sbuild (Debian sbuild) 0.85.10 (30 May 2024) on carme.larted.org.uk +==============================================================================+ | jellyfish 2.3.1-3+b6 (amd64) Sat, 03 Aug 2024 11:34:24 +0000 | +==============================================================================+ Package: jellyfish Version: 2.3.1-3+b6 Source Version: 2.3.1-3 Distribution: perl-5.40 Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/perl-5.40-amd64-debomatic-ef1fcdef-313e-45e8-bc86-43cfed73b8a8' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup jellyfish_2.3.1-3 perl-5.40 amd64 -------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup jellyfish_2.3.1-3 perl-5.40 amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/jellyfish-pFs7kI/resolver-7iFlGq' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Get:2 http://localhost:3142/debian sid InRelease [198 kB] Get:3 http://deb.debian.org/debian unstable InRelease [198 kB] Get:4 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:5 http://localhost:3142/debian sid/main Sources T-2024-08-03-0808.05-F-2024-08-03-0808.05.pdiff [16.0 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:5 http://localhost:3142/debian sid/main Sources T-2024-08-03-0808.05-F-2024-08-03-0808.05.pdiff [16.0 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2024-08-03-0808.05-F-2024-08-03-0808.05.pdiff [10.5 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2024-08-03-0808.05-F-2024-08-03-0808.05.pdiff [10.5 kB] Fetched 550 kB in 8s (71.6 kB/s) 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 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/jellyfish_2.3.1-3.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/jellyfish-pFs7kI/jellyfish-2.3.1' with '<>' I: NOTICE: Log filtering will replace 'build/jellyfish-pFs7kI' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ 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, fakeroot 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, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [845 B] Get:5 copy:/<>/apt_archive ./ Packages [878 B] Fetched 2332 B in 0s (180 kB/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 d-shlibs debhelper dh-autoreconf dh-python dh-strip-nondeterminism dos2unix dwz fakeroot file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli-dev libbrotli1 libcom-err2 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libedit2 libelf1t64 libevent-2.1-7t64 libexpat1 libexpat1-dev libfakeroot libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgssapi-krb5-2 libhts-dev libhts3t64 libhtscodecs2 libicu72 libidn2-dev libjs-jquery libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 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 libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 librtmp-dev librtmp1 libruby libruby3.1t64 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-dev python3-minimal python3-pkg-resources python3-setuptools python3.12 python3.12-dev python3.12-minimal rake ruby ruby-net-telnet ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.1 rubygems-integration samtools sensible-utils swig time tzdata yaggo zlib1g-dev Suggested packages: gnu-standards autoconf-doc dh-make flit python3-build python3-installer python3-wheel gettext-doc libasprintf-dev libgettextpo-dev groff libcurl4-doc libidn-dev libkrb5-dev libldap2-dev gmp-doc libgmp10-doc libmpfr-dev dns-root-data gnutls-bin gnutls-doc krb5-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 python3.12-venv python3.12-doc binfmt-support ri ruby-dev bundler cwltool swig-doc swig-examples Recommended packages: curl | wget | lynx libarchive-cpio-perl javascript-common krb5-locales libgpm2 publicsuffix 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 d-shlibs debhelper dh-autoreconf dh-python dh-strip-nondeterminism dos2unix dwz fakeroot file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli-dev libbrotli1 libcom-err2 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libedit2 libelf1t64 libevent-2.1-7t64 libexpat1 libexpat1-dev libfakeroot libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgssapi-krb5-2 libhts-dev libhts3t64 libhtscodecs2 libicu72 libidn2-dev libjs-jquery libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 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 libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 librtmp-dev librtmp1 libruby libruby3.1t64 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-dev python3-minimal python3-pkg-resources python3-setuptools python3.12 python3.12-dev python3.12-minimal rake ruby ruby-net-telnet ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.1 rubygems-integration samtools sbuild-build-depends-main-dummy sensible-utils swig time tzdata yaggo zlib1g-dev 0 upgraded, 133 newly installed, 0 to remove and 0 not upgraded. Need to get 64.1 MB of archives. After this operation, 252 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [1012 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 libpython3.12-minimal amd64 3.12.4-3 [812 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.4-3 [2137 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.4-1 [26.5 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.4-3 [1950 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.4-3 [664 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.4-1 [9500 B] Get:13 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.4-1 [27.6 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-5 [64.7 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-5 [878 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.2.2-1 [1364 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-1 [96.1 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-2 [1411 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 architecture-properties amd64 0.1.1+b1 [1888 B] Get:29 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 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 0.16-2+b1 [17.1 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 d-shlibs all 0.106 [10.9 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.16 [88.6 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:43 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-3+b1 [671 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.16 [891 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 70.3.0-2 [264 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 70.3.0-2 [504 