sbuild (Debian sbuild) 0.89.1 (28 April 2025) on carme.larted.org.uk +==============================================================================+ | jellyfish 2.3.1-4+b2 (amd64) Sun, 29 Jun 2025 18:11:28 +0000 | +==============================================================================+ Package: jellyfish Version: 2.3.1-4+b2 Source Version: 2.3.1-4 Distribution: perl-5.40 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 Sun, 29 Jun 2025 18:11:29 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup jellyfish_2.3.1-4 perl-5.40 amd64 -------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup jellyfish_2.3.1-4 perl-5.40 amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Sun, 29 Jun 2025 18:11:29 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3039 B] Get:1 file:/srv/reprepro perl-5.40 InRelease [3039 B] Get:2 file:/srv/reprepro perl-5.40/main amd64 Packages [199 kB] Hit:3 http://deb.debian.org/debian unstable InRelease Hit:4 http://localhost:3142/debian sid InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files Sun, 29 Jun 2025 18:11:35 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/jellyfish_2.3.1-4.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Sun, 29 Jun 2025 18:11:35 +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, dh-sequence-python3, python3-setuptools, 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, dh-sequence-python3, python3-setuptools, perl, chrpath, libhts-dev, dos2unix, samtools, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/jellyfish-eW46fQ/resolver-OTpSsR/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/jellyfish-eW46fQ/resolver-OTpSsR/apt_archive ./ InRelease Get:2 copy:/build/jellyfish-eW46fQ/resolver-OTpSsR/apt_archive ./ Release [609 B] Ign:3 copy:/build/jellyfish-eW46fQ/resolver-OTpSsR/apt_archive ./ Release.gpg Get:4 copy:/build/jellyfish-eW46fQ/resolver-OTpSsR/apt_archive ./ Sources [828 B] Get:5 copy:/build/jellyfish-eW46fQ/resolver-OTpSsR/apt_archive ./ Packages [867 B] Fetched 2304 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... 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-jquery libjs-sphinxdoc libjs-underscore 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 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 librtmp-dev librtmp1 libruby libruby3.3 libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libxml2 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 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 gcj-jdk 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 ri ruby-dev bundler cwltool swig-doc swig-examples Recommended packages: curl | wget | lynx bzip2-doc libarchive-cpio-perl javascript-common krb5-locales libgpm2 publicsuffix ruby-sdbm libtasn1-doc libltdl-dev libmail-sendmail-perl psmisc linux-sysctl-defaults zip fonts-lato 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-jquery libjs-sphinxdoc libjs-underscore 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 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 librtmp-dev librtmp1 libruby libruby3.3 libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libxml2 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 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, 149 newly installed, 0 to remove and 0 not upgraded. Need to get 58.6 MB of archives. After this operation, 227 MB of additional disk space will be used. Get:1 copy:/build/jellyfish-eW46fQ/resolver-OTpSsR/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [980 B] Get:2 http://deb.debian.org/debian unstable/main amd64 autoconf-archive all 20220903-3 [775 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.5-2 [862 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.1-1 [108 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.5-2 [2224 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.4-1 [27.3 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-4 [260 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.5-2 [1956 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.5-2 [757 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.4-1 [10.2 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.4-1 [28.3 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-8 [65.4 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-8 [881 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.5.0-2 [1490 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20250419 [162 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 architecture-properties amd64 0.2.6 [2336 B] Get:29 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-8 [294 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 bc amd64 1.07.1-4 [103 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 chrpath amd64 0.18-1 [13.5 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b1 [25.0 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-3+b1 [56.7 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 d-shlibs all 0.109 [11.1 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get:45 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-1 [698 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.2 [919 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250414 [116 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 dos2unix amd64 7.5.2-1 [518 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get:57 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-5 [60.0 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-5 [42.5 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-5 [42.6 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-5 [54.2 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-5 [126 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.14.1-2 [384 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.9-2 [455 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.9-2 [455 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-2 [103 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.9-2 [1401 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-5 [16.1 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.6.10+dfsg-1 [312 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1.1 [116 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.8.0-1 [91.3 kB] Get:93 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.11.0-1 [34.0 kB] Get:94 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.11.0-1 [179 kB] Get:95 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get:96 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get:97 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get:98 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.5.0-2 [2950 kB] Get:99 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get:100 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-1 [371 kB] Get:101 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.14.1-2 [503 kB] Get:102 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get:103 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.23-2 [55.9 kB] Get:104 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.7.1-1 [161 kB] Get:105 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get:106 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get:107 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.1-1 [348 kB] Get:108 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.21+ds-1 [1733 kB] Get:109 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:110 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get:111 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Get:112 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5+20250216-2 [105 kB] Get:113 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.5-2 [2160 kB] Get:114 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.5-2 [5291 kB] Get:115 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.4-1 [10.4 kB] Get:116 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.13.4-1 [1064 B] Get:117 http://deb.debian.org/debian unstable/main amd64 rubygems-integration all 1.19 [5488 B] Get:118 http://deb.debian.org/debian unstable/main amd64 ruby3.3 amd64 3.3.8-2 [834 kB] Get:119 http://deb.debian.org/debian unstable/main amd64 ruby-rubygems all 3.6.7-2 [407 kB] Get:120 http://deb.debian.org/debian unstable/main amd64 ruby amd64 1:3.3+b1 [6560 B] Get:121 http://deb.debian.org/debian unstable/main amd64 rake all 13.2.1-1 [65.2 kB] Get:122 http://deb.debian.org/debian unstable/main amd64 ruby-csv all 3.3.4-1 [42.2 kB] Get:123 http://deb.debian.org/debian unstable/main amd64 ruby-did-you-mean all 1.6.3-2 [20.9 kB] Get:124 http://deb.debian.org/debian unstable/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get:125 http://deb.debian.org/debian unstable/main amd64 ruby-ruby2-keywords all 0.0.5-1 [4300 B] Get:126 http://deb.debian.org/debian unstable/main amd64 ruby-webrick all 1.9.1-1 [59.6 kB] Get:127 http://deb.debian.org/debian unstable/main amd64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get:128 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get:129 http://deb.debian.org/debian unstable/main amd64 libruby3.3 amd64 3.3.8-2 [6301 kB] Get:130 http://deb.debian.org/debian unstable/main amd64 libruby amd64 1:3.3+b1 [5440 B] Get:131 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.13.4-1 [1044 B] Get:132 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.5-2 [504 kB] Get:133 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.4-1 [26.1 kB] Get:134 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.13.4-1 [1064 B] Get:135 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:136 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.7.0-1 [67.4 kB] Get:137 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.13.2-1 [90.5 kB] Get:138 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.2-1 [37.3 kB] Get:139 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get:140 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get:141 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get:142 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get:143 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get:144 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get:145 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get:146 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.21-1 [667 kB] Get:147 http://deb.debian.org/debian unstable/main amd64 swig amd64 4.3.0-1 [1503 kB] Get:148 http://deb.debian.org/debian unstable/main amd64 time amd64 1.9-0.2 [50.8 kB] Get:149 http://deb.debian.org/debian unstable/main amd64 yaggo all 1.5.11-2 [21.4 kB] Preconfiguring packages ... 