.14-minimal (= 3.14.0-5), rake (= 13.2.1-1), readline-common (= 8.3-3), rpcsvc-proto (= 1.4.3-1), ruby (= 1:3.3+b1), ruby-csv (= 3.3.4-1), ruby-did-you-mean (= 1.6.3-2), ruby-net-telnet (= 0.2.0-1), ruby-ruby2-keywords (= 0.0.5-1), ruby-rubygems (= 3.6.7-2), ruby-webrick (= 1.9.1-1), ruby-xmlrpc (= 0.3.3-2), ruby3.3 (= 3.3.8-2), rubygems-integration (= 1.19), samtools (= 1.22.1-1), sed (= 4.9-2), sensible-utils (= 0.0.26), sqv (= 1.3.0-3+b1), swig (= 4.4.0-1), sysvinit-utils (= 3.15-6), tar (= 1.35+dfsg-3.1), time (= 1.9-0.3), tzdata (= 2025b-5), util-linux (= 2.41.2-4), xz-utils (= 5.8.1-2), yaggo (= 1.5.11-2), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1+b1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1764737936" +------------------------------------------------------------------------------+ | Package contents Wed, 03 Dec 2025 05:05:58 +0000 | +------------------------------------------------------------------------------+ jellyfish-dbgsym_2.3.1-5+b2_amd64.deb ------------------------------------- new Debian package, version 2.0. size 7689536 bytes: control archive=760 bytes. 518 bytes, 12 lines control 510 bytes, 5 lines md5sums Package: jellyfish-dbgsym Source: jellyfish (2.3.1-5) Version: 2.3.1-5+b2 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 8854 Depends: jellyfish (= 2.3.1-5+b2) Section: debug Priority: optional Description: debug symbols for jellyfish Build-Ids: a76d6db91aedcc59814fd79c73d58788a06107cd a8db437e3ec8e7ac49a2433170513fe02cb8bd75 adb5b7f98daf9bb28fc2803d6e62c697e262ad3a e81f3239d67ea7baa0a3011a174a63f2457407d6 drwxr-xr-x root/root 0 2025-12-03 04:58 ./ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/debug/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/debug/.build-id/a7/ -rw-r--r-- root/root 7294608 2025-12-03 04:58 ./usr/lib/debug/.build-id/a7/6d6db91aedcc59814fd79c73d58788a06107cd.debug drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/debug/.build-id/a8/ -rw-r--r-- root/root 1523960 2025-12-03 04:58 ./usr/lib/debug/.build-id/a8/db437e3ec8e7ac49a2433170513fe02cb8bd75.debug drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/debug/.build-id/ad/ -rw-r--r-- root/root 84888 2025-12-03 04:58 ./usr/lib/debug/.build-id/ad/b5b7f98daf9bb28fc2803d6e62c697e262ad3a.debug drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/debug/.build-id/e8/ -rw-r--r-- root/root 66000 2025-12-03 04:58 ./usr/lib/debug/.build-id/e8/1f3239d67ea7baa0a3011a174a63f2457407d6.debug drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 79032 2025-12-03 04:58 ./usr/lib/debug/.dwz/x86_64-linux-gnu/jellyfish.debug drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/share/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/share/doc/ lrwxrwxrwx root/root 0 2025-12-03 04:58 ./usr/share/doc/jellyfish-dbgsym -> jellyfish jellyfish_2.3.1-5+b2_amd64.deb ------------------------------ new Debian package, version 2.0. size 811248 bytes: control archive=1368 bytes. 1183 bytes, 24 lines control 988 bytes, 14 lines md5sums Package: jellyfish Source: jellyfish (2.3.1-5) Version: 2.3.1-5+b2 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 2559 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libhts3t64 (>= 1.17), libjellyfish-2.0-2 (= 2.3.1-5+b2), 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 2025-12-03 04:58 ./ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/bin/ -rwxr-xr-x root/root 351736 2025-12-03 04:58 ./usr/bin/jellyfish drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/jellyfish/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/jellyfish/bin/ -rwxr-xr-x root/root 27168 2025-12-03 04:58 ./usr/lib/jellyfish/bin/fastq2sam -rwxr-xr-x root/root 39656 2025-12-03 04:58 ./usr/lib/jellyfish/bin/generate_sequence -rwxr-xr-x root/root 1940160 2025-12-03 04:58 ./usr/lib/jellyfish/bin/test_all drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/share/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/share/doc-base/ -rw-r--r-- root/root 987 2024-01-01 10:16 ./usr/share/doc-base/jellyfish.jellyfish drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/share/doc/jellyfish/ -rw-r--r-- root/root 321 2024-01-01 10:16 ./usr/share/doc/jellyfish/README.test -rw-r--r-- root/root 208 2025-12-03 04:58 ./usr/share/doc/jellyfish/changelog.Debian.amd64.gz -rw-r--r-- root/root 3064 2025-12-03 04:58 ./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 2025-11-13 18:53 ./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 2024-01-01 10:16 ./usr/share/doc/jellyfish/run-unit-test drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/share/lintian/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 144 2024-01-01 10:16 ./usr/share/lintian/overrides/jellyfish drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/share/man/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/share/man/man1/ -rw-r--r-- root/root 4554 2025-12-03 04:58 ./usr/share/man/man1/jellyfish.1.gz libjellyfish-2.0-2-dbgsym_2.3.1-5+b2_amd64.deb ---------------------------------------------- new Debian package, version 2.0. size 545276 bytes: control archive=568 bytes. 438 bytes, 13 lines control 106 bytes, 1 lines md5sums Package: libjellyfish-2.0-2-dbgsym Source: jellyfish (2.3.1-5) Version: 2.3.1-5+b2 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 579 Depends: libjellyfish-2.0-2 (= 2.3.1-5+b2) Section: debug Priority: optional Multi-Arch: same Description: debug symbols for libjellyfish-2.0-2 Build-Ids: 0a5adcf3c0edcf8a4ad118708c4e97d6c33b7b97 drwxr-xr-x root/root 0 2025-12-03 04:58 ./ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/debug/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/debug/.build-id/0a/ -rw-r--r-- root/root 581792 2025-12-03 04:58 ./usr/lib/debug/.build-id/0a/5adcf3c0edcf8a4ad118708c4e97d6c33b7b97.debug drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/share/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/share/doc/ lrwxrwxrwx root/root 0 2025-12-03 04:58 ./usr/share/doc/libjellyfish-2.0-2-dbgsym -> libjellyfish-2.0-2 libjellyfish-2.0-2_2.3.1-5+b2_amd64.deb --------------------------------------- new Debian package, version 2.0. size 68300 bytes: control archive=1328 bytes. 1386 bytes, 31 lines control 503 bytes, 6 lines md5sums 49 bytes, 1 lines shlibs 66 bytes, 2 lines triggers Package: libjellyfish-2.0-2 Source: jellyfish (2.3.1-5) Version: 2.3.1-5+b2 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 205 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 (= 2.3.1-5+b2) 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 2025-12-03 04:58 ./ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/x86_64-linux-gnu/ lrwxrwxrwx root/root 0 2025-12-03 04:58 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2 -> libjellyfish-2.0.so.2.0.0 -rw-r--r-- root/root 182296 2025-12-03 04:58 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/share/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/share/doc/libjellyfish-2.0-2/ -rw-r--r-- root/root 208 2025-12-03 04:58 ./usr/share/doc/libjellyfish-2.0-2/changelog.Debian.amd64.gz -rw-r--r-- root/root 3064 2025-12-03 04:58 ./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 2025-11-13 18:53 ./usr/share/doc/libjellyfish-2.0-2/copyright drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/share/lintian/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 178 2025-11-13 18:53 ./usr/share/lintian/overrides/libjellyfish-2.0-2 libjellyfish-2.0-dev_2.3.1-5+b2_amd64.deb ----------------------------------------- new Debian package, version 2.0. size 139168 bytes: control archive=2544 bytes. 