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20240603 [109 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 dos2unix amd64 7.5.2-1 [518 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libfakeroot amd64 1.35.1-1 [28.6 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 fakeroot amd64 1.35.1-1 [74.5 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b4 [300 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b4 [313 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:63 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.62.1-2 [74.9 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.4.0-1 [63.1 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-7 [216 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.9.1-1 [470 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10 [181 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.20.0-1+b1 [583 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.6-2 [439 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.6-2 [439 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.7-2 [123 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-2 [208 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.19.0-3+b2 [98.0 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-2+b1 [329 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-2+b1 [640 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10-1 [1316 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.6-2 [1381 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-3 [36.2 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-3 [29.9 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-3 [26.1 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.62.1-2 [115 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.4.0-1 [86.5 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.6.0-1 [23.8 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.6.0-1 [170 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1 [77.4 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get:93 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b4 [67.7 kB] Get:94 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.2.2-1 [2701 kB] Get:95 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.0-7 [357 kB] Get:96 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.6+dfsg-1 [368 kB] Get:97 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.9.1-1 [582 kB] Get:98 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get:99 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.20-1 [54.5 kB] Get:100 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20240517-1 [93.3 kB] Get:101 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.2-1 [155 kB] Get:102 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get:103 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.20+ds-1 [452 kB] Get:104 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.2-2 [299 kB] Get:105 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.20+ds-1 [1684 kB] Get:106 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:107 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get:108 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 7.3.7-4 [154 kB] Get:109 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2 [104 kB] Get:110 http://deb.debian.org/debian unstable/main amd64 libpython3.12t64 amd64 3.12.4-3 [2114 kB] Get:111 http://deb.debian.org/debian unstable/main amd64 libpython3.12-dev amd64 3.12.4-3 [5077 kB] Get:112 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.12.4-1 [9736 B] Get:113 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.12.4-1 [1068 B] Get:114 http://deb.debian.org/debian unstable/main amd64 rubygems-integration all 1.18 [6704 B] Get:115 http://deb.debian.org/debian unstable/main amd64 ruby3.1 amd64 3.1.2-8.3 [664 kB] Get:116 http://deb.debian.org/debian unstable/main amd64 ruby-rubygems all 3.4.20-1 [309 kB] Get:117 http://deb.debian.org/debian unstable/main amd64 ruby amd64 1:3.1+nmu1 [5584 B] Get:118 http://deb.debian.org/debian unstable/main amd64 rake all 13.2.1-1 [65.2 kB] Get:119 http://deb.debian.org/debian unstable/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get:120 http://deb.debian.org/debian unstable/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB] Get:121 http://deb.debian.org/debian unstable/main amd64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get:122 http://deb.debian.org/debian unstable/main amd64 ruby-sdbm amd64 1.0.0-5+b4 [15.4 kB] Get:123 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-1+b1 [52.6 kB] Get:124 http://deb.debian.org/debian unstable/main amd64 libruby3.1t64 amd64 3.1.2-8.3 [5399 kB] Get:125 http://deb.debian.org/debian unstable/main amd64 libruby amd64 1:3.1+nmu1 [4664 B] Get:126 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.12.4-1 [1044 B] Get:127 http://deb.debian.org/debian unstable/main amd64 python3.12-dev amd64 3.12.4-3 [499 kB] Get:128 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.12.4-1 [26.2 kB] Get:129 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.12.4-1 [1068 B] Get:130 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.20-3 [653 kB] Get:131 http://deb.debian.org/debian unstable/main amd64 swig amd64 4.2.1-1 [1437 kB] Get:132 http://deb.debian.org/debian unstable/main amd64 time amd64 1.9-0.2 [50.8 kB] Get:133 http://deb.debian.org/debian unstable/main amd64 yaggo all 1.5.11-1 [21.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 64.1 MB in 1s (95.4 MB/s) Selecting previously unselected package autoconf-archive. (Reading database ... 22966 files and directories currently installed.) Preparing to unpack .../autoconf-archive_20220903-3_all.deb ... Unpacking autoconf-archive (20220903-3) ... Selecting previously unselected package libpython3.12-minimal:amd64. Preparing to unpack .../libpython3.12-minimal_3.12.4-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.4-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.4-3_amd64.deb ... Unpacking python3.12-minimal (3.12.4-3) ... Setting up libpython3.12-minimal:amd64 (3.12.4-3) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.12-minimal (3.12.4-3) ... Selecting previously unselected package python3-minimal. (Reading database ... 