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Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../098-libjs-sphinxdoc_8.1.3-5_all.deb ... Unpacking libjs-sphinxdoc (8.1.3-5) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../099-libncurses6_6.5+20250216-2_amd64.deb ... Unpacking libncurses6:amd64 (6.5+20250216-2) ... Selecting previously unselected package libpython3.13:amd64. Preparing to unpack .../100-libpython3.13_3.13.5-2_amd64.deb ... Unpacking libpython3.13:amd64 (3.13.5-2) ... Selecting previously unselected package libpython3.13-dev:amd64. Preparing to unpack .../101-libpython3.13-dev_3.13.5-2_amd64.deb ... Unpacking libpython3.13-dev:amd64 (3.13.5-2) ... Selecting previously unselected package libpython3-dev:amd64. Preparing to unpack .../102-libpython3-dev_3.13.4-1_amd64.deb ... Unpacking libpython3-dev:amd64 (3.13.4-1) ... Selecting previously unselected package libpython3-all-dev:amd64. 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Selecting previously unselected package libruby3.3:amd64. Preparing to unpack .../116-libruby3.3_3.3.8-2_amd64.deb ... Unpacking libruby3.3:amd64 (3.3.8-2) ... Selecting previously unselected package libruby:amd64. Preparing to unpack .../117-libruby_1%3a3.3+b1_amd64.deb ... Unpacking libruby:amd64 (1:3.3+b1) ... Selecting previously unselected package python3-all. Preparing to unpack .../118-python3-all_3.13.4-1_amd64.deb ... Unpacking python3-all (3.13.4-1) ... Selecting previously unselected package python3.13-dev. Preparing to unpack .../119-python3.13-dev_3.13.5-2_amd64.deb ... Unpacking python3.13-dev (3.13.5-2) ... Selecting previously unselected package python3-dev. Preparing to unpack .../120-python3-dev_3.13.4-1_amd64.deb ... Unpacking python3-dev (3.13.4-1) ... Selecting previously unselected package python3-all-dev. Preparing to unpack .../121-python3-all-dev_3.13.4-1_amd64.deb ... Unpacking python3-all-dev (3.13.4-1) ... 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Selecting previously unselected package samtools. Preparing to unpack .../133-samtools_1.21-1_amd64.deb ... Unpacking samtools (1.21-1) ... Selecting previously unselected package swig. Preparing to unpack .../134-swig_4.3.0-1_amd64.deb ... Unpacking swig (4.3.0-1) ... Selecting previously unselected package time. Preparing to unpack .../135-time_1.9-0.2_amd64.deb ... Unpacking time (1.9-0.2) ... Selecting previously unselected package yaggo. Preparing to unpack .../136-yaggo_1.5.11-2_all.deb ... Unpacking yaggo (1.5.11-2) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../137-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libhtscodecs2:amd64 (1.6.1-2) ... Setting up media-types (13.0.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libgnutls-openssl27t64:amd64 (3.8.9-2) ... Setting up time (1.9-0.2) ... Setting up libkeyutils1:amd64 (1.6.3-6) ... Setting up ruby-ruby2-keywords (0.0.5-1) ... Setting up swig (4.3.0-1) ... Setting up libzstd-dev:amd64 (1.5.7+dfsg-1) ... Setting up bsdextrautils (2.41-5) ... 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 libdebhelper-perl (13.24.2) ... Setting up libbrotli1:amd64 (1.1.0-2+b7) ... 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) ... Setting up libdeflate0:amd64 (1.23-2) ... Setting up bc (1.07.1-4) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up autoconf-archive (20220903-3) ... Setting up libcom-err2:amd64 (1.47.2-3+b1) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libkrb5support0:amd64 (1.21.3-5) ... Setting up tzdata (2025b-4) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Jun 29 18:11:46 UTC 2025. Universal Time is now: Sun Jun 29 18:11:46 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libunbound8:amd64 (1.22.0-1+b1) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-3) ... Setting up libexpat1-dev:amd64 (2.7.1-1) ... Setting up libgnutls-dane0t64:amd64 (3.8.9-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libldap-dev:amd64 (2.6.10+dfsg-1) ... Setting up libncurses6:amd64 (6.5+20250216-2) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up ruby-csv (3.3.4-1) ... Setting up libproc2-0:amd64 (2:4.0.4-8) ... Setting up comerr-dev:amd64 (2.1-1.47.2-3+b1) ... Setting up libssl-dev:amd64 (3.5.0-2) ... Setting up autopoint (0.23.1-2) ... Setting up d-shlibs (0.109) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libidn2-dev:amd64 (2.3.8-2) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:amd64 (1.8.0-1) ... Setting up libnghttp3-dev:amd64 (1.8.0-1) ... Setting up ruby-webrick (1.9.1-1) ... Setting up liblzma-dev:amd64 (5.8.1-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-8) ... 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 (1.11.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up dos2unix (7.5.2-1) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up ruby-did-you-mean (1.6.3-2) ... Setting up libtasn1-6-dev:amd64 (4.20.0-2) ... Setting up openssl (3.5.0-2) ... Setting up libdeflate-dev:amd64 (1.23-2) ... Setting up libpython3.13-stdlib:amd64 (3.13.5-2) ... Setting up ruby-xmlrpc (0.3.3-2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b7) ... Setting up chrpath (0.18-1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Setting up libp11-kit-dev:amd64 (0.25.5-3) ... Setting up libpython3-stdlib:amd64 (3.13.4-1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up libpython3.13:amd64 (3.13.5-2) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-3) ... Setting up nettle-dev:amd64 (3.10.1-1) ... Setting up libtool (2.5.4-4) ... Setting up python3.13 (3.13.5-2) ... Setting up python3 (3.13.4-1) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.11.0-1) ... Setting up libngtcp2-dev:amd64 (1.11.0-1) ... Setting up python3-zipp (3.21.0-1) ... 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 (20) ... Setting up ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 150 added, 0 removed; done. Setting up libpython3.13-dev:amd64 (3.13.5-2) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up python3-typing-extensions (4.13.2-1) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up libjs-sphinxdoc (8.1.3-5) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up dh-python (6.20250414) ... Setting up libgnutls28-dev:amd64 (3.8.9-2) ... Setting up python3-more-itertools (10.7.0-1) ... Setting up libnghttp2-dev:amd64 (1.64.0-1.1) ... Setting up libpython3-dev:amd64 (3.13.4-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3.13-dev (3.13.5-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3-typeguard (4.4.2-1) ... Setting up libcurl3t64-gnutls:amd64 (8.14.1-2) ... Setting up python3-all (3.13.4-1) ... 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 (7.3.1-2) ... Setting up libpython3-all-dev:amd64 (3.13.4-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up libgssrpc4t64:amd64 (1.21.3-5) ... Setting up python3-dev (3.13.4-1) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libhts3t64:amd64 (1.21+ds-1) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-5) ... Setting up python3-pkg-resources (78.1.1-0.1) ... Setting up python3-all-dev (3.13.4-1) ... Setting up python3-setuptools (78.1.1-0.1) ... Setting up libkdb5-10t64:amd64 (1.21.3-5) ... Setting up debhelper (13.24.2) ... Setting up samtools (1.21-1) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-5) ... Setting up krb5-multidev:amd64 (1.21.3-5) ... Setting up libkrb5-dev:amd64 (1.21.3-5) ... Setting up libcurl4-gnutls-dev:amd64 (8.14.1-2) ... Setting up libhts-dev:amd64 (1.21+ds-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 (2.41-9) ... 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 Sun, 29 Jun 2025 18:11:52 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment Sun, 29 Jun 2025 18:11:52 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.25-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.25-1 (2025-04-25) amd64 (x86_64) Toolchain package versions: binutils_2.44-3 dpkg-dev_1.22.20 g++-13_13.4.0-1 g++-14_14.2.0-19 gcc-13_13.4.0-1 gcc-14_14.2.0-19 libc6-dev_2.41-9 libstdc++-13-dev_13.4.0-1 libstdc++-14-dev_14.2.0-19 libstdc++6_14.2.0-19 linux-libc-dev_6.12.33-1 Package versions: adduser_3.152 apt_3.0.3 architecture-properties_0.2.6 autoconf_2.72-3.1 autoconf-archive_20220903-3 automake_1:1.17-4 autopoint_0.23.1-2 autotools-dev_20240727.1 base-files_13.8 base-passwd_3.6.7 bash_5.2.37-2+b3 bc_1.07.1-4 binutils_2.44-3 binutils-common_2.44-3 binutils-x86-64-linux-gnu_2.44-3 bsdextrautils_2.41-5 bsdutils_1:2.41-5 build-essential_12.12 bzip2_1.0.8-6 ca-certificates_20250419 chrpath_0.18-1 comerr-dev_2.1-1.47.2-3+b1 coreutils_9.7-3 cpp_4:14.2.0-1 cpp-13_13.4.0-1 cpp-13-x86-64-linux-gnu_13.4.0-1 cpp-14_14.2.0-19 cpp-14-x86-64-linux-gnu_14.2.0-19 cpp-x86-64-linux-gnu_4:14.2.0-1 d-shlibs_0.109 dash_0.5.12-12 debconf_1.5.91 debhelper_13.24.2 debian-archive-keyring_2025.1 debianutils_5.23.1 dh-autoreconf_20 dh-python_6.20250414 dh-strip-nondeterminism_1.14.1-2 diffutils_1:3.10-4 dirmngr_2.4.7-21+b1 dos2unix_7.5.2-1 dpkg_1.22.20 dpkg-dev_1.22.20 dwz_0.15-1+b1 eatmydata_131-2 file_1:5.46-5 findutils_4.10.0-3 g++_4:14.2.0-1 g++-13_13.4.0-1 g++-13-x86-64-linux-gnu_13.4.0-1 g++-14_14.2.0-19 g++-14-x86-64-linux-gnu_14.2.0-19 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-13_13.4.0-1 gcc-13-base_13.4.0-1 gcc-13-x86-64-linux-gnu_13.4.0-1 gcc-14_14.2.0-19 gcc-14-base_14.2.0-19 gcc-14-x86-64-linux-gnu_14.2.0-19 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.23.1-2 gettext-base_0.23.1-2 gnupg_2.4.7-21 gnupg-l10n_2.4.7-21 gnupg-utils_2.4.7-21+b1 gpg_2.4.7-21+b1 gpg-agent_2.4.7-21+b1 gpg-wks-client_2.4.7-21+b1 gpgconf_2.4.7-21+b1 gpgsm_2.4.7-21+b1 gpgv_2.4.7-21+b1 grep_3.11-4 groff-base_1.23.0-9 gzip_1.13-1 hostname_3.25 init-system-helpers_1.68 intltool-debian_0.35.0+20060710.6 krb5-multidev_1.21.3-5 libacl1_2.3.2-2+b1 libapt-pkg6.0t64_2.9.25 libapt-pkg7.0_3.0.3 libarchive-zip-perl_1.68-1 libasan8_14.2.0-19 libassuan0_2.5.6-1+b1 libassuan9_3.0.2-2 libatomic1_14.2.0-19 libattr1_1:2.5.2-3 libaudit-common_1:4.0.2-2 libaudit1_1:4.0.2-2+b2 libbinutils_2.44-3 libblkid1_2.41-5 libbrotli-dev_1.1.0-2+b7 libbrotli1_1.1.0-2+b7 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libbz2-dev_1.0.8-6 libc-bin_2.41-9 libc-dev-bin_2.41-9 libc-l10n_2.41-9 libc6_2.41-9 libc6-dev_2.41-9 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-9 libcc1-0_14.2.0-19 libcom-err2_1.47.2-3+b1 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.44-3 libctf0_2.44-3 libcurl3t64-gnutls_8.14.1-2 libcurl4-gnutls-dev_8.14.1-2 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.279 libdebhelper-perl_13.24.2 