1231 bytes, 27 lines control 4278 bytes, 57 lines md5sums Package: libjellyfish-2.0-dev Source: jellyfish (2.3.1-5) Version: 2.3.1-5+b2 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 694 Depends: libjellyfish-2.0-2 (= 2.3.1-5+b2) 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 2025-12-03 04:58 ./ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/include/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/include/jellyfish/ -rw-r--r-- root/root 1596 2025-12-03 04:58 ./usr/include/jellyfish/allocators_mmap.hpp -rw-r--r-- root/root 5898 2025-12-03 04:58 ./usr/include/jellyfish/atomic_bits_array.hpp -rw-r--r-- root/root 4770 2025-12-03 04:58 ./usr/include/jellyfish/atomic_field.hpp -rw-r--r-- root/root 1392 2025-12-03 04:58 ./usr/include/jellyfish/atomic_gcc.hpp -rw-r--r-- root/root 272 2025-12-03 04:58 ./usr/include/jellyfish/backtrace.hpp -rw-r--r-- root/root 6829 2025-12-03 04:58 ./usr/include/jellyfish/binary_dumper.hpp -rw-r--r-- root/root 3480 2025-12-03 04:58 ./usr/include/jellyfish/bloom_common.hpp -rw-r--r-- root/root 6778 2025-12-03 04:58 ./usr/include/jellyfish/bloom_counter2.hpp -rw-r--r-- root/root 5447 2025-12-03 04:58 ./usr/include/jellyfish/bloom_filter.hpp -rw-r--r-- root/root 5211 2025-12-03 04:58 ./usr/include/jellyfish/circular_buffer.hpp -rw-r--r-- root/root 2408 2025-12-03 04:58 ./usr/include/jellyfish/compare_and_swap.hpp -rw-r--r-- root/root 7472 2025-12-03 04:58 ./usr/include/jellyfish/cooperative_pool.hpp -rw-r--r-- root/root 8494 2025-12-03 04:58 ./usr/include/jellyfish/cooperative_pool2.hpp -rw-r--r-- root/root 4125 2025-12-03 04:58 ./usr/include/jellyfish/cpp_array.hpp -rw-r--r-- root/root 2742 2025-12-03 04:58 ./usr/include/jellyfish/divisor.hpp -rw-r--r-- root/root 2710 2025-12-03 04:58 ./usr/include/jellyfish/dumper.hpp -rw-r--r-- root/root 2257 2025-12-03 04:58 ./usr/include/jellyfish/err.hpp -rw-r--r-- root/root 4033 2025-12-03 04:58 ./usr/include/jellyfish/file_header.hpp -rw-r--r-- root/root 4637 2025-12-03 04:58 ./usr/include/jellyfish/generator_manager.hpp -rw-r--r-- root/root 6814 2025-12-03 04:58 ./usr/include/jellyfish/generic_file_header.hpp -rw-r--r-- root/root 8326 2025-12-03 04:58 ./usr/include/jellyfish/hash_counter.hpp -rw-r--r-- root/root 7025 2025-12-03 04:58 ./usr/include/jellyfish/int128.hpp -rw-r--r-- root/root 1118 2025-12-03 04:58 ./usr/include/jellyfish/jellyfish.hpp -rw-r--r-- root/root 61697 2025-12-03 04:58 ./usr/include/jellyfish/json.h -rw-r--r-- root/root 40578 2025-12-03 04:58 ./usr/include/jellyfish/large_hash_array.hpp -rw-r--r-- root/root 7564 2025-12-03 04:58 ./usr/include/jellyfish/large_hash_iterator.hpp -rw-r--r-- root/root 4328 2025-12-03 04:58 ./usr/include/jellyfish/locks_pthread.hpp -rw-r--r-- root/root 5181 2025-12-03 04:58 ./usr/include/jellyfish/mapped_file.hpp -rw-r--r-- root/root 23839 2025-12-03 04:58 ./usr/include/jellyfish/mer_dna.hpp -rw-r--r-- root/root 1296 2025-12-03 04:58 ./usr/include/jellyfish/mer_dna_bloom_counter.hpp -rw-r--r-- root/root 3076 2025-12-03 04:58 ./usr/include/jellyfish/mer_heap.hpp -rw-r--r-- root/root 2588 2025-12-03 04:58 ./usr/include/jellyfish/mer_iterator.hpp -rw-r--r-- root/root 9371 2025-12-03 04:58 ./usr/include/jellyfish/mer_overlap_sequence_parser.hpp -rw-r--r-- root/root 3247 2025-12-03 04:58 ./usr/include/jellyfish/mer_qual_iterator.hpp -rw-r--r-- root/root 8066 2025-12-03 04:58 ./usr/include/jellyfish/misc.hpp -rw-r--r-- root/root 10025 2025-12-03 04:58 ./usr/include/jellyfish/offsets_key_value.hpp -rw-r--r-- root/root 960 2025-12-03 04:58 ./usr/include/jellyfish/parser_common.hpp -rw-r--r-- root/root 12859 2025-12-03 04:58 ./usr/include/jellyfish/rectangular_binary_matrix.hpp -rw-r--r-- root/root 2311 2025-12-03 04:58 ./usr/include/jellyfish/sam_format.hpp -rw-r--r-- root/root 3504 2025-12-03 04:58 ./usr/include/jellyfish/simple_circular_buffer.hpp -rw-r--r-- root/root 3346 2025-12-03 04:58 ./usr/include/jellyfish/sorted_dumper.hpp -rw-r--r-- root/root 5069 2025-12-03 04:58 ./usr/include/jellyfish/stdio_filebuf.hpp -rw-r--r-- root/root 602 2025-12-03 04:58 ./usr/include/jellyfish/storage.hpp -rw-r--r-- root/root 2036 2025-12-03 04:58 ./usr/include/jellyfish/stream_iterator.hpp -rw-r--r-- root/root 6318 2025-12-03 04:58 ./usr/include/jellyfish/stream_manager.hpp -rw-r--r-- root/root 2063 2025-12-03 04:58 ./usr/include/jellyfish/text_dumper.hpp -rw-r--r-- root/root 994 2025-12-03 04:58 ./usr/include/jellyfish/thread_exec.hpp -rw-r--r-- root/root 1884 2025-12-03 04:58 ./usr/include/jellyfish/time.hpp -rw-r--r-- root/root 1599 2025-12-03 04:58 ./usr/include/jellyfish/token_ring.hpp -rw-r--r-- root/root 6761 2025-12-03 04:58 ./usr/include/jellyfish/whole_sequence_parser.hpp drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/x86_64-linux-gnu/ -rw-r--r-- root/root 321038 2025-12-03 04:58 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a -rw-r--r-- root/root 1005 2025-12-03 04:58 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.la lrwxrwxrwx root/root 0 2025-12-03 04:58 ./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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jellyfish (2.3.1-5) Version: 2.3.1-5+b2 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 371 Depends: libjellyfish-perl (= 2.3.1-5+b2) Section: debug Priority: optional Multi-Arch: same Description: debug symbols for libjellyfish-perl Build-Ids: 2e0c56bc1977a355966011a3f5bda4c5ba7c546e drwxr-xr-x root/root 0 2025-12-03 04:58 ./ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/debug/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/debug/.build-id/2e/ -rw-r--r-- root/root 368928 2025-12-03 04:58 ./usr/lib/debug/.build-id/2e/0c56bc1977a355966011a3f5bda4c5ba7c546e.debug drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/share/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/share/doc/ lrwxrwxrwx root/root 0 2025-12-03 04:58 ./usr/share/doc/libjellyfish-perl-dbgsym -> libjellyfish-perl libjellyfish-perl_2.3.1-5+b2_amd64.deb -------------------------------------- new Debian package, version 2.0. size 58420 bytes: control archive=1168 bytes. 1250 bytes, 27 lines control 494 bytes, 6 lines md5sums Package: libjellyfish-perl Source: jellyfish (2.3.1-5) Version: 2.3.1-5+b2 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 177 Depends: perl (>= 5.42.0-3), perlapi-5.42.0, 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 2025-12-03 04:58 ./ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/x86_64-linux-gnu/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/x86_64-linux-gnu/perl5/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/x86_64-linux-gnu/perl5/5.42/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/x86_64-linux-gnu/perl5/5.42/auto/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/x86_64-linux-gnu/perl5/5.42/auto/jellyfish/ -rw-r--r-- root/root 146664 2025-12-03 04:58 ./usr/lib/x86_64-linux-gnu/perl5/5.42/auto/jellyfish/jellyfish.so drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/share/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/share/doc/libjellyfish-perl/ -rw-r--r-- root/root 208 2025-12-03 04:58 ./usr/share/doc/libjellyfish-perl/changelog.Debian.amd64.gz -rw-r--r-- root/root 3067 2025-12-03 04:58 ./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 2025-11-13 18:53 ./usr/share/doc/libjellyfish-perl/copyright drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/share/perl5/ -rw-r--r-- root/root 7414 2025-12-03 04:58 ./usr/share/perl5/jellyfish.pm python3-dna-jellyfish-dbgsym_2.3.1-5+b2_amd64.deb ------------------------------------------------- new Debian package, version 2.0. size 637208 bytes: control archive=656 bytes. 