24468 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.12.4-1_amd64.deb ... Unpacking python3-minimal (3.12.4-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../4-libpython3.12-stdlib_3.12.4-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.4-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../5-python3.12_3.12.4-3_amd64.deb ... Unpacking python3.12 (3.12.4-3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../6-libpython3-stdlib_3.12.4-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.4-1) ... Setting up python3-minimal (3.12.4-1) ... Selecting previously unselected package python3. (Reading database ... 25438 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.4-1_amd64.deb ... Unpacking python3 (3.12.4-1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-5_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-5) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.4-5_amd64.deb ... Unpacking procps (2:4.0.4-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../004-openssl_3.2.2-1_amd64.deb ... Unpacking openssl (3.2.2-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../005-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../006-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../007-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../008-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../009-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../010-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../011-groff-base_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../012-bsdextrautils_2.40.2-1_amd64.deb ... Unpacking bsdextrautils (2.40.2-1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../013-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../014-man-db_2.12.1-2_amd64.deb ... Unpacking man-db (2.12.1-2) ... Selecting previously unselected package architecture-properties:amd64. Preparing to unpack .../015-architecture-properties_0.1.1+b1_amd64.deb ... Unpacking architecture-properties:amd64 (0.1.1+b1) ... Selecting previously unselected package m4. Preparing to unpack .../016-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../017-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../018-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../019-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../020-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package bc. Preparing to unpack .../021-bc_1.07.1-4_amd64.deb ... Unpacking bc (1.07.1-4) ... Selecting previously unselected package chrpath. Preparing to unpack .../022-chrpath_0.16-2+b1_amd64.deb ... Unpacking chrpath (0.16-2+b1) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../023-d-shlibs_0.106_all.deb ... Unpacking d-shlibs (0.106) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../024-libdebhelper-perl_13.16_all.deb ... Unpacking libdebhelper-perl (13.16) ... Selecting previously unselected package libtool. Preparing to unpack .../025-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../026-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../027-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../028-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../029-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../030-libelf1t64_0.191-2_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-2) ... Selecting previously unselected package dwz. Preparing to unpack .../031-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../032-libicu72_72.1-5_amd64.deb ... Unpacking libicu72:amd64 (72.1-5) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../033-libxml2_2.12.7+dfsg-3+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg-3+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../034-gettext_0.22.5-2_amd64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../035-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../036-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../037-debhelper_13.16_all.deb ... Unpacking debhelper (13.16) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../038-python3-pkg-resources_70.3.0-2_all.deb ... Unpacking python3-pkg-resources (70.3.0-2) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../039-python3-setuptools_70.3.0-2_all.deb ... Unpacking python3-setuptools (70.3.0-2) ... Selecting previously unselected package dh-python. Preparing to unpack .../040-dh-python_6.20240603_all.deb ... Unpacking dh-python (6.20240603) ... Selecting previously unselected package dos2unix. Preparing to unpack .../041-dos2unix_7.5.2-1_amd64.deb ... Unpacking dos2unix (7.5.2-1) ... Selecting previously unselected package libfakeroot:amd64. Preparing to unpack .../042-libfakeroot_1.35.1-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.35.1-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../043-fakeroot_1.35.1-1_amd64.deb ... Unpacking fakeroot (1.35.1-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../044-libbrotli1_1.1.0-2+b4_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b4) ... Selecting previously unselected package libbrotli-dev:amd64. Preparing to unpack .../045-libbrotli-dev_1.1.0-2+b4_amd64.deb ... Unpacking libbrotli-dev:amd64 (1.1.0-2+b4) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../046-libcom-err2_1.47.1-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../047-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../048-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../049-libkeyutils1_1.6.3-3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../050-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../051-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../052-libnghttp2-14_1.62.1-2_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.62.1-2) ... Selecting previously unselected package libnghttp3-9:amd64. Preparing to unpack .../053-libnghttp3-9_1.4.0-1_amd64.deb ... Unpacking libnghttp3-9:amd64 (1.4.0-1) ... Selecting previously unselected package libngtcp2-16:amd64. Preparing to unpack .../054-libngtcp2-16_1.6.0-1_amd64.deb ... Unpacking libngtcp2-16:amd64 (1.6.0-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:amd64. Preparing to unpack .../055-libngtcp2-crypto-gnutls8_1.6.0-1_amd64.deb ... Unpacking libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../056-libpsl5t64_0.21.2-1.1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../057-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../058-libssh2-1t64_1.11.0-7_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.0-7) ... Selecting previously unselected package libcurl3t64-gnutls:amd64. Preparing to unpack .../059-libcurl3t64-gnutls_8.9.1-1_amd64.deb ... Unpacking libcurl3t64-gnutls:amd64 (8.9.1-1) ... Selecting