libdeflate-dev_1.23-2 libdeflate0_1.23-2 libdpkg-perl_1.22.20 libeatmydata1_131-2+b1 libelf1t64_0.192-4 libevent-2.1-7t64_2.1.12-stable-10+b1 libexpat1_2.7.1-1 libexpat1-dev_2.7.1-1 libffi8_3.4.8-2 libfile-stripnondeterminism-perl_1.14.1-2 libgcc-13-dev_13.4.0-1 libgcc-14-dev_14.2.0-19 libgcc-s1_14.2.0-19 libgcrypt20_1.11.0-7 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgmp-dev_2:6.3.0+dfsg-3 libgmp10_2:6.3.0+dfsg-3 libgmpxx4ldbl_2:6.3.0+dfsg-3 libgnutls-dane0t64_3.8.9-2 libgnutls-openssl27t64_3.8.9-2 libgnutls28-dev_3.8.9-2 libgnutls30t64_3.8.9-2 libgomp1_14.2.0-19 libgpg-error0_1.51-4 libgprofng0_2.44-3 libgssapi-krb5-2_1.21.3-5 libgssrpc4t64_1.21.3-5 libhogweed6t64_3.10.1-1 libhts-dev_1.21+ds-1 libhts3t64_1.21+ds-1 libhtscodecs2_1.6.1-2 libhwasan0_14.2.0-19 libidn2-0_2.3.8-2 libidn2-dev_2.3.8-2 libisl23_0.27-1 libitm1_14.2.0-19 libjansson4_2.14-2+b3 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-sphinxdoc_8.1.3-5 libjs-underscore_1.13.4~dfsg+~1.11.4-3 libk5crypto3_1.21.3-5 libkadm5clnt-mit12_1.21.3-5 libkadm5srv-mit12_1.21.3-5 libkdb5-10t64_1.21.3-5 libkeyutils1_1.6.3-6 libkrb5-3_1.21.3-5 libkrb5-dev_1.21.3-5 libkrb5support0_1.21.3-5 libksba8_1.6.7-2+b1 liblastlog2-2_2.41-5 libldap-2.5-0_2.5.19+dfsg-1 libldap-dev_2.6.10+dfsg-1 libldap2_2.6.10+dfsg-1 liblsan0_14.2.0-19 liblz4-1_1.10.0-4 liblzma-dev_5.8.1-1 liblzma5_5.8.1-1 libmagic-mgc_1:5.46-5 libmagic1t64_1:5.46-5 libmd0_1.1.0-2+b1 libmount1_2.41-5 libmpc3_1.3.1-1+b3 libmpfr6_4.2.2-1 libncurses6_6.5+20250216-2 libncursesw6_6.5+20250216-2 libnettle8t64_3.10.1-1 libnghttp2-14_1.64.0-1.1 libnghttp2-dev_1.64.0-1.1 libnghttp3-9_1.8.0-1 libnghttp3-dev_1.8.0-1 libngtcp2-16_1.11.0-1 libngtcp2-crypto-gnutls-dev_1.11.0-1 libngtcp2-crypto-gnutls8_1.11.0-1 libngtcp2-dev_1.11.0-1 libnpth0t64_1.8-3 libp11-kit-dev_0.25.5-3 libp11-kit0_0.25.5-3 libpam-modules_1.7.0-3 libpam-modules-bin_1.7.0-3 libpam-runtime_1.7.0-3 libpam0g_1.7.0-3 libpcre2-8-0_10.45-1 libperl5.38t64_5.38.2-5 libperl5.40_5.40.1-4 libpipeline1_1.5.8-1 libpkgconf3_1.8.1-4 libproc2-0_2:4.0.4-8 libpsl-dev_0.21.2-1.1+b1 libpsl5t64_0.21.2-1.1+b1 libpython3-all-dev_3.13.4-1 libpython3-dev_3.13.4-1 libpython3-stdlib_3.13.4-1 libpython3.13_3.13.5-2 libpython3.13-dev_3.13.5-2 libpython3.13-minimal_3.13.5-2 libpython3.13-stdlib_3.13.5-2 libquadmath0_14.2.0-19 libreadline8t64_8.2-6 librtmp-dev_2.4+20151223.gitfa8646d.1-2+b5 librtmp1_2.4+20151223.gitfa8646d.1-2+b5 libruby_1:3.3+b1 libruby3.3_3.3.8-2 libsasl2-2_2.1.28+dfsg1-9 libsasl2-modules-db_2.1.28+dfsg1-9 libseccomp2_2.6.0-2 libselinux1_3.8.1-1 libsemanage-common_3.8.1-1 libsemanage2_3.8.1-1 libsepol2_3.8.1-1 libsframe1_2.44-3 libsmartcols1_2.41-5 libsqlite3-0_3.46.1-6 libssh2-1-dev_1.11.1-1 libssh2-1t64_1.11.1-1 libssl-dev_3.5.0-2 libssl3t64_3.5.0-2 libstdc++-13-dev_13.4.0-1 libstdc++-14-dev_14.2.0-19 libstdc++6_14.2.0-19 libsystemd0_257.7-1 libtasn1-6_4.20.0-2 libtasn1-6-dev_4.20.0-2 libtinfo6_6.5+20250216-2 libtool_2.5.4-4 libtsan2_14.2.0-19 libubsan1_14.2.0-19 libuchardet0_0.0.8-1+b2 libudev1_257.7-1 libunbound8_1.22.0-1+b1 libunistring5_1.3-2 libuuid1_2.41-5 libxml2_2.12.7+dfsg+really2.9.14-1 libxxhash0_0.8.3-2 libyaml-0-2_0.2.5-2 libzstd-dev_1.5.7+dfsg-1 libzstd1_1.5.7+dfsg-1 linux-libc-dev_6.12.33-1 locales-all_2.41-9 login_1:4.16.0-2+really2.41-5 login.defs_1:4.17.4-2 m4_1.4.19-8 make_4.4.1-2 man-db_2.13.1-1 mawk_1.3.4.20250131-1 media-types_13.0.0 ncurses-base_6.5+20250216-2 ncurses-bin_6.5+20250216-2 netbase_6.5 nettle-dev_3.10.1-1 openssl_3.5.0-2 openssl-provider-legacy_3.5.0-2 passwd_1:4.17.4-2 patch_2.8-2 perl_5.40.1-4 perl-base_5.40.1-4 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.1-4 pinentry-curses_1.3.1-2 pkgconf_1.8.1-4 pkgconf-bin_1.8.1-4 po-debconf_1.0.21+nmu1 procps_2:4.0.4-8 python3_3.13.4-1 python3-all_3.13.4-1 python3-all-dev_3.13.4-1 python3-autocommand_2.2.2-3 python3-dev_3.13.4-1 python3-inflect_7.3.1-2 python3-jaraco.context_6.0.1-1 python3-jaraco.functools_4.1.0-1 python3-jaraco.text_4.0.0-1 python3-minimal_3.13.4-1 python3-more-itertools_10.7.0-1 python3-pkg-resources_78.1.1-0.1 python3-setuptools_78.1.1-0.1 python3-typeguard_4.4.2-1 python3-typing-extensions_4.13.2-1 python3-zipp_3.21.0-1 python3.13_3.13.5-2 python3.13-dev_3.13.5-2 python3.13-minimal_3.13.5-2 rake_13.2.1-1 readline-common_8.2-6 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_1.21-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.25 sqv_1.3.0-3 swig_4.3.0-1 sysvinit-utils_3.14-4 tar_1.35+dfsg-3.1 time_1.9-0.2 tzdata_2025b-4 usr-is-merged_39+nmu2 util-linux_2.41-5 xz-utils_5.8.1-1 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 Sun, 29 Jun 2025 18:11:52 +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: 2.3.1-4 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: 4.7.0 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, dh-sequence-python3, python3-setuptools, perl, 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 59b7c662f3178716a5fc3ae5d6362e1c28b4acf0 13296 jellyfish_2.3.1-4.debian.tar.xz Checksums-Sha256: 540d09457fb4e14b98c7f1428cf885c333e2d6ef4f6a3735aa06be13eb523d69 681990 jellyfish_2.3.1.orig.tar.gz 3a6f5547acad0c0e6cb3df644dd2ab6e62fecdc689fd5928637dcb2ad5049964 13296 jellyfish_2.3.1-4.debian.tar.xz Files: 27fb29ad3edfe25d776cfbf98dcc8c0e 681990 jellyfish_2.3.1.orig.tar.gz 8f26d8c3a313498ac0ad7bed8573f0a5 13296 jellyfish_2.3.1-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmdWlqoRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFXiQ/+L2XxFlkMc74oxuTErut/NdSdGedjMB+F 1W+3xN+wuXaiEYkVYjat0OZJdJut6mFPKwhaAICnJzU1idZ2U3OPF1p/fyQkOX7a vlfIzpT3xSVhLdiBmJ0kOuKMgi5U9gqsNSKTt0E2xh+3tUcjf8qA3jE/cq3hwHzW jn4whQbTqmbe2Lpk/hSKWurOMUmB7VXyVIVNoK8VOpWhOg8F4FpKFzLkbkXSc/jW oQ19zrulU9Esz/1r9OHiO2065u4K4iHp7odN+RLeItdGW1uxK/qVd5o2MA7obBTN PHm69JxF+xaxgckDQxQH+c8qZTDu1wLgXUPWXJ4yHjWbsh497BzFfoX9i5ePudSO ozwp0FqkywVctq7I/YcGERlsj6dwBWrMfFEPMRAKL6o3HpWF/WXWJNh+TEQi8UWd jIVvGtJ183GGXHKjuESxVRTqPYfbYI+CUKHyl/mbZZrbravYpzZd1TmisJ13wOzm 4UJZam2hHcgHcwW2lvpkyxQiXhMp2wc3+BHNhe5Ls8fjz7YLWJ5yVDz7SWncrv29 53nY3Ov/m1/Fm40HzkMSRjCSXdlMSb0i4kS4aMHRh0yd28Ho5vJb3IYkmwR8eotE f8gnoboMobZ5JTLkdmL4c8nkXxUns3xMYy3olKJ5H8KY/AJrbA15PdckjHWldaCy 28dkC4DO50g= =nDSH -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./jellyfish_2.3.1-4.dsc: no acceptable signature found dpkg-source: info: extracting jellyfish in /build/jellyfish-eW46fQ/jellyfish-2.3.1 dpkg-source: info: unpacking jellyfish_2.3.1.orig.tar.gz dpkg-source: info: unpacking jellyfish_2.3.1-4.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 2.3.1-4+b2 +------------------------------------------------------------------------------+ | Starting Timed Build Commands Sun, 29 Jun 2025 18:11:52 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network jellyfish_2.3.1-4 perl-5.40 amd64 -------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network jellyfish_2.3.1-4 perl-5.40 amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/jellyfish-eW46fQ/jellyfish-2.3.1 SCHROOT_ALIAS_NAME=perl-5.40-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-af3bf1a8-ccce-4232-84e9-17126f703ffc 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 2.3.1-4+b2 dpkg-buildpackage: info: source distribution perl-5.40 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-eW46fQ/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-eW46fQ/jellyfish-2.3.1' debian/rules binary-arch dh binary-arch debian/rules override_dh_update_autotools_config make[1]: Entering directory '/build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/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 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/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for 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/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for ld... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking for shared library run path origin... done checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking 32-bit host C ABI... no checking for egrep -e... (cached) /usr/bin/grep -E checking for ELF binary format... yes checking for the common suffixes of directories in the library search path... lib,lib,lib64 checking for htslib... yes checking for samtools... /usr/bin/samtools checking for unix2dos... /usr/bin/unix2dos checking for md5sum... md5sum checking for yaggo... /usr/bin/yaggo checking for x86 cpuid output... unknown checking for x86-AVX xgetbv output... unknown checking for x86 cpuid 0x00000000 output... 12:756e6547:6c65746e:49656e69 checking for x86 cpuid 0x80000000 output... 80000008:756e6547:6c65746e:49656e69 checking for x86 cpuid 0x00000001 output... 506e3:800:fffa3223:f8bfbff checking for x86 cpuid 0x00000007 output... 0:9c07af:4:ac000400 checking for x86 cpuid 0x80000001 output... 506e3:0:121:2c100800 checking for x86-AVX xgetbv 0x00000000 output... 7:0 checking whether RDRND is supported by the processor... yes checking whether RDRND is supported by the processor and OS... yes checking whether C++ compiler accepts -mrdrnd... yes checking whether BMI1 is supported by the processor... yes checking whether BMI1 is supported by the processor and OS... yes checking whether C++ compiler accepts -mbmi... yes checking whether BMI2 is supported by the processor... yes checking whether BMI2 is supported by the processor and OS... yes checking whether C++ compiler accepts -mbmi2... yes checking whether ADX is supported by the processor... yes checking whether ADX is supported by the processor and OS... yes checking whether C++ compiler accepts -madx... yes checking whether MPX is supported by the processor... no checking whether PREFETCHWT1 is supported by the processor... no checking whether ABM is supported by the processor... yes checking whether ABM is supported by the processor and OS... yes checking whether C++ compiler accepts -mabm... yes checking whether MMX is supported by the processor... yes checking whether MMX is supported by the processor and OS... yes checking whether C++ compiler accepts -mmmx... yes checking whether SSE is supported by the processor... yes checking whether SSE is supported by the processor and OS... yes checking whether C++ compiler accepts -msse... yes checking whether SSE2 is supported by the processor... yes checking whether SSE2 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse2... yes checking whether SSE3 is supported by the processor... yes checking whether SSE3 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse3... yes checking whether SSSE3 is supported by the processor... yes checking whether SSSE3 is supported by the