471 bytes, 12 lines control 310 bytes, 3 lines md5sums Package: python3-dna-jellyfish-dbgsym Source: jellyfish (2.3.1-5) Version: 2.3.1-5+b2 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 692 Depends: python3-dna-jellyfish (= 2.3.1-5+b2) Section: debug Priority: optional Description: debug symbols for python3-dna-jellyfish Build-Ids: 29640c0f252af02bad4e49c6e81ac57311b3ba58 ddc6b36b0977a3c57a0c2bda61f9fc1d0d9cd4e9 drwxr-xr-x root/root 0 2025-12-03 04:58 ./ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/debug/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/debug/.build-id/29/ -rw-r--r-- root/root 289952 2025-12-03 04:58 ./usr/lib/debug/.build-id/29/640c0f252af02bad4e49c6e81ac57311b3ba58.debug drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/debug/.build-id/dd/ -rw-r--r-- root/root 289216 2025-12-03 04:58 ./usr/lib/debug/.build-id/dd/c6b36b0977a3c57a0c2bda61f9fc1d0d9cd4e9.debug drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 114304 2025-12-03 04:58 ./usr/lib/debug/.dwz/x86_64-linux-gnu/python3-dna-jellyfish.debug drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/share/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/share/doc/ lrwxrwxrwx root/root 0 2025-12-03 04:58 ./usr/share/doc/python3-dna-jellyfish-dbgsym -> python3-dna-jellyfish python3-dna-jellyfish_2.3.1-5+b2_amd64.deb ------------------------------------------ new Debian package, version 2.0. size 67160 bytes: control archive=1644 bytes. 1312 bytes, 26 lines control 975 bytes, 10 lines md5sums 289 bytes, 12 lines * postinst #!/bin/sh 435 bytes, 12 lines * prerm #!/bin/sh Package: python3-dna-jellyfish Source: jellyfish (2.3.1-5) Version: 2.3.1-5+b2 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 334 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 2025-12-03 04:58 ./ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/python3/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/python3/dist-packages/ -rw-r--r-- root/root 149856 2025-12-03 04:58 ./usr/lib/python3/dist-packages/_dna_jellyfish.cpython-313-x86_64-linux-gnu.so -rw-r--r-- root/root 149856 2025-12-03 04:58 ./usr/lib/python3/dist-packages/_dna_jellyfish.cpython-314-x86_64-linux-gnu.so drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/lib/python3/dist-packages/dna_jellyfish-0.0.1.egg-info/ -rw-r--r-- root/root 160 2025-12-03 04:58 ./usr/lib/python3/dist-packages/dna_jellyfish-0.0.1.egg-info/PKG-INFO -rw-r--r-- root/root 1 2025-12-03 04:58 ./usr/lib/python3/dist-packages/dna_jellyfish-0.0.1.egg-info/dependency_links.txt -rw-r--r-- root/root 29 2025-12-03 04:58 ./usr/lib/python3/dist-packages/dna_jellyfish-0.0.1.egg-info/top_level.txt -rw-r--r-- root/root 12643 2025-12-03 04:58 ./usr/lib/python3/dist-packages/dna_jellyfish.py drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/share/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-12-03 04:58 ./usr/share/doc/python3-dna-jellyfish/ -rw-r--r-- root/root 208 2025-12-03 04:58 ./usr/share/doc/python3-dna-jellyfish/changelog.Debian.amd64.gz -rw-r--r-- root/root 3064 2025-12-03 04:58 ./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 2025-11-13 18:53 ./usr/share/doc/python3-dna-jellyfish/copyright +------------------------------------------------------------------------------+ | Post Build Wed, 03 Dec 2025 05:06:00 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Wed, 03 Dec 2025 05:06:00 +0000 | +------------------------------------------------------------------------------+ Purging /build/jellyfish-YgfDsN Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Wed, 03 Dec 2025 05:06:01 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 1795360 Build-Time: 375 Distribution: perl-5.42 Host Architecture: amd64 Install-Time: 40 Job: /srv/debomatic/incoming/jellyfish_2.3.1-5.dsc Machine Architecture: amd64 Package: jellyfish Package-Time: 421 Source-Version: 2.3.1-5 Space: 1795360 Status: successful Version: 2.3.1-5+b2 -------------------------------------------------------------------------------- Finished at 2025-12-03T05:05:57Z Build needed 00:07:01, 1795360k disk space