previously unselected package libevent-2.1-7t64:amd64. Preparing to unpack .../060-libevent-2.1-7t64_2.1.12-stable-10_amd64.deb ... Unpacking libevent-2.1-7t64:amd64 (2.1.12-stable-10) ... Selecting previously unselected package libunbound8:amd64. Preparing to unpack .../061-libunbound8_1.20.0-1+b1_amd64.deb ... Unpacking libunbound8:amd64 (1.20.0-1+b1) ... Selecting previously unselected package libgnutls-dane0t64:amd64. Preparing to unpack .../062-libgnutls-dane0t64_3.8.6-2_amd64.deb ... Unpacking libgnutls-dane0t64:amd64 (3.8.6-2) ... Selecting previously unselected package libgnutls-openssl27t64:amd64. Preparing to unpack .../063-libgnutls-openssl27t64_3.8.6-2_amd64.deb ... Unpacking libgnutls-openssl27t64:amd64 (3.8.6-2) ... Selecting previously unselected package libidn2-dev:amd64. Preparing to unpack .../064-libidn2-dev_2.3.7-2_amd64.deb ... Unpacking libidn2-dev:amd64 (2.3.7-2) ... Selecting previously unselected package libp11-kit-dev:amd64. Preparing to unpack .../065-libp11-kit-dev_0.25.5-2_amd64.deb ... Unpacking libp11-kit-dev:amd64 (0.25.5-2) ... Selecting previously unselected package libtasn1-6-dev:amd64. Preparing to unpack .../066-libtasn1-6-dev_4.19.0-3+b2_amd64.deb ... Unpacking libtasn1-6-dev:amd64 (4.19.0-3+b2) ... Selecting previously unselected package libgmpxx4ldbl:amd64. Preparing to unpack .../067-libgmpxx4ldbl_2%3a6.3.0+dfsg-2+b1_amd64.deb ... Unpacking libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-2+b1) ... Selecting previously unselected package libgmp-dev:amd64. Preparing to unpack .../068-libgmp-dev_2%3a6.3.0+dfsg-2+b1_amd64.deb ... Unpacking libgmp-dev:amd64 (2:6.3.0+dfsg-2+b1) ... Selecting previously unselected package nettle-dev:amd64. Preparing to unpack .../069-nettle-dev_3.10-1_amd64.deb ... Unpacking nettle-dev:amd64 (3.10-1) ... Selecting previously unselected package libgnutls28-dev:amd64. Preparing to unpack .../070-libgnutls28-dev_3.8.6-2_amd64.deb ... Unpacking libgnutls28-dev:amd64 (3.8.6-2) ... Selecting previously unselected package libpkgconf3:amd64. Preparing to unpack .../071-libpkgconf3_1.8.1-3_amd64.deb ... Unpacking libpkgconf3:amd64 (1.8.1-3) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../072-pkgconf-bin_1.8.1-3_amd64.deb ... Unpacking pkgconf-bin (1.8.1-3) ... Selecting previously unselected package pkgconf:amd64. Preparing to unpack .../073-pkgconf_1.8.1-3_amd64.deb ... Unpacking pkgconf:amd64 (1.8.1-3) ... Selecting previously unselected package libnghttp2-dev:amd64. Preparing to unpack .../074-libnghttp2-dev_1.62.1-2_amd64.deb ... Unpacking libnghttp2-dev:amd64 (1.62.1-2) ... Selecting previously unselected package libnghttp3-dev:amd64. Preparing to unpack .../075-libnghttp3-dev_1.4.0-1_amd64.deb ... Unpacking libnghttp3-dev:amd64 (1.4.0-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls-dev:amd64. Preparing to unpack .../076-libngtcp2-crypto-gnutls-dev_1.6.0-1_amd64.deb ... Unpacking libngtcp2-crypto-gnutls-dev:amd64 (1.6.0-1) ... Selecting previously unselected package libngtcp2-dev:amd64. Preparing to unpack .../077-libngtcp2-dev_1.6.0-1_amd64.deb ... Unpacking libngtcp2-dev:amd64 (1.6.0-1) ... Selecting previously unselected package libpsl-dev:amd64. Preparing to unpack .../078-libpsl-dev_0.21.2-1.1_amd64.deb ... Unpacking libpsl-dev:amd64 (0.21.2-1.1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../079-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Selecting previously unselected package librtmp-dev:amd64. Preparing to unpack .../080-librtmp-dev_2.4+20151223.gitfa8646d.1-2+b4_amd64.deb ... Unpacking librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssl-dev:amd64. Preparing to unpack .../081-libssl-dev_3.2.2-1_amd64.deb ... Unpacking libssl-dev:amd64 (3.2.2-1) ... Selecting previously unselected package libssh2-1-dev:amd64. Preparing to unpack .../082-libssh2-1-dev_1.11.0-7_amd64.deb ... Unpacking libssh2-1-dev:amd64 (1.11.0-7) ... Selecting previously unselected package libzstd-dev:amd64. Preparing to unpack .../083-libzstd-dev_1.5.6+dfsg-1_amd64.deb ... Unpacking libzstd-dev:amd64 (1.5.6+dfsg-1) ... Selecting previously unselected package libcurl4-gnutls-dev:amd64. Preparing to unpack .../084-libcurl4-gnutls-dev_8.9.1-1_amd64.deb ... Unpacking libcurl4-gnutls-dev:amd64 (8.9.1-1) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../085-libdeflate0_1.20-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.20-1) ... Selecting previously unselected package libdeflate-dev:amd64. Preparing to unpack .../086-libdeflate-dev_1.20-1_amd64.deb ... Unpacking libdeflate-dev:amd64 (1.20-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../087-libedit2_3.1-20240517-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20240517-1) ... Selecting previously unselected package libexpat1-dev:amd64. Preparing to unpack .../088-libexpat1-dev_2.6.2-1_amd64.deb ... Unpacking libexpat1-dev:amd64 (2.6.2-1) ... Selecting previously unselected package libhtscodecs2:amd64. Preparing to unpack .../089-libhtscodecs2_1.6.0-1+b1_amd64.deb ... Unpacking libhtscodecs2:amd64 (1.6.0-1+b1) ... Selecting previously unselected package libhts3t64:amd64. Preparing to unpack .../090-libhts3t64_1.20+ds-1_amd64.deb ... Unpacking libhts3t64:amd64 (1.20+ds-1) ... Selecting previously unselected package liblzma-dev:amd64. Preparing to unpack .../091-liblzma-dev_5.6.2-2_amd64.deb ... Unpacking liblzma-dev:amd64 (5.6.2-2) ... Selecting previously unselected package libhts-dev:amd64. Preparing to unpack .../092-libhts-dev_1.20+ds-1_amd64.deb ... Unpacking libhts-dev:amd64 (1.20+ds-1) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../093-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../094-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../095-libjs-sphinxdoc_7.3.7-4_all.deb ... Unpacking libjs-sphinxdoc (7.3.7-4) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../096-libncurses6_6.5-2_amd64.deb ... Unpacking libncurses6:amd64 (6.5-2) ... Selecting previously unselected package libpython3.12t64:amd64. Preparing to unpack .../097-libpython3.12t64_3.12.4-3_amd64.deb ... Unpacking libpython3.12t64:amd64 (3.12.4-3) ... Selecting previously unselected package libpython3.12-dev:amd64. Preparing to unpack .../098-libpython3.12-dev_3.12.4-3_amd64.deb ... Unpacking libpython3.12-dev:amd64 (3.12.4-3) ... Selecting previously unselected package libpython3-dev:amd64. Preparing to unpack .../099-libpython3-dev_3.12.4-1_amd64.deb ... Unpacking libpython3-dev:amd64 (3.12.4-1) ... Selecting previously unselected package libpython3-all-dev:amd64. Preparing to unpack .../100-libpython3-all-dev_3.12.4-1_amd64.deb ... Unpacking libpython3-all-dev:amd64 (3.12.4-1) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../101-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package ruby3.1. Preparing to unpack .../102-ruby3.1_3.1.2-8.3_amd64.deb ... Unpacking ruby3.1 (3.1.2-8.3) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../103-ruby-rubygems_3.4.20-1_all.deb ... Unpacking ruby-rubygems (3.4.20-1) ... Selecting previously unselected package ruby. Preparing to unpack .../104-ruby_1%3a3.1+nmu1_amd64.deb ... Unpacking ruby (1:3.1+nmu1) ... Selecting previously unselected package rake. Preparing to unpack .../105-rake_13.2.1-1_all.deb ... Unpacking rake (13.2.1-1) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../106-ruby-net-telnet_0.2.0-1_all.deb ... Unpacking ruby-net-telnet (0.2.0-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../107-ruby-webrick_1.8.1-1_all.deb ... Unpacking ruby-webrick (1.8.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../108-ruby-xmlrpc_0.3.3-2_all.deb ... Unpacking ruby-xmlrpc (0.3.3-2) ... Selecting previously unselected package ruby-sdbm:amd64. Preparing to unpack .../109-ruby-sdbm_1.0.0-5+b4_amd64.deb ... Unpacking ruby-sdbm:amd64 (1.0.0-5+b4) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../110-libyaml-0-2_0.2.5-1+b1_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.2.5-1+b1) ... Selecting previously unselected package libruby3.1t64:amd64. Preparing to unpack .../111-libruby3.1t64_3.1.2-8.3_amd64.deb ... Unpacking libruby3.1t64:amd64 (3.1.2-8.3) ... Selecting previously unselected package libruby:amd64. Preparing to unpack .../112-libruby_1%3a3.1+nmu1_amd64.deb ... Unpacking libruby:amd64 (1:3.1+nmu1) ... Selecting previously unselected package python3-all. Preparing to unpack .../113-python3-all_3.12.4-1_amd64.deb ... Unpacking python3-all (3.12.4-1) ... Selecting previously unselected package python3.12-dev. Preparing to unpack .../114-python3.12-dev_3.12.4-3_amd64.deb ... Unpacking python3.12-dev (3.12.4-3) ... Selecting previously unselected package python3-dev. Preparing to unpack .../115-python3-dev_3.12.4-1_amd64.deb ... Unpacking python3-dev (3.12.4-1) ... Selecting previously unselected package python3-all-dev. Preparing to unpack .../116-python3-all-dev_3.12.4-1_amd64.deb ... Unpacking python3-all-dev (3.12.4-1) ... Selecting previously unselected package samtools. Preparing to unpack .../117-samtools_1.20-3_amd64.deb ... Unpacking samtools (1.20-3) ... Selecting previously unselected package swig. Preparing to unpack .../118-swig_4.2.1-1_amd64.deb ... Unpacking swig (4.2.1-1) ... Selecting previously unselected package time. Preparing to unpack .../119-time_1.9-0.2_amd64.deb ... Unpacking time (1.9-0.2) ... Selecting previously unselected package yaggo. Preparing to unpack .../120-yaggo_1.5.11-1_all.deb ... Unpacking yaggo (1.5.11-1) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../121-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libhtscodecs2:amd64 (1.6.0-1+b1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up libgnutls-openssl27t64:amd64 (3.8.6-2) ... Setting up time (1.9-0.2) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up swig (4.2.1-1) ... Setting up libicu72:amd64 (72.1-5) ... Setting up libzstd-dev:amd64 (1.5.6+dfsg-1) ... Setting up bsdextrautils (2.40.2-1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.5-1+b1) ... Setting up architecture-properties:amd64 (0.1.1+b1) ... Setting up libdebhelper-perl (13.16) ... Setting up libbrotli1:amd64 (1.1.0-2+b4) ... Setting up libedit2:amd64 (3.1-20240517-1) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.62.1-2) ... Setting up libdeflate0:amd64 (1.20-1) ... Setting up bc (1.07.1-4) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10) ... Setting up autoconf-archive (20220903-3) ... Setting up libcom-err2:amd64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libfakeroot:amd64 (1.35.1-1) ... Setting up libelf1t64:amd64 (0.191-2) ... Setting up libpsl-dev:amd64 (0.21.2-1.1) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Aug 3 11:34:51 UTC 2024. Universal Time is now: Sat Aug 3 11:34:51 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.35.1-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up autotools-dev (20220109.1) ... Setting up libunbound8:amd64 (1.20.0-1+b1) ... Setting up libpkgconf3:amd64 (1.8.1-3) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-2+b1) ... Setting up libexpat1-dev:amd64 (2.6.2-1) ... Setting up libgnutls-dane0t64:amd64 (3.8.6-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libncurses6:amd64 (6.5-2) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up libproc2-0:amd64 (2:4.0.4-5) ... Setting up libssl-dev:amd64 (3.2.2-1) ... Setting up autopoint (0.22.5-2) ... Setting up d-shlibs (0.106) ... Setting up pkgconf-bin (1.8.1-3) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libidn2-dev:amd64 (2.3.7-2) ... Setting up autoconf (2.71-3) ... Setting up libnghttp3-9:amd64 (1.4.0-1) ... Setting up libnghttp3-dev:amd64 (1.4.0-1) ... Setting up ruby-webrick (1.8.1-1) ... Setting up liblzma-dev:amd64 (5.6.2-2) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up procps (2:4.0.4-5) ... Setting up netbase (6.4) ... 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 (1.6.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up dos2unix (7.5.2-1) ... Setting up libssh2-1t64:amd64 (1.11.0-7) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libtasn1-6-dev:amd64 (4.19.0-3+b2) ... Setting up openssl (3.2.2-1) ... Setting up libdeflate-dev:amd64 (1.20-1) ... Setting up ruby-xmlrpc (0.3.3-2) ... Setting up libxml2:amd64 (2.12.7+dfsg-3+b1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b4) ... Setting up chrpath (0.16-2+b1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Setting up libp11-kit-dev:amd64 (0.25.5-2) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-2+b1) ... Setting up libpython3.12-stdlib:amd64 (3.12.4-3) ... Setting up nettle-dev:amd64 (3.10-1) ... Setting up libtool (2.4.7-7) ... Setting up python3.12 (3.12.4-3) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.6.0-1) ... Setting up libngtcp2-dev:amd64 (1.6.0-1) ... Setting up pkgconf:amd64 (1.8.1-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libpython3.12t64:amd64 (3.12.4-3) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libssh2-1-dev:amd64 (1.11.0-7) ... Setting up libjs-sphinxdoc (7.3.7-4) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libpython3-stdlib:amd64 (3.12.4-1) ... Setting up libgnutls28-dev:amd64 (3.8.6-2) ... Setting up libnghttp2-dev:amd64 (1.62.1-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.9.1-1) ... Setting up python3 (3.12.4-1) ... Setting up libpython3.12-dev:amd64 (3.12.4-3) ... Setting up rubygems-integration (1.18) ... Setting up man-db (2.12.