processor and OS... yes checking whether C++ compiler accepts -mssse3... yes checking whether SSE4.1 is supported by the processor... yes checking whether SSE4.1 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse4.1... yes checking whether SSE4.2 is supported by the processor... yes checking whether SSE4.2 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse4.2... yes checking whether SSE4a is supported by the processor... no checking whether SHA is supported by the processor... no checking whether AES is supported by the processor... yes checking whether AES is supported by the processor and OS... yes checking whether C++ compiler accepts -maes... yes checking whether AVX is supported by the processor... yes checking whether AVX is supported by the processor and OS... yes checking whether C++ compiler accepts -mavx... yes checking whether FMA3 is supported by the processor... yes checking whether FMA3 is supported by the processor and OS... yes checking whether C++ compiler accepts -mfma... yes checking whether FMA4 is supported by the processor... no checking whether XOP is supported by the processor... no checking whether AVX2 is supported by the processor... yes checking whether AVX2 is supported by the processor and OS... yes checking whether C++ compiler accepts -mavx2... yes checking whether AVX512-F is supported by the processor... no checking whether AVX512-CD is supported by the processor... no checking whether AVX512-PF is supported by the processor... no checking whether AVX512-ER is supported by the processor... no checking whether AVX512-VL is supported by the processor... no checking whether AVX512-BW is supported by the processor... no checking whether AVX512-DQ is supported by the processor... no checking whether AVX512-IFMA is supported by the processor... no checking whether AVX512-VBMI is supported by the processor... no checking for __int128... yes checking for std::numeric_limits<__int128>... yes checking for _NSGetExecutablePath... no checking for execinfo.h... yes checking for ext/stdio_filebuf.h... yes checking for sys/syscall.h... yes checking for sys/prctl.h... yes checking for siginfo_t.si_int... yes checking for swig... /usr/bin/swig checking SWIG version... 4.3.0 checking for SWIG library... /usr/share/swig/4.3.0 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/5.40/CORE checking for Perl extension target directory... /usr/lib/perl/5.40.0 checking for Perl extensions C preprocessor flags... -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include checking for Perl extensions linker flags... -shared -L/usr/local/lib -fstack-protector-strong checking for posix_memalign... yes checking for aligned_alloc... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating compat.sh config.status: creating jellyfish-2.0.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_configure --sourcedirectory=swig/perl5 cd swig/perl5 && /usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1 -L/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -lpthread -L/build/jellyfish-eW46fQ/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:311: python3.13 setup.py config running config mv /tmp/m4-ax_python_devel.m4 m4 make[1]: Leaving directory '/build/jellyfish-eW46fQ/jellyfish-2.3.1' debian/rules override_dh_auto_build make[1]: Entering directory '/build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/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 -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o sub_commands/info_main.o sub_commands/info_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o sub_commands/dump_main.o sub_commands/dump_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o sub_commands/histo_main.o sub_commands/histo_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o sub_commands/stats_main.o sub_commands/stats_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o sub_commands/merge_main.o sub_commands/merge_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o sub_commands/bc_main.o sub_commands/bc_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o sub_commands/query_main.o sub_commands/query_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o sub_commands/cite_main.o sub_commands/cite_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o sub_commands/mem_main.o sub_commands/mem_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o jellyfish/merge_files.o jellyfish/merge_files.cc /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o lib/rectangular_binary_matrix.lo lib/rectangular_binary_matrix.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-DHAVE_CONFIG_H -I. -I/usr/include/python3.13 -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/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++ 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'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-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o 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-I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1=. -fstack-protector-strong 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-I/build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include 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g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -pthread -L/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -lhts -R/build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu make[2]: Leaving directory '/build/jellyfish-eW46fQ/jellyfish-2.3.1' dh_auto_install -- install-data make -j1 install DESTDIR=/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp AM_UPDATE_INFO_DIR=no install-data make[2]: Entering directory '/build/jellyfish-eW46fQ/jellyfish-2.3.1' make install-am make[3]: Entering directory '/build/jellyfish-eW46fQ/jellyfish-2.3.1' make[4]: Entering directory '/build/jellyfish-eW46fQ/jellyfish-2.3.1' /usr/bin/mkdir -p '/build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/bin' /bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/bin/jellyfish /usr/bin/mkdir -p '/build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/mkdir -p '/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/jellyfish-eW46fQ/jellyfish-2.3.1; /bin/bash "/build/jellyfish-eW46fQ/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/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/5.40.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/14/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-eW46fQ/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/14 -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/14/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crtn.o -Werror -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so.0 || { rm -f jellyfish.so.0 && ln -s jellyfish.so.0.0.0 jellyfish.so.0; }; }) libtool: install: (cd /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so || { rm -f jellyfish.so && ln -s jellyfish.so.0.0.0 jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.lai /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: chmod 644 /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: ranlib /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.40.0' /usr/bin/mkdir -p '/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/mkdir -p '/build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/mkdir -p '/build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1; /bin/bash "/build/jellyfish-eW46fQ/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/14/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-eW46fQ/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/14 -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/14/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crtn.o -Werror -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' make[4]: Leaving directory '/build/jellyfish-eW46fQ/jellyfish-2.3.1' make[3]: Leaving directory '/build/jellyfish-eW46fQ/jellyfish-2.3.1' /usr/bin/mkdir -p '/build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/mkdir -p '/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/jellyfish-eW46fQ/jellyfish-2.3.1; /bin/bash "/build/jellyfish-eW46fQ/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/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/5.40.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/14/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-eW46fQ/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/14 -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/14/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crtn.o -Werror -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so.0 || { rm -f jellyfish.so.0 && ln -s jellyfish.so.0.0.0 jellyfish.so.0; }; }) libtool: install: (cd /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so || { rm -f jellyfish.so && ln -s jellyfish.so.0.0.0 jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.lai /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: chmod 644 /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: ranlib /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.40.0' /usr/bin/mkdir -p '/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/mkdir -p '/build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/mkdir -p '/build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1; /bin/bash "/build/jellyfish-eW46fQ/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/14/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-eW46fQ/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/14 -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/14/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crtn.o -Werror -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' make[2]: Leaving directory '/build/jellyfish-eW46fQ/jellyfish-2.3.1' dh_auto_build --sourcedirectory=swig/perl5 cd swig/perl5 && make -j2 make[2]: Entering directory '/build/jellyfish-eW46fQ/jellyfish-2.3.1/swig/perl5' Running Mkbootstrap for jellyfish () g++ -c -std=c++0x -I/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/jellyfish-eW46fQ/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.0.1\" -DXS_VERSION=\"0.0.1\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" swig_wrap.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ chmod 644 "jellyfish.bs" "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- jellyfish.bs blib/arch/auto/jellyfish/jellyfish.bs 644 rm -f blib/arch/auto/jellyfish/jellyfish.so x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/swig/perl5' dh_auto_build --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build build_ext -L/build/jellyfish-eW46fQ/jellyfish-2.3.1/.libs running build running build_py copying dna_jellyfish.py -> /build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -L/build/jellyfish-eW46fQ/jellyfish-2.3.1/.libs -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -lpthread -o /build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu make[1]: Leaving directory '/build/jellyfish-eW46fQ/jellyfish-2.3.1' debian/rules override_dh_auto_test make[1]: Entering directory '/build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1' make check-am make[3]: Entering directory '/build/jellyfish-eW46fQ/jellyfish-2.3.1' make bin/generate_sequence bin/fastq2sam bin/test_all libgtest.la libgtest_main.la make[4]: Entering directory '/build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -pthread -L/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu -lhts -R/build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1' make check-TESTS make[4]: Entering directory '/build/jellyfish-eW46fQ/jellyfish-2.3.1' make[5]: Entering directory '/build/jellyfish-eW46fQ/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: tests/subset_hashing.sh PASS: unit_tests/unit_tests.sh PASS: tests/bloom_counter.sh PASS: tests/large_key.sh PASS: tests/multi_file.sh PASS: tests/sam.sh PASS: tests/small_mers.sh SKIP: tests/swig_ruby.sh PASS: tests/swig_python.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-eW46fQ/jellyfish-2.3.1' make[4]: Leaving directory '/build/jellyfish-eW46fQ/jellyfish-2.3.1' make[3]: Leaving directory '/build/jellyfish-eW46fQ/jellyfish-2.3.1' make[2]: Leaving directory '/build/jellyfish-eW46fQ/jellyfish-2.3.1' make[1]: Leaving directory '/build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1' chrpath --delete bin/.libs/* dh_auto_install -- install-data make -j1 install DESTDIR=/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp AM_UPDATE_INFO_DIR=no install-data make[2]: Entering directory '/build/jellyfish-eW46fQ/jellyfish-2.3.1' make install-am make[3]: Entering directory '/build/jellyfish-eW46fQ/jellyfish-2.3.1' make[4]: Entering directory '/build/jellyfish-eW46fQ/jellyfish-2.3.1' /usr/bin/mkdir -p '/build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/bin' /bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/bin/jellyfish /usr/bin/mkdir -p '/build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/mkdir -p '/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/jellyfish-eW46fQ/jellyfish-2.3.1; /bin/bash "/build/jellyfish-eW46fQ/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/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/5.40.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/14/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-eW46fQ/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/14 -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/14/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crtn.o -Werror -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so.0 || { rm -f jellyfish.so.0 && ln -s jellyfish.so.0.0.0 jellyfish.so.0; }; }) libtool: install: (cd /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so || { rm -f jellyfish.so && ln -s jellyfish.so.0.0.0 jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.lai /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: chmod 644 /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: ranlib /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.40.0' /usr/bin/mkdir -p '/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/mkdir -p '/build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/mkdir -p '/build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1; /bin/bash "/build/jellyfish-eW46fQ/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/14/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-eW46fQ/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/14 -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/14/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crtn.o -Werror -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' make[4]: Leaving directory '/build/jellyfish-eW46fQ/jellyfish-2.3.1' make[3]: Leaving directory '/build/jellyfish-eW46fQ/jellyfish-2.3.1' /usr/bin/mkdir -p '/build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/mkdir -p '/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/jellyfish-eW46fQ/jellyfish-2.3.1; /bin/bash "/build/jellyfish-eW46fQ/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/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/5.40.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/14/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-eW46fQ/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/14 -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/14/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crtn.o -Werror -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so.0 || { rm -f jellyfish.so.0 && ln -s jellyfish.so.0.0.0 jellyfish.so.0; }; }) libtool: install: (cd /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so || { rm -f jellyfish.so && ln -s jellyfish.so.0.0.0 jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.lai /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: chmod 644 /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: ranlib /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.40.0' /usr/bin/mkdir -p '/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/mkdir -p '/build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/mkdir -p '/build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1; /bin/bash "/build/jellyfish-eW46fQ/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/14/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-eW46fQ/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/14 -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/14/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crtn.o -Werror -g -O2 -ffile-prefix-map=/build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/python3.13/site-packages/dna_jellyfish' make[2]: Leaving directory '/build/jellyfish-eW46fQ/jellyfish-2.3.1' dh_auto_install --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/.pybuild/cpython3_3.13_dna_jellyfish/build running build_ext running install_lib creating /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.13/dist-packages copying /build/jellyfish-eW46fQ/jellyfish-2.3.1/.pybuild/cpython3_3.13_dna_jellyfish/build/_dna_jellyfish.cpython-313-x86_64-linux-gnu.so -> /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.13/dist-packages copying /build/jellyfish-eW46fQ/jellyfish-2.3.1/.pybuild/cpython3_3.13_dna_jellyfish/build/dna_jellyfish.py -> /build/jellyfish-eW46fQ/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.13/dist-packages byte-compiling /build/jellyfish-eW46fQ/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 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-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr make[2]: Entering directory '/build/jellyfish-eW46fQ/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-eW46fQ/jellyfish-2.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/jellyfish/jellyfish.so make[2]: Leaving directory '/build/jellyfish-eW46fQ/jellyfish-2.3.1/swig/perl5' ls -l debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so -r-xr-xr-x 1 debomatic sbuild 1143840 Jun 29 18:14 debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/jellyfish/jellyfish.so if [ ! -e debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so ] ; then sleep 1; fi chmod +w debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so chrpath --delete debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so dh_install d-shlibmove --commit \ --multiarch \ --devunversioned \ --movedev "debian/tmp/usr/include/jellyfish*/jellyfish/*.hpp" usr/include/jellyfish \ --movedev "debian/tmp/usr/include/jellyfish*/jellyfish/*.h" usr/include/jellyfish \ --movedev config.h usr/include/jellyfish \ debian/tmp/usr/lib/*/libjellyfish-*.so Library package automatic movement utility set -e install -d -m 755 debian/libjellyfish-2.0-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/libjellyfish-2.0-2/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a debian/libjellyfish-2.0-dev/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.la debian/libjellyfish-2.0-dev/usr/lib/x86_64-linux-gnu || true mv debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so debian/libjellyfish-2.0-dev/usr/lib/x86_64-linux-gnu mv /build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/jellyfish-2.3.1' dh_install -a debian/rules execute_after_dh_install make[1]: Entering directory '/build/jellyfish-eW46fQ/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-eW46fQ/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-eW46fQ/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-eW46fQ/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_2.3.1-4+b2_amd64.deb'. dpkg-deb: building package 'python3-dna-jellyfish' in '../python3-dna-jellyfish_2.3.1-4+b2_amd64.deb'. dpkg-deb: building package 'python3-dna-jellyfish-dbgsym' in '../python3-dna-jellyfish-dbgsym_2.3.1-4+b2_amd64.deb'. dpkg-deb: building package 'libjellyfish-perl' in '../libjellyfish-perl_2.3.1-4+b2_amd64.deb'. dpkg-deb: building package 'libjellyfish-perl-dbgsym' in '../libjellyfish-perl-dbgsym_2.3.1-4+b2_amd64.deb'. dpkg-deb: building package 'jellyfish-dbgsym' in '../jellyfish-dbgsym_2.3.1-4+b2_amd64.deb'. dpkg-deb: building package 'libjellyfish-2.0-2' in '../libjellyfish-2.0-2_2.3.1-4+b2_amd64.deb'. dpkg-deb: building package 'libjellyfish-2.0-2-dbgsym' in '../libjellyfish-2.0-2-dbgsym_2.3.1-4+b2_amd64.deb'. dpkg-deb: building package 'libjellyfish-2.0-dev' in '../libjellyfish-2.0-dev_2.3.1-4+b2_amd64.deb'. dpkg-genbuildinfo --build=any -O../jellyfish_2.3.1-4+b2_amd64.buildinfo dpkg-genchanges --build=any -mDebian Perl autobuilder -O../jellyfish_2.3.1-4+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 2025-06-29T18:16:41Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Sun, 29 Jun 2025 18:16:41 +0000 | +------------------------------------------------------------------------------+ jellyfish_2.3.1-4+b2_amd64.changes: ----------------------------------- Format: 1.8 Date: Sun, 29 Jun 2025 18:11:28 +0000 Source: jellyfish (2.3.1-4) 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: 2.3.1-4+b2 Distribution: perl-5.40 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 (2.3.1-4+b2) perl-5.40; urgency=low, binary-only=yes . * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild for Perl 5.40 Checksums-Sha1: 543e9c35a82a26e3d797eeff47c600e2597567cc 7603688 