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up python3.12-dev (3.12.4-3) ... Setting up libhts3t64:amd64 (1.20+ds-1) ... Setting up python3-pkg-resources (70.3.0-2) ... Setting up libpython3-dev:amd64 (3.12.4-1) ... Setting up python3-setuptools (70.3.0-2) ... Setting up python3-all (3.12.4-1) ... Setting up debhelper (13.16) ... Setting up libcurl4-gnutls-dev:amd64 (8.9.1-1) ... Setting up samtools (1.20-3) ... Setting up libpython3-all-dev:amd64 (3.12.4-1) ... Setting up python3-dev (3.12.4-1) ... Setting up dh-python (6.20240603) ... Setting up python3-all-dev (3.12.4-1) ... Setting up libhts-dev:amd64 (1.20+ds-1) ... Setting up rake (13.2.1-1) ... Setting up ruby-sdbm:amd64 (1.0.0-5+b4) ... Setting up ruby-rubygems (3.4.20-1) ... Setting up libruby3.1t64:amd64 (3.1.2-8.3) ... Setting up ruby3.1 (3.1.2-8.3) ... Setting up libruby:amd64 (1:3.1+nmu1) ... Setting up ruby (1:3.1+nmu1) ... Setting up yaggo (1.5.11-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.39-6) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.9.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.9.7-1 (2024-06-27) amd64 (x86_64) Toolchain package versions: binutils_2.42.90.20240720-2 dpkg-dev_1.22.11 g++-13_13.3.0-4 g++-14_14.2.0-1 gcc-13_13.3.0-4 gcc-14_14.2.0-1 libc6-dev_2.39-6 libstdc++-13-dev_13.3.0-4 libstdc++-14-dev_14.2.0-1 libstdc++6_14.2.0-1 linux-libc-dev_6.9.12-1 Package versions: adduser_3.137 apt_2.9.7 architecture-properties_0.1.1+b1 autoconf_2.71-3 autoconf-archive_20220903-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.4 base-passwd_3.6.4 bash_5.2.21-2.1 bc_1.07.1-4 binutils_2.42.90.20240720-2 binutils-common_2.42.90.20240720-2 binutils-x86-64-linux-gnu_2.42.90.20240720-2 bsdextrautils_2.40.2-1 bsdutils_1:2.40.2-1 build-essential_12.10 bzip2_1.0.8-5.1 ca-certificates_20240203 chrpath_0.16-2+b1 coreutils_9.4-3.1 cpp_4:14.1.0-2 cpp-13_13.3.0-4 cpp-13-x86-64-linux-gnu_13.3.0-4 cpp-14_14.2.0-1 cpp-14-x86-64-linux-gnu_14.2.0-1 cpp-x86-64-linux-gnu_4:14.1.0-2 d-shlibs_0.106 dash_0.5.12-9 debconf_1.5.87 debhelper_13.16 debian-archive-keyring_2023.4 debianutils_5.20 dh-autoreconf_20 dh-python_6.20240603 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.43-8 dos2unix_7.5.2-1 dpkg_1.22.11 dpkg-dev_1.22.11 dwz_0.15-1+b1 eatmydata_131-2 fakeroot_1.35.1-1 file_1:5.45-3 findutils_4.10.0-2 g++_4:14.1.0-2 g++-13_13.3.0-4 g++-13-x86-64-linux-gnu_13.3.0-4 g++-14_14.2.0-1 g++-14-x86-64-linux-gnu_14.2.0-1 g++-x86-64-linux-gnu_4:14.1.0-2 gcc_4:14.1.0-2 gcc-13_13.3.0-4 gcc-13-base_13.3.0-4 gcc-13-x86-64-linux-gnu_13.3.0-4 gcc-14_14.2.0-1 gcc-14-base_14.2.0-1 gcc-14-x86-64-linux-gnu_14.2.0-1 gcc-x86-64-linux-gnu_4:14.1.0-2 gettext_0.22.5-2 gettext-base_0.22.5-2 gnupg_2.2.43-8 gnupg-l10n_2.2.43-8 gnupg-utils_2.2.43-8 gpg_2.2.43-8 gpg-agent_2.2.43-8 gpg-wks-client_2.2.43-8 gpgconf_2.2.43-8 gpgsm_2.2.43-8 gpgv_2.2.43-8 grep_3.11-4 groff-base_1.23.0-5 gzip_1.12-1.1 hostname_3.23+nmu2 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2 libapt-pkg6.0t64_2.9.7 libarchive-zip-perl_1.68-1 libasan8_14.2.0-1 libassuan0_2.5.6-1+b1 libatomic1_14.2.0-1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-4 libaudit1_1:3.1.2-4+b1 libbinutils_2.42.90.20240720-2 libblkid1_2.40.2-1 libbrotli-dev_1.1.0-2+b4 libbrotli1_1.1.0-2+b4 libbsd0_0.12.2-1 libbz2-1.0_1.0.8-5.1 libc-bin_2.39-6 libc-dev-bin_2.39-6 libc-l10n_2.39-6 libc6_2.39-6 libc6-dev_2.39-6 libcap-ng0_0.8.5-1+b1 libcap2_1:2.66-5 libcc1-0_14.2.0-1 libcom-err2_1.47.1-1 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libctf-nobfd0_2.42.90.20240720-2 libctf0_2.42.90.20240720-2 libcurl3t64-gnutls_8.9.1-1 libcurl4-gnutls-dev_8.9.1-1 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.272 libdebhelper-perl_13.16 libdeflate-dev_1.20-1 libdeflate0_1.20-1 libdpkg-perl_1.22.11 libeatmydata1_131-2 libedit2_3.1-20240517-1 libelf1t64_0.191-2 libevent-2.1-7t64_2.1.12-stable-10 libexpat1_2.6.2-1 libexpat1-dev_2.6.2-1 libfakeroot_1.35.1-1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.0-1 libgcc-13-dev_13.3.0-4 libgcc-14-dev_14.2.0-1 libgcc-s1_14.2.0-1 libgcrypt20_1.11.0-5 libgdbm-compat4t64_1.23-6 libgdbm6t64_1.23-6 libgmp-dev_2:6.3.0+dfsg-2+b1 libgmp10_2:6.3.0+dfsg-2+b1 libgmpxx4ldbl_2:6.3.0+dfsg-2+b1 libgnutls-dane0t64_3.8.6-2 libgnutls-openssl27t64_3.8.6-2 libgnutls28-dev_3.8.6-2 libgnutls30t64_3.8.6-2 libgomp1_14.2.0-1 libgpg-error0_1.49-2 libgprofng0_2.42.90.20240720-2 libgssapi-krb5-2_1.21.3-3 libhogweed6t64_3.10-1 libhts-dev_1.20+ds-1 libhts3t64_1.20+ds-1 libhtscodecs2_1.6.0-1+b1 libhwasan0_14.2.0-1 libicu72_72.1-5 libidn2-0_2.3.7-2 libidn2-dev_2.3.7-2 libisl23_0.26-3+b2 libitm1_14.2.0-1 libjansson4_2.14-2+b2 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-sphinxdoc_7.3.7-4 libjs-underscore_1.13.4~dfsg+~1.11.4-3 libk5crypto3_1.21.3-3 libkeyutils1_1.6.3-3 libkrb5-3_1.21.3-3 libkrb5support0_1.21.3-3 libksba8_1.6.7-2 libldap-2.5-0_2.5.18+dfsg-2+b1 liblsan0_14.2.0-1 liblz4-1_1.9.4-3 liblzma-dev_5.6.2-2 liblzma5_5.6.2-2 libmagic-mgc_1:5.45-3 libmagic1t64_1:5.45-3 libmd0_1.1.0-2 libmount1_2.40.2-1 libmpc3_1.3.1-1+b2 libmpfr6_4.2.1-1+b1 libncurses6_6.5-2 libncursesw6_6.5-2 libnettle8t64_3.10-1 libnghttp2-14_1.62.1-2 libnghttp2-dev_1.62.1-2 libnghttp3-9_1.4.0-1 libnghttp3-dev_1.4.0-1 libngtcp2-16_1.6.0-1 libngtcp2-crypto-gnutls-dev_1.6.0-1 libngtcp2-crypto-gnutls8_1.6.0-1 libngtcp2-dev_1.6.0-1 libnpth0t64_1.6-3.1 libp11-kit-dev_0.25.5-2 libp11-kit0_0.25.5-2 libpam-modules_1.5.3-7 libpam-modules-bin_1.5.3-7 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7 libpcre2-8-0_10.42-4+b1 libperl5.38t64_5.38.2-5 libperl5.40_5.40.0-1 libpipeline1_1.5.7-2 libpkgconf3_1.8.1-3 libproc2-0_2:4.0.4-5 libpsl-dev_0.21.2-1.1 libpsl5t64_0.21.2-1.1 libpython3-all-dev_3.12.4-1 libpython3-dev_3.12.4-1 libpython3-stdlib_3.12.4-1 libpython3.12-dev_3.12.4-3 libpython3.12-minimal_3.12.4-3 libpython3.12-stdlib_3.12.4-3 libpython3.12t64_3.12.4-3 libquadmath0_14.2.0-1 