jellyfish-dbgsym_2.3.1-4+b2_amd64.deb 33319ec6843249f81a69ea8fe0d073468cd6ae7a 11855 jellyfish_2.3.1-4+b2_amd64.buildinfo 15d5cb26648b44abe70195526c49e2cdb8cf4d53 808136 jellyfish_2.3.1-4+b2_amd64.deb 318501a2e6157fc40d0c15219bad8e4ea5af7bff 545356 libjellyfish-2.0-2-dbgsym_2.3.1-4+b2_amd64.deb 9786f2c6918ce7f61680529a6364ef5dedf6089d 67396 libjellyfish-2.0-2_2.3.1-4+b2_amd64.deb 860b43ea64f946194465cd50fa6ce4d07f3d7b47 138960 libjellyfish-2.0-dev_2.3.1-4+b2_amd64.deb 470970f6ddec889f94e869b195ff6af3e68e80d9 353336 libjellyfish-perl-dbgsym_2.3.1-4+b2_amd64.deb 97940dff49ea929863811ae23a736ecbc071acdb 57020 libjellyfish-perl_2.3.1-4+b2_amd64.deb 071fba5a630632c8b7cb0650786b0adbf0dc50d9 344096 python3-dna-jellyfish-dbgsym_2.3.1-4+b2_amd64.deb ec14bb16f92d024ff585170d0f12f9a85fa5ce1a 56996 python3-dna-jellyfish_2.3.1-4+b2_amd64.deb Checksums-Sha256: 6e1c5cc926deec909724983efaaf1cd8ad60d86a09c5679b2c968ed9aa26c79d 7603688 jellyfish-dbgsym_2.3.1-4+b2_amd64.deb 5493dee3be25714d98392f0fba830248f0041ac6db5549097945495900b22347 11855 jellyfish_2.3.1-4+b2_amd64.buildinfo c6c80d22d646251d75df9c545cfad304559ba1784408dd1d4e1ab716efe14bd2 808136 jellyfish_2.3.1-4+b2_amd64.deb 068036d84495da69097c9e317b6e367bed74841576ed6f2c75adeed2cb601c77 545356 libjellyfish-2.0-2-dbgsym_2.3.1-4+b2_amd64.deb 540e937246b0199f796da7b1860262828e8e85b4c42e86933fad7e7419e8ad04 67396 libjellyfish-2.0-2_2.3.1-4+b2_amd64.deb 15ac2e56f30fc082d5fb17478684d2b1f4ccb8c4c258634d4aede53ad337303b 138960 libjellyfish-2.0-dev_2.3.1-4+b2_amd64.deb 285be0de5c41f41488e6d33642e391827b02ff93b2a4ec1affadac98feb6a45c 353336 libjellyfish-perl-dbgsym_2.3.1-4+b2_amd64.deb 3f6dd370105cb074ddbac1461ebb36d7135419c8a1e40f7aa5549369a44c500e 57020 libjellyfish-perl_2.3.1-4+b2_amd64.deb d467e79cb723885406f20274e9fcddc97bcd254b9633f4a22410b2211d5af1e7 344096 python3-dna-jellyfish-dbgsym_2.3.1-4+b2_amd64.deb 6f0fbce01cb286579bb3d22ca6e5590b816c79798ace2a147b985cee8411d4f3 56996 python3-dna-jellyfish_2.3.1-4+b2_amd64.deb Files: 8342aef0de021638077cdf42e2e4546b 7603688 debug optional jellyfish-dbgsym_2.3.1-4+b2_amd64.deb 6cc454620199b548e91ae10766fe3116 11855 science optional jellyfish_2.3.1-4+b2_amd64.buildinfo 45e348be0cdabc595852c89a2d0b18f3 808136 science optional jellyfish_2.3.1-4+b2_amd64.deb aa8139e7bd32c485e660009ca72d1bd9 545356 debug optional libjellyfish-2.0-2-dbgsym_2.3.1-4+b2_amd64.deb 50c8914566590cfe3fd034e920477edf 67396 libs optional libjellyfish-2.0-2_2.3.1-4+b2_amd64.deb 80470be6acd967454ebc70fa42d6f1e9 138960 libdevel optional libjellyfish-2.0-dev_2.3.1-4+b2_amd64.deb d4644e2109fd49eb0a2c48cb7d0f07a7 353336 debug optional libjellyfish-perl-dbgsym_2.3.1-4+b2_amd64.deb f552449e2375ad36139e7219d7d7e8d6 57020 perl optional libjellyfish-perl_2.3.1-4+b2_amd64.deb f5975edee542d975f733f817b7808fca 344096 debug optional python3-dna-jellyfish-dbgsym_2.3.1-4+b2_amd64.deb 5b3b1b7a9b719fe76815cb0e67691224 56996 python optional python3-dna-jellyfish_2.3.1-4+b2_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Sun, 29 Jun 2025 18:16:42 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: jellyfish (2.3.1-4) 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: 2.3.1-4+b2 Binary-Only-Changes: jellyfish (2.3.1-4+b2) perl-5.40; urgency=low, binary-only=yes . * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild for Perl 5.40 . -- Debian Perl autobuilder Sun, 29 Jun 2025 18:11:28 +0000 Checksums-Md5: 8342aef0de021638077cdf42e2e4546b 7603688 jellyfish-dbgsym_2.3.1-4+b2_amd64.deb 45e348be0cdabc595852c89a2d0b18f3 808136 jellyfish_2.3.1-4+b2_amd64.deb aa8139e7bd32c485e660009ca72d1bd9 545356 libjellyfish-2.0-2-dbgsym_2.3.1-4+b2_amd64.deb 50c8914566590cfe3fd034e920477edf 67396 libjellyfish-2.0-2_2.3.1-4+b2_amd64.deb 80470be6acd967454ebc70fa42d6f1e9 138960 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libjellyfish-perl_2.3.1-4+b2_amd64.deb 071fba5a630632c8b7cb0650786b0adbf0dc50d9 344096 python3-dna-jellyfish-dbgsym_2.3.1-4+b2_amd64.deb ec14bb16f92d024ff585170d0f12f9a85fa5ce1a 56996 python3-dna-jellyfish_2.3.1-4+b2_amd64.deb Checksums-Sha256: 6e1c5cc926deec909724983efaaf1cd8ad60d86a09c5679b2c968ed9aa26c79d 7603688 jellyfish-dbgsym_2.3.1-4+b2_amd64.deb c6c80d22d646251d75df9c545cfad304559ba1784408dd1d4e1ab716efe14bd2 808136 jellyfish_2.3.1-4+b2_amd64.deb 068036d84495da69097c9e317b6e367bed74841576ed6f2c75adeed2cb601c77 545356 libjellyfish-2.0-2-dbgsym_2.3.1-4+b2_amd64.deb 540e937246b0199f796da7b1860262828e8e85b4c42e86933fad7e7419e8ad04 67396 libjellyfish-2.0-2_2.3.1-4+b2_amd64.deb 15ac2e56f30fc082d5fb17478684d2b1f4ccb8c4c258634d4aede53ad337303b 138960 libjellyfish-2.0-dev_2.3.1-4+b2_amd64.deb 285be0de5c41f41488e6d33642e391827b02ff93b2a4ec1affadac98feb6a45c 353336 libjellyfish-perl-dbgsym_2.3.1-4+b2_amd64.deb 3f6dd370105cb074ddbac1461ebb36d7135419c8a1e40f7aa5549369a44c500e 57020 libjellyfish-perl_2.3.1-4+b2_amd64.deb d467e79cb723885406f20274e9fcddc97bcd254b9633f4a22410b2211d5af1e7 344096 python3-dna-jellyfish-dbgsym_2.3.1-4+b2_amd64.deb 6f0fbce01cb286579bb3d22ca6e5590b816c79798ace2a147b985cee8411d4f3 56996 python3-dna-jellyfish_2.3.1-4+b2_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 29 Jun 2025 18:16:41 +0000 Build-Path: /build/jellyfish-eW46fQ/jellyfish-2.3.1 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: adduser (= 3.152), apt (= 3.0.3), architecture-properties (= 0.2.6), autoconf (= 2.72-3.1), autoconf-archive (= 20220903-3), automake (= 1:1.17-4), autopoint (= 0.23.1-2), autotools-dev (= 20240727.1), base-files (= 13.8), base-passwd (= 3.6.7), bash (= 5.2.37-2+b3), bc (= 1.07.1-4), binutils (= 2.44-3), binutils-common (= 2.44-3), binutils-x86-64-linux-gnu (= 2.44-3), bsdextrautils (= 2.41-5), bsdutils (= 1:2.41-5), build-essential (= 12.12), bzip2 (= 1.0.8-6), ca-certificates (= 20250419), chrpath (= 0.18-1), comerr-dev (= 2.1-1.47.2-3+b1), coreutils (= 9.7-3), cpp (= 4:14.2.0-1), cpp-13 (= 13.4.0-1), cpp-13-x86-64-linux-gnu (= 13.4.0-1), cpp-14 (= 14.2.0-19), cpp-14-x86-64-linux-gnu (= 14.2.0-19), cpp-x86-64-linux-gnu (= 4:14.2.0-1), d-shlibs (= 0.109), dash (= 0.5.12-12), debconf (= 1.5.91), debhelper (= 13.24.2), debian-archive-keyring (= 2025.1), debianutils (= 5.23.1), dh-autoreconf (= 20), dh-python (= 6.20250414), dh-strip-nondeterminism (= 1.14.1-2), diffutils (= 1:3.10-4), dos2unix (= 7.5.2-1), dpkg (= 1.22.20), dpkg-dev (= 1.22.20), dwz (= 0.15-1+b1), file (= 1:5.46-5), findutils (= 4.10.0-3), g++ (= 4:14.2.0-1), g++-14 (= 14.2.0-19), g++-14-x86-64-linux-gnu (= 14.2.0-19), g++-x86-64-linux-gnu (= 4:14.2.0-1), gcc (= 4:14.2.0-1), gcc-13 (= 13.4.0-1), gcc-13-base (= 13.4.0-1), gcc-13-x86-64-linux-gnu (= 13.4.0-1), gcc-14 (= 14.2.0-19), gcc-14-base (= 14.2.0-19), gcc-14-x86-64-linux-gnu (= 14.2.0-19), gcc-x86-64-linux-gnu (= 4:14.2.0-1), gettext (= 0.23.1-2), gettext-base (= 0.23.1-2), grep (= 3.11-4), groff-base (= 1.23.0-9), gzip (= 1.13-1), hostname (= 3.25), init-system-helpers (= 1.68), intltool-debian (= 0.35.0+20060710.6), krb5-multidev (= 1.21.3-5), libacl1 (= 2.3.2-2+b1), libapt-pkg7.0 (= 3.0.3), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.2.0-19), libatomic1 (= 14.2.0-19), libattr1 (= 1:2.5.2-3), libaudit-common (= 1:4.0.2-2), libaudit1 (= 1:4.0.2-2+b2), libbinutils (= 2.44-3), libblkid1 (= 2.41-5), libbrotli-dev (= 1.1.0-2+b7), libbrotli1 (= 1.1.0-2+b7), libbsd0 (= 0.12.2-2), libbz2-1.0 (= 1.0.8-6), libbz2-dev (= 1.0.8-6), libc-bin (= 2.41-9), libc-dev-bin (= 2.41-9), libc6 (= 2.41-9), libc6-dev (= 2.41-9), libcap-ng0 (= 0.8.5-4+b1), libcap2 (= 1:2.75-9), libcc1-0 (= 14.2.0-19), libcom-err2 (= 1.47.2-3+b1), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libctf-nobfd0 (= 2.44-3), libctf0 (= 2.44-3), libcurl3t64-gnutls (= 8.14.1-2), libcurl4-gnutls-dev (= 8.14.1-2), libdb5.3t64 (= 5.3.28+dfsg2-9), libdebconfclient0 (= 0.279), libdebhelper-perl (= 13.24.2), libdeflate-dev (= 1.23-2), libdeflate0 (= 1.23-2), libdpkg-perl (= 1.22.20), libelf1t64 (= 0.192-4), libevent-2.1-7t64 (= 2.1.12-stable-10+b1), libexpat1 (= 2.7.1-1), libexpat1-dev (= 2.7.1-1), libffi8 (= 3.4.8-2), libfile-stripnondeterminism-perl (= 1.14.1-2), libgcc-13-dev (= 13.4.0-1), libgcc-14-dev (= 14.2.0-19), libgcc-s1 (= 14.2.0-19), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgmp-dev (= 2:6.3.0+dfsg-3), libgmp10 (= 2:6.3.0+dfsg-3), libgmpxx4ldbl (= 2:6.3.0+dfsg-3), libgnutls-dane0t64 (= 3.8.9-2), libgnutls-openssl27t64 (= 3.8.9-2), libgnutls28-dev (= 3.8.9-2), libgnutls30t64 (= 3.8.9-2), libgomp1 (= 14.2.0-19), libgprofng0 (= 2.44-3), libgssapi-krb5-2 (= 1.21.3-5), libgssrpc4t64 (= 1.21.3-5), libhogweed6t64 (= 3.10.1-1), libhts-dev (= 1.21+ds-1), libhts3t64 (= 1.21+ds-1), libhtscodecs2 (= 1.6.1-2), libhwasan0 (= 14.2.0-19), libidn2-0 (= 2.3.8-2), libidn2-dev (= 2.3.8-2), libisl23 (= 0.27-1), libitm1 (= 14.2.0-19), libjansson4 (= 2.14-2+b3), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libjs-sphinxdoc (= 8.1.3-5), libjs-underscore (= 1.13.4~dfsg+~1.11.4-3), libk5crypto3 (= 1.21.3-5), libkadm5clnt-mit12 (= 1.21.3-5), libkadm5srv-mit12 (= 1.21.3-5), libkdb5-10t64 (= 1.21.3-5), libkeyutils1 (= 1.6.3-6), libkrb5-3 (= 1.21.3-5), libkrb5-dev (= 1.21.3-5), libkrb5support0 (= 1.21.3-5), liblastlog2-2 (= 2.41-5), libldap-dev (= 2.6.10+dfsg-1), libldap2 (= 2.6.10+dfsg-1), liblsan0 (= 14.2.0-19), liblz4-1 (= 1.10.0-4), liblzma-dev (= 5.8.1-1), liblzma5 (= 5.8.1-1), libmagic-mgc (= 1:5.46-5), libmagic1t64 (= 1:5.46-5), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.41-5), libmpc3 (= 1.3.1-1+b3), libmpfr6 (= 4.2.2-1), libncurses6 (= 6.5+20250216-2), libncursesw6 (= 6.5+20250216-2), libnettle8t64 (= 3.10.1-1), libnghttp2-14 (= 1.64.0-1.1), libnghttp2-dev (= 1.64.0-1.1), libnghttp3-9 (= 1.8.0-1), libnghttp3-dev (= 1.8.0-1), libngtcp2-16 (= 1.11.0-1), libngtcp2-crypto-gnutls-dev (= 1.11.0-1), libngtcp2-crypto-gnutls8 (= 1.11.0-1), libngtcp2-dev (= 1.11.0-1), libp11-kit-dev (= 0.25.5-3), libp11-kit0 (= 0.25.5-3), libpam-modules (= 1.7.0-3), libpam-modules-bin (= 1.7.0-3), libpam-runtime (= 1.7.0-3), libpam0g (= 1.7.0-3), libpcre2-8-0 (= 10.45-1), libperl5.40 (= 5.40.1-4), libpipeline1 (= 1.5.8-1), libpkgconf3 (= 1.8.1-4), libproc2-0 (= 2:4.0.4-8), libpsl-dev (= 0.21.2-1.1+b1), libpsl5t64 (= 0.21.2-1.1+b1), libpython3-all-dev (= 3.13.4-1), libpython3-dev (= 3.13.4-1), libpython3-stdlib (= 3.13.4-1), libpython3.13 (= 3.13.5-2), libpython3.13-dev (= 3.13.5-2), libpython3.13-minimal (= 3.13.5-2), libpython3.13-stdlib (= 3.13.5-2), libquadmath0 (= 14.2.0-19), libreadline8t64 (= 8.2-6), librtmp-dev (= 2.4+20151223.gitfa8646d.1-2+b5), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b5), libruby (= 1:3.3+b1), libruby3.3 (= 3.3.8-2), libsasl2-2 (= 2.1.28+dfsg1-9), libsasl2-modules-db (= 2.1.28+dfsg1-9), libseccomp2 (= 2.6.0-2), libselinux1 (= 3.8.1-1), libsemanage-common (= 3.8.1-1), libsemanage2 (= 3.8.1-1), libsepol2 (= 3.8.1-1), libsframe1 (= 2.44-3), libsmartcols1 (= 2.41-5), libsqlite3-0 (= 3.46.1-6), libssh2-1-dev (= 1.11.1-1), libssh2-1t64 (= 1.11.1-1), libssl-dev (= 3.5.0-2), libssl3t64 (= 3.5.0-2), libstdc++-14-dev (= 14.2.0-19), libstdc++6 (= 14.2.0-19), libsystemd0 (= 257.7-1), libtasn1-6 (= 4.20.0-2), libtasn1-6-dev (= 4.20.0-2), libtinfo6 (= 6.5+20250216-2), libtool (= 2.5.4-4), libtsan2 (= 14.2.0-19), libubsan1 (= 14.2.0-19), libuchardet0 (= 0.0.8-1+b2), libudev1 (= 257.7-1), libunbound8 (= 1.22.0-1+b1), libunistring5 (= 1.3-2), libuuid1 (= 2.41-5), libxml2 (= 2.12.7+dfsg+really2.9.14-1), libxxhash0 (= 0.8.3-2), libyaml-0-2 (= 0.2.5-2), libzstd-dev (= 1.5.7+dfsg-1), libzstd1 (= 1.5.7+dfsg-1), linux-libc-dev (= 6.12.33-1), login.defs (= 1:4.17.4-2), m4 (= 1.4.19-8), make (= 4.4.1-2), man-db (= 2.13.1-1), mawk (= 1.3.4.20250131-1), media-types (= 13.0.0), ncurses-base (= 6.5+20250216-2), ncurses-bin (= 6.5+20250216-2), netbase (= 6.5), nettle-dev (= 3.10.1-1), openssl (= 3.5.0-2), openssl-provider-legacy (= 3.5.0-2), passwd (= 1:4.17.4-2), patch (= 2.8-2), perl (= 5.40.1-4), perl-base (= 5.40.1-4), perl-modules-5.40 (= 5.40.1-4), pkgconf (= 1.8.1-4), pkgconf-bin (= 1.8.1-4), po-debconf (= 1.0.21+nmu1), procps (= 2:4.0.4-8), python3 (= 3.13.4-1), python3-all (= 3.13.4-1), python3-all-dev (= 3.13.4-1), python3-autocommand (= 2.2.2-3), python3-dev (= 3.13.4-1), python3-inflect (= 7.3.1-2), python3-jaraco.context (= 6.0.1-1), python3-jaraco.functools (= 4.1.0-1), python3-jaraco.text (= 4.0.0-1), python3-minimal (= 3.13.4-1), python3-more-itertools (= 10.7.0-1), python3-pkg-resources (= 78.1.1-0.1), python3-setuptools (= 78.1.1-0.1), python3-typeguard (= 4.4.2-1), python3-typing-extensions (= 4.13.2-1), python3-zipp (= 3.21.0-1), python3.13 (= 3.13.5-2), python3.13-dev (= 3.13.5-2), python3.13-minimal (= 3.13.5-2), rake (= 13.2.1-1), readline-common (= 8.2-6), 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 (= 1.21-1), sed (= 4.9-2), sensible-utils (= 0.0.25), sqv (= 1.3.0-3), swig (= 4.3.0-1), sysvinit-utils (= 3.14-4), tar (= 1.35+dfsg-3.1), time (= 1.9-0.2), tzdata (= 2025b-4), util-linux (= 2.41-5), xz-utils (= 5.8.1-1), 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="1751220688" +------------------------------------------------------------------------------+ | Package contents Sun, 29 Jun 2025 18:16:42 +0000 | +------------------------------------------------------------------------------+ jellyfish-dbgsym_2.3.1-4+b2_amd64.deb ------------------------------------- new Debian package, version 2.0. size 7603688 bytes: control archive=768 bytes. 518 bytes, 12 lines control 510 bytes, 5 lines md5sums Package: jellyfish-dbgsym Source: jellyfish (2.3.1-4) Version: 2.3.1-4+b2 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 8773 Depends: jellyfish (= 2.3.1-4+b2) Section: debug Priority: optional Description: debug symbols for jellyfish Build-Ids: 3b2b4c1a3b4be85bab7f461b275db28f4fdb47ea 788d0d86eb9fc8c82dcd64c1f094189ed81cde89 9f914772ab45cfab129e59fa41bf504556b1a989 ff42c232ae44e3b9e3e3a90d407b642f72ec97a6 drwxr-xr-x root/root 0 2025-06-29 18:11 ./ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/debug/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/debug/.build-id/3b/ -rw-r--r-- root/root 7222424 2025-06-29 18:11 ./usr/lib/debug/.build-id/3b/2b4c1a3b4be85bab7f461b275db28f4fdb47ea.debug drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/debug/.build-id/78/ -rw-r--r-- root/root 66584 2025-06-29 18:11 ./usr/lib/debug/.build-id/78/8d0d86eb9fc8c82dcd64c1f094189ed81cde89.debug drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/debug/.build-id/9f/ -rw-r--r-- root/root 1512440 2025-06-29 18:11 ./usr/lib/debug/.build-id/9f/914772ab45cfab129e59fa41bf504556b1a989.debug drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/debug/.build-id/ff/ -rw-r--r-- root/root 84416 2025-06-29 18:11 ./usr/lib/debug/.build-id/ff/42c232ae44e3b9e3e3a90d407b642f72ec97a6.debug drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 79024 2025-06-29 18:11 ./usr/lib/debug/.dwz/x86_64-linux-gnu/jellyfish.debug drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/doc/ lrwxrwxrwx root/root 0 2025-06-29 18:11 ./usr/share/doc/jellyfish-dbgsym -> jellyfish jellyfish_2.3.1-4+b2_amd64.deb ------------------------------ new Debian package, version 2.0. size 808136 bytes: control archive=1368 bytes. 1183 bytes, 24 lines control 988 bytes, 14 lines md5sums Package: jellyfish Source: jellyfish (2.3.1-4) Version: 2.3.1-4+b2 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 2527 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libhts3t64 (>= 1.17), libjellyfish-2.0-2 (= 2.3.1-4+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 2025-06-29 18:11 ./ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/bin/ -rwxr-xr-x root/root 347640 2025-06-29 18:11 ./usr/bin/jellyfish drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/jellyfish/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/jellyfish/bin/ -rwxr-xr-x root/root 27168 2025-06-29 18:11 ./usr/lib/jellyfish/bin/fastq2sam -rwxr-xr-x root/root 35560 2025-06-29 18:11 ./usr/lib/jellyfish/bin/generate_sequence -rwxr-xr-x root/root 1915584 2025-06-29 18:11 ./usr/lib/jellyfish/bin/test_all drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/doc-base/ -rw-r--r-- root/root 987 2024-12-09 06:54 ./usr/share/doc-base/jellyfish.jellyfish drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/doc/jellyfish/ -rw-r--r-- root/root 321 2024-12-09 06:54 ./usr/share/doc/jellyfish/README.test -rw-r--r-- root/root 209 2025-06-29 18:11 ./usr/share/doc/jellyfish/changelog.Debian.amd64.gz -rw-r--r-- root/root 2833 2025-06-29 18:11 ./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 2024-12-09 06:54 ./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 2024-12-09 06:54 ./usr/share/doc/jellyfish/run-unit-test drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/lintian/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 144 2024-12-09 06:54 ./usr/share/lintian/overrides/jellyfish drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/man/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/man/man1/ -rw-r--r-- root/root 4554 2025-06-29 18:11 ./usr/share/man/man1/jellyfish.1.gz libjellyfish-2.0-2-dbgsym_2.3.1-4+b2_amd64.deb ---------------------------------------------- new Debian package, version 2.0. size 545356 bytes: control archive=564 bytes. 438 bytes, 13 lines control 106 bytes, 1 lines md5sums Package: libjellyfish-2.0-2-dbgsym Source: jellyfish (2.3.1-4) Version: 2.3.1-4+b2 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 579 Depends: libjellyfish-2.0-2 (= 2.3.1-4+b2) Section: debug Priority: optional Multi-Arch: same Description: debug symbols for libjellyfish-2.0-2 Build-Ids: df64cb43736d93695381883977f3f0921ed0df27 drwxr-xr-x root/root 0 2025-06-29 18:11 ./ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/debug/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/debug/.build-id/df/ -rw-r--r-- root/root 582024 2025-06-29 18:11 ./usr/lib/debug/.build-id/df/64cb43736d93695381883977f3f0921ed0df27.debug drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/doc/ lrwxrwxrwx root/root 0 2025-06-29 18:11 ./usr/share/doc/libjellyfish-2.0-2-dbgsym -> libjellyfish-2.0-2 libjellyfish-2.0-2_2.3.1-4+b2_amd64.deb --------------------------------------- new Debian package, version 2.0. size 67396 bytes: control archive=1328 bytes. 1386 bytes, 31 lines control 503 bytes, 6 lines md5sums 49 bytes, 1 lines shlibs 68 bytes, 2 lines triggers Package: libjellyfish-2.0-2 Source: jellyfish (2.3.1-4) Version: 2.3.1-4+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 (= 2.3.1-4+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 2025-06-29 18:11 ./ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/x86_64-linux-gnu/ lrwxrwxrwx root/root 0 2025-06-29 18:11 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2 -> libjellyfish-2.0.so.2.0.0 -rw-r--r-- root/root 182296 2025-06-29 18:11 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/doc/libjellyfish-2.0-2/ -rw-r--r-- root/root 209 2025-06-29 18:11 ./usr/share/doc/libjellyfish-2.0-2/changelog.Debian.amd64.gz -rw-r--r-- root/root 2834 2025-06-29 18:11 ./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 2024-12-09 06:54 ./usr/share/doc/libjellyfish-2.0-2/copyright drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/lintian/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 178 2024-12-09 06:54 ./usr/share/lintian/overrides/libjellyfish-2.0-2 libjellyfish-2.0-dev_2.3.1-4+b2_amd64.deb ----------------------------------------- new Debian package, version 2.0. size 138960 bytes: control archive=2544 bytes. 1231 bytes, 27 lines control 4278 bytes, 57 lines md5sums Package: libjellyfish-2.0-dev Source: jellyfish (2.3.1-4) Version: 2.3.1-4+b2 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 696 Depends: libjellyfish-2.0-2 (= 2.3.1-4+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 2025-06-29 18:11 ./ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/include/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/include/jellyfish/ -rw-r--r-- root/root 1596 2025-06-29 18:11 ./usr/include/jellyfish/allocators_mmap.hpp -rw-r--r-- root/root 5898 2025-06-29 18:11 ./usr/include/jellyfish/atomic_bits_array.hpp -rw-r--r-- root/root 4770 2025-06-29 18:11 ./usr/include/jellyfish/atomic_field.hpp -rw-r--r-- root/root 1392 2025-06-29 18:11 ./usr/include/jellyfish/atomic_gcc.hpp -rw-r--r-- root/root 272 2025-06-29 18:11 ./usr/include/jellyfish/backtrace.hpp -rw-r--r-- root/root 6829 2025-06-29 18:11 ./usr/include/jellyfish/binary_dumper.hpp -rw-r--r-- root/root 3480 2025-06-29 18:11 ./usr/include/jellyfish/bloom_common.hpp -rw-r--r-- root/root 6778 2025-06-29 18:11 ./usr/include/jellyfish/bloom_counter2.hpp -rw-r--r-- root/root 5447 2025-06-29 18:11 ./usr/include/jellyfish/bloom_filter.hpp -rw-r--r-- root/root 5211 2025-06-29 18:11 ./usr/include/jellyfish/circular_buffer.hpp -rw-r--r-- root/root 2408 2025-06-29 18:11 ./usr/include/jellyfish/compare_and_swap.hpp -rw-r--r-- root/root 7472 2025-06-29 18:11 ./usr/include/jellyfish/cooperative_pool.hpp -rw-r--r-- root/root 8494 2025-06-29 18:11 ./usr/include/jellyfish/cooperative_pool2.hpp -rw-r--r-- root/root 4125 2025-06-29 18:11 ./usr/include/jellyfish/cpp_array.hpp -rw-r--r-- root/root 2742 2025-06-29 18:11 ./usr/include/jellyfish/divisor.hpp -rw-r--r-- root/root 2710 2025-06-29 18:11 ./usr/include/jellyfish/dumper.hpp -rw-r--r-- root/root 2257 2025-06-29 18:11 ./usr/include/jellyfish/err.hpp -rw-r--r-- root/root 4033 2025-06-29 18:11 ./usr/include/jellyfish/file_header.hpp -rw-r--r-- root/root 4637 2025-06-29 18:11 ./usr/include/jellyfish/generator_manager.hpp -rw-r--r-- root/root 6814 2025-06-29 18:11 ./usr/include/jellyfish/generic_file_header.hpp -rw-r--r-- root/root 8326 2025-06-29 18:11 ./usr/include/jellyfish/hash_counter.hpp -rw-r--r-- root/root 7025 2025-06-29 18:11 ./usr/include/jellyfish/int128.hpp -rw-r--r-- root/root 1118 2025-06-29 18:11 ./usr/include/jellyfish/jellyfish.hpp -rw-r--r-- root/root 61697 2025-06-29 18:11 ./usr/include/jellyfish/json.h -rw-r--r-- root/root 40578 2025-06-29 18:11 ./usr/include/jellyfish/large_hash_array.hpp -rw-r--r-- root/root 7564 2025-06-29 18:11 ./usr/include/jellyfish/large_hash_iterator.hpp -rw-r--r-- root/root 4328 2025-06-29 18:11 ./usr/include/jellyfish/locks_pthread.hpp -rw-r--r-- root/root 5181 2025-06-29 18:11 ./usr/include/jellyfish/mapped_file.hpp -rw-r--r-- root/root 23839 2025-06-29 18:11 ./usr/include/jellyfish/mer_dna.hpp -rw-r--r-- root/root 1296 2025-06-29 18:11 ./usr/include/jellyfish/mer_dna_bloom_counter.hpp -rw-r--r-- root/root 3076 2025-06-29 18:11 ./usr/include/jellyfish/mer_heap.hpp -rw-r--r-- root/root 2588 2025-06-29 18:11 ./usr/include/jellyfish/mer_iterator.hpp -rw-r--r-- root/root 9371 2025-06-29 18:11 ./usr/include/jellyfish/mer_overlap_sequence_parser.hpp -rw-r--r-- root/root 3247 2025-06-29 18:11 ./usr/include/jellyfish/mer_qual_iterator.hpp -rw-r--r-- root/root 8066 2025-06-29 18:11 ./usr/include/jellyfish/misc.hpp -rw-r--r-- root/root 10025 2025-06-29 18:11 ./usr/include/jellyfish/offsets_key_value.hpp -rw-r--r-- root/root 960 2025-06-29 18:11 ./usr/include/jellyfish/parser_common.hpp -rw-r--r-- root/root 12859 2025-06-29 18:11 ./usr/include/jellyfish/rectangular_binary_matrix.hpp -rw-r--r-- root/root 2311 2025-06-29 18:11 ./usr/include/jellyfish/sam_format.hpp -rw-r--r-- root/root 3504 2025-06-29 18:11 ./usr/include/jellyfish/simple_circular_buffer.hpp -rw-r--r-- root/root 3346 2025-06-29 18:11 ./usr/include/jellyfish/sorted_dumper.hpp -rw-r--r-- root/root 5069 2025-06-29 18:11 ./usr/include/jellyfish/stdio_filebuf.hpp -rw-r--r-- root/root 602 2025-06-29 18:11 ./usr/include/jellyfish/storage.hpp -rw-r--r-- root/root 2036 2025-06-29 18:11 ./usr/include/jellyfish/stream_iterator.hpp -rw-r--r-- root/root 6318 2025-06-29 18:11 ./usr/include/jellyfish/stream_manager.hpp -rw-r--r-- root/root 2063 2025-06-29 18:11 ./usr/include/jellyfish/text_dumper.hpp -rw-r--r-- root/root 994 2025-06-29 18:11 ./usr/include/jellyfish/thread_exec.hpp -rw-r--r-- root/root 1884 2025-06-29 18:11 ./usr/include/jellyfish/time.hpp -rw-r--r-- root/root 1599 2025-06-29 18:11 ./usr/include/jellyfish/token_ring.hpp -rw-r--r-- root/root 6761 2025-06-29 18:11 ./usr/include/jellyfish/whole_sequence_parser.hpp drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/x86_64-linux-gnu/ -rw-r--r-- root/root 322864 2025-06-29 18:11 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a -rw-r--r-- root/root 1005 2025-06-29 18:11 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.la lrwxrwxrwx root/root 0 2025-06-29 18:11 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so -> libjellyfish-2.0.so.2.0.0 drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/x86_64-linux-gnu/pkgconfig/ -rw-r--r-- root/root 273 2025-06-29 18:11 ./usr/lib/x86_64-linux-gnu/pkgconfig/jellyfish-2.0.pc drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/doc/libjellyfish-2.0-dev/ -rw-r--r-- root/root 209 2025-06-29 18:11 ./usr/share/doc/libjellyfish-2.0-dev/changelog.Debian.amd64.gz -rw-r--r-- root/root 2834 2025-06-29 18:11 ./usr/share/doc/libjellyfish-2.0-dev/changelog.Debian.gz -rw-r--r-- root/root 284 2023-12-06 21:50 ./usr/share/doc/libjellyfish-2.0-dev/changelog.gz -rw-r--r-- root/root 6395 2024-12-09 06:54 ./usr/share/doc/libjellyfish-2.0-dev/copyright libjellyfish-perl-dbgsym_2.3.1-4+b2_amd64.deb --------------------------------------------- new Debian package, version 2.0. size 353336 bytes: control archive=564 bytes. 435 bytes, 13 lines control 106 bytes, 1 lines md5sums Package: libjellyfish-perl-dbgsym Source: jellyfish (2.3.1-4) Version: 2.3.1-4+b2 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 373 Depends: libjellyfish-perl (= 2.3.1-4+b2) Section: debug Priority: optional Multi-Arch: same Description: debug symbols for libjellyfish-perl Build-Ids: 3cd9e45a58b0f8d6a16d350229f33250a340c703 drwxr-xr-x root/root 0 2025-06-29 18:11 ./ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/debug/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/debug/.build-id/3c/ -rw-r--r-- root/root 371184 2025-06-29 18:11 ./usr/lib/debug/.build-id/3c/d9e45a58b0f8d6a16d350229f33250a340c703.debug drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/doc/ lrwxrwxrwx root/root 0 2025-06-29 18:11 ./usr/share/doc/libjellyfish-perl-dbgsym -> libjellyfish-perl libjellyfish-perl_2.3.1-4+b2_amd64.deb -------------------------------------- new Debian package, version 2.0. size 57020 bytes: control archive=1164 bytes. 1250 bytes, 27 lines control 494 bytes, 6 lines md5sums Package: libjellyfish-perl Source: jellyfish (2.3.1-4) Version: 2.3.1-4+b2 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 177 Depends: perl (>= 5.40.1-4), perlapi-5.40.1, libc6 (>= 2.38), libgcc-s1 (>= 3.0) Section: perl Priority: optional Multi-Arch: same Homepage: https://www.genome.umd.edu/jellyfish.html Description: count k-mers in DNA sequences (Perl bindings of jellyfish) JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. . JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish dump" command. . This package contains the Perl bindings of jellyfish. drwxr-xr-x root/root 0 2025-06-29 18:11 ./ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/x86_64-linux-gnu/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/x86_64-linux-gnu/perl5/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/x86_64-linux-gnu/perl5/5.40/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/x86_64-linux-gnu/perl5/5.40/auto/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/x86_64-linux-gnu/perl5/5.40/auto/jellyfish/ -rw-r--r-- root/root 146664 2025-06-29 18:11 ./usr/lib/x86_64-linux-gnu/perl5/5.40/auto/jellyfish/jellyfish.so drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/doc/libjellyfish-perl/ -rw-r--r-- root/root 209 2025-06-29 18:11 ./usr/share/doc/libjellyfish-perl/changelog.Debian.amd64.gz -rw-r--r-- root/root 2836 2025-06-29 18:11 ./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 2024-12-09 06:54 ./usr/share/doc/libjellyfish-perl/copyright drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/perl5/ -rw-r--r-- root/root 7414 2025-06-29 18:11 ./usr/share/perl5/jellyfish.pm python3-dna-jellyfish-dbgsym_2.3.1-4+b2_amd64.deb ------------------------------------------------- new Debian package, version 2.0. size 344096 bytes: control archive=556 bytes. 430 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: python3-dna-jellyfish-dbgsym Source: jellyfish (2.3.1-4) Version: 2.3.1-4+b2 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 368 Depends: python3-dna-jellyfish (= 2.3.1-4+b2) Section: debug Priority: optional Description: debug symbols for python3-dna-jellyfish Build-Ids: d3d531e2c6900d67e031cd9e4bf0667cb0743e5e drwxr-xr-x root/root 0 2025-06-29 18:11 ./ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/debug/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/debug/.build-id/d3/ -rw-r--r-- root/root 366152 2025-06-29 18:11 ./usr/lib/debug/.build-id/d3/d531e2c6900d67e031cd9e4bf0667cb0743e5e.debug drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/doc/ lrwxrwxrwx root/root 0 2025-06-29 18:11 ./usr/share/doc/python3-dna-jellyfish-dbgsym -> python3-dna-jellyfish python3-dna-jellyfish_2.3.1-4+b2_amd64.deb ------------------------------------------ new Debian package, version 2.0. size 56996 bytes: control archive=1604 bytes. 1312 bytes, 26 lines control 864 bytes, 9 lines md5sums 289 bytes, 12 lines * postinst #!/bin/sh 402 bytes, 12 lines * prerm #!/bin/sh Package: python3-dna-jellyfish Source: jellyfish (2.3.1-4) Version: 2.3.1-4+b2 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 186 Depends: python3 (<< 3.14), 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 2025-06-29 18:11 ./ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/python3/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/python3/dist-packages/ -rw-r--r-- root/root 149496 2025-06-29 18:11 ./usr/lib/python3/dist-packages/_dna_jellyfish.cpython-313-x86_64-linux-gnu.so drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/lib/python3/dist-packages/dna_jellyfish-0.0.1.egg-info/ -rw-r--r-- root/root 160 2025-06-29 18:11 ./usr/lib/python3/dist-packages/dna_jellyfish-0.0.1.egg-info/PKG-INFO -rw-r--r-- root/root 1 2025-06-29 18:11 ./usr/lib/python3/dist-packages/dna_jellyfish-0.0.1.egg-info/dependency_links.txt -rw-r--r-- root/root 29 2025-06-29 18:11 ./usr/lib/python3/dist-packages/dna_jellyfish-0.0.1.egg-info/top_level.txt -rw-r--r-- root/root 12643 2025-06-29 18:11 ./usr/lib/python3/dist-packages/dna_jellyfish.py drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-06-29 18:11 ./usr/share/doc/python3-dna-jellyfish/ -rw-r--r-- root/root 209 2025-06-29 18:11 ./usr/share/doc/python3-dna-jellyfish/changelog.Debian.amd64.gz -rw-r--r-- root/root 2834 2025-06-29 18:11 ./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 2024-12-09 06:54 ./usr/share/doc/python3-dna-jellyfish/copyright +------------------------------------------------------------------------------+ | Post Build Sun, 29 Jun 2025 18:16:43 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Sun, 29 Jun 2025 18:16:43 +0000 | +------------------------------------------------------------------------------+ Purging /build/jellyfish-eW46fQ Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Sun, 29 Jun 2025 18:16:44 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 1810140 Build-Time: 289 Distribution: perl-5.40 Host Architecture: amd64 Install-Time: 17 Job: /srv/debomatic/incoming/jellyfish_2.3.1-4.dsc Machine Architecture: amd64 Package: jellyfish Package-Time: 313 Source-Version: 2.3.1-4 Space: 1810140 Status: successful Version: 2.3.1-4+b2 -------------------------------------------------------------------------------- Finished at 2025-06-29T18:16:41Z Build needed 00:05:13, 1810140k disk space