libreadline8t64_8.2-4 librtmp-dev_2.4+20151223.gitfa8646d.1-2+b4 librtmp1_2.4+20151223.gitfa8646d.1-2+b4 libruby_1:3.1+nmu1 libruby3.1t64_3.1.2-8.3 libsasl2-2_2.1.28+dfsg1-6 libsasl2-modules-db_2.1.28+dfsg1-6 libseccomp2_2.5.5-1+b1 libselinux1_3.5-2+b3 libsemanage-common_3.5-1 libsemanage2_3.5-1+b4 libsepol2_3.5-2+b1 libsframe1_2.42.90.20240720-2 libsmartcols1_2.40.2-1 libsqlite3-0_3.46.0-1 libssh2-1-dev_1.11.0-7 libssh2-1t64_1.11.0-7 libssl-dev_3.2.2-1 libssl3t64_3.2.2-1 libstdc++-13-dev_13.3.0-4 libstdc++-14-dev_14.2.0-1 libstdc++6_14.2.0-1 libsystemd0_256.4-2 libtasn1-6_4.19.0-3+b2 libtasn1-6-dev_4.19.0-3+b2 libtinfo6_6.5-2 libtool_2.4.7-7 libtsan2_14.2.0-1 libubsan1_14.2.0-1 libuchardet0_0.0.8-1+b1 libudev1_256.4-2 libunbound8_1.20.0-1+b1 libunistring5_1.2-1 libuuid1_2.40.2-1 libxml2_2.12.7+dfsg-3+b1 libxxhash0_0.8.2-2+b1 libyaml-0-2_0.2.5-1+b1 libzstd-dev_1.5.6+dfsg-1 libzstd1_1.5.6+dfsg-1 linux-libc-dev_6.9.12-1 locales-all_2.39-6 login_1:4.15.3-3 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.1-2 mawk_1.3.4.20240622-2 media-types_10.1.0 ncurses-base_6.5-2 ncurses-bin_6.5-2 netbase_6.4 nettle-dev_3.10-1 openssl_3.2.2-1 passwd_1:4.15.3-3 patch_2.7.6-7 perl_5.40.0-1 perl-base_5.40.0-1 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.0-1 pinentry-curses_1.2.1-3+b2 pkgconf_1.8.1-3 pkgconf-bin_1.8.1-3 po-debconf_1.0.21+nmu1 procps_2:4.0.4-5 python3_3.12.4-1 python3-all_3.12.4-1 python3-all-dev_3.12.4-1 python3-dev_3.12.4-1 python3-minimal_3.12.4-1 python3-pkg-resources_70.3.0-2 python3-setuptools_70.3.0-2 python3.12_3.12.4-3 python3.12-dev_3.12.4-3 python3.12-minimal_3.12.4-3 rake_13.2.1-1 readline-common_8.2-4 rpcsvc-proto_1.4.3-1 ruby_1:3.1+nmu1 ruby-net-telnet_0.2.0-1 ruby-rubygems_3.4.20-1 ruby-sdbm_1.0.0-5+b4 ruby-webrick_1.8.1-1 ruby-xmlrpc_0.3.3-2 ruby3.1_3.1.2-8.3 rubygems-integration_1.18 samtools_1.20-3 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 swig_4.2.1-1 sysvinit-utils_3.09-2 tar_1.35+dfsg-3 time_1.9-0.2 tzdata_2024a-4 usr-is-merged_39 util-linux_2.40.2-1 xz-utils_5.6.2-2 yaggo_1.5.11-1 zlib1g_1:1.3.dfsg+really1.3.1-1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ 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: 2.3.1-3 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: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/jellyfish Vcs-Git: https://salsa.debian.org/med-team/jellyfish.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@ Build-Depends: debhelper-compat (= 13), architecture-is-little-endian, architecture-is-64-bit, d-shlibs, autoconf-archive, yaggo, pkgconf, bc, time, procps, swig, python3-all-dev, 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 32f49f1dd8cebe75a863a9b20b29e4a41223e1cc 13340 jellyfish_2.3.1-3.debian.tar.xz Checksums-Sha256: 540d09457fb4e14b98c7f1428cf885c333e2d6ef4f6a3735aa06be13eb523d69 681990 jellyfish_2.3.1.orig.tar.gz 476e52f24cf5f7ac0bc1b047372d16fcbbc057e71ce5a5098c93d8726a9154b5 13340 jellyfish_2.3.1-3.debian.tar.xz Files: 27fb29ad3edfe25d776cfbf98dcc8c0e 681990 jellyfish_2.3.1.orig.tar.gz c7928f076800e7bc8f60f2ff07c5ce31 13340 jellyfish_2.3.1-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmX5yeAACgkQPCZ2P2xn 5uLHWw//SVUwz4TiVUuonq8W2QFJXhKBZH3YCNYX+PUbAW2x67HmvOFdEJXcDeoM nzfp08XxpMcwzb6/Lcah74vS/bcP8JBR3LJxhml78f4zx/xpGJeL8VP/c0w3i0WN /FXFiKuGRNVeQo/JY77Vd4idgu7SkaxtTF5Pmc55mOeXtkcLJ5r6p3XN5wPUkQDY kd0k1oxTX5vira3JooP5jHwaQUDuWJ+nWN1EFtco8DA2zzVirunJFHw2zeLMPGcX PAlMCJDLshSFN/su0Uq38iDxBKrNbqiD8FA+Y1IYzEr9QC77eBqDVA8yMZLY8638 S3lkTE0Yf8ixwvxaaBjQKADGsNMEu3z5cmRcLEiRp9Irbcn6boalqwBr9ZvaCSWS UJnBPAMGVRNgetHTybVLK6jQN9bXMueDieGaSkXZEj0x1zxi2UKXLZ+SwZlouxj6 65DYNkksxsFjjj18p8fmw1/mmpI4o75KfhF0uwjEhbMrpkfagd0HQsLnvn5L9Z62 I7uowOmrPL6G1I9y+m5JC8ZLJCWlujUrikncejM2Al87Z9rhUFxpt3a1Shc7HSqm q+HUkybAB6egGhcXHehLYi+s9h1JKNJ0cr97DryldNZUbtGhG+tL0E7ky5Ed7EeP fse2+Z0fwPDdx6qtwHDKUGYE8LH9MYNjyq+/ozC0H02j4hZZZ+I= =88VS -----END PGP SIGNATURE----- gpgv: Signature made Tue Mar 19 17:22:40 2024 UTC gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./jellyfish_2.3.1-3.dsc: no acceptable signature found dpkg-source: info: extracting jellyfish in /<> dpkg-source: info: unpacking jellyfish_2.3.1.orig.tar.gz dpkg-source: info: unpacking jellyfish_2.3.1-3.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 2.3.1-3+b6 +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network jellyfish_2.3.1-3 perl-5.40 amd64 -------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network jellyfish_2.3.1-3 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=/<> 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-ef1fcdef-313e-45e8-bc86-43cfed73b8a8 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -mDebian Perl autobuilder -B -rfakeroot -Zxz dpkg-buildpackage: info: source package jellyfish dpkg-buildpackage: info: source version 2.3.1-3+b6 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 '/<>' if [ -d debian/tmp_save_tests ] ; then \ mv debian/tmp_save_tests/* tests ; \ rmdir debian/tmp_save_tests ; \ fi make[1]: Leaving directory '/<>' debian/rules binary-arch dh binary-arch debian/rules override_dh_update_autotools_config make[1]: Entering directory '/<>' # use python configuration from autoconf-archive mv m4/m4-ax_python_devel.m4 /tmp dh_update_autotools_config make[1]: Leaving directory '/<>' 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 '/<>' dh_auto_configure -- --enable-swig --enable-perl-binding --enable-htslib --enable-python-binding PYTHON=/usr/bin/python3 ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-swig --enable-perl-binding --enable-htslib --enable-python-binding PYTHON=/usr/bin/python3 checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /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 whether make supports nested variables... (cached) yes checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /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 ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /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 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... d:756e6547:6c65746e:49656e69 checking for x86 cpuid 0x80000000 output... 80000008:756e6547:6c65746e:49656e69 checking for x86 cpuid 0x00000001 output... 506e3:1000800:fffa3223:f8bfbff checking for x86 cpuid 0x00000007 output... 0:9c0fbb: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... 4.2.1 checking for SWIG library... /usr/share/swig/4.2.1 checking for python... /usr/bin/python3 checking for a version of Python >= '2.1.0'... yes checking for the sysconfig Python package... yes checking for Python include path... -I/usr/include/python3.12 checking for Python library path... -L/usr/lib/x86_64-linux-gnu -lpython3.12 checking for Python site-packages path... /usr/lib/python3.12/site-packages checking for Python platform specific site-packages path... /usr/lib/python3.12/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=/<>=. -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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -lpthread" -I/<>/debian/tmp/usr/include/jellyfish-2.3.1 -L/<>/debian/tmp/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -lpthread -L/<>/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: python3.12 setup.py config running config mv /tmp/m4-ax_python_devel.m4 m4 make[1]: Leaving directory '/<>' debian/rules override_dh_auto_build make[1]: Entering directory '/<>' 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 '/<>' /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 '/<>' g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c lib/rectangular_binary_matrix.cc -fPIC -DPIC -o lib/.libs/rectangular_binary_matrix.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c lib/rectangular_binary_matrix.cc -o lib/rectangular_binary_matrix.o >/dev/null 2>&1 /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/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o lib/mer_dna.lo lib/mer_dna.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c lib/mer_dna.cc -fPIC -DPIC -o lib/.libs/mer_dna.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c lib/mer_dna.cc -o lib/mer_dna.o >/dev/null 2>&1 /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/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o lib/storage.lo lib/storage.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c lib/storage.cc -fPIC -DPIC -o lib/.libs/storage.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c lib/storage.cc -o lib/storage.o >/dev/null 2>&1 /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/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o lib/allocators_mmap.lo lib/allocators_mmap.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c lib/allocators_mmap.cc -fPIC -DPIC -o lib/.libs/allocators_mmap.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c lib/allocators_mmap.cc -o lib/allocators_mmap.o >/dev/null 2>&1 /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/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o lib/misc.lo lib/misc.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c lib/misc.cc -fPIC -DPIC -o lib/.libs/misc.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c lib/misc.cc -o lib/misc.o >/dev/null 2>&1 /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/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o lib/int128.lo lib/int128.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c lib/int128.cc -fPIC -DPIC -o lib/.libs/int128.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c lib/int128.cc -o lib/int128.o >/dev/null 2>&1 /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/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o lib/thread_exec.lo lib/thread_exec.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c lib/thread_exec.cc -fPIC -DPIC -o lib/.libs/thread_exec.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c lib/thread_exec.cc -o lib/thread_exec.o >/dev/null 2>&1 /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/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o lib/jsoncpp.lo lib/jsoncpp.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c lib/jsoncpp.cpp -fPIC -DPIC -o lib/.libs/jsoncpp.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c lib/jsoncpp.cpp -o lib/jsoncpp.o >/dev/null 2>&1 /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/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o lib/time.lo lib/time.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c lib/time.cc -fPIC -DPIC -o lib/.libs/time.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c lib/time.cc -o lib/time.o >/dev/null 2>&1 /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/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o lib/generator_manager.lo lib/generator_manager.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c lib/generator_manager.cc -fPIC -DPIC -o lib/.libs/generator_manager.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c lib/generator_manager.cc -o lib/generator_manager.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -version-info 2:0:0 -Wl,-z,relro -Wl,-z,now -lpthread -o libjellyfish-2.0.la -rpath /usr/lib/x86_64-linux-gnu lib/rectangular_binary_matrix.lo lib/mer_dna.lo lib/storage.lo lib/allocators_mmap.lo lib/misc.lo lib/int128.lo lib/thread_exec.lo lib/jsoncpp.lo lib/time.lo lib/generator_manager.lo libtool: link: 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 lib/.libs/rectangular_binary_matrix.o lib/.libs/mer_dna.o lib/.libs/storage.o lib/.libs/allocators_mmap.o lib/.libs/misc.o lib/.libs/int128.o lib/.libs/thread_exec.o lib/.libs/jsoncpp.o lib/.libs/time.o lib/.libs/generator_manager.o -lpthread -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/x86_64-linux-gnu -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 -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libjellyfish-2.0.so.2 -o .libs/libjellyfish-2.0.so.2.0.0 libtool: link: (cd ".libs" && rm -f "libjellyfish-2.0.so.2" && ln -s "libjellyfish-2.0.so.2.0.0" "libjellyfish-2.0.so.2") libtool: link: (cd ".libs" && rm -f "libjellyfish-2.0.so" && ln -s "libjellyfish-2.0.so.2.0.0" "libjellyfish-2.0.so") libtool: link: ar cr .libs/libjellyfish-2.0.a lib/rectangular_binary_matrix.o lib/mer_dna.o lib/storage.o lib/allocators_mmap.o lib/misc.o lib/int128.o lib/thread_exec.o lib/jsoncpp.o lib/time.o lib/generator_manager.o libtool: link: ranlib .libs/libjellyfish-2.0.a libtool: link: ( cd ".libs" && rm -f "libjellyfish-2.0.la" && ln -s "../libjellyfish-2.0.la" "libjellyfish-2.0.la" ) /bin/bash ./libtool --tag=CXX --mode=link g++ -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -pthread -L/<>/debian/tmp/usr/lib/x86_64-linux-gnu -lhts -R/<>/debian/tmp/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o bin/jellyfish sub_commands/jellyfish.o sub_commands/count_main.o sub_commands/info_main.o sub_commands/dump_main.o sub_commands/histo_main.o sub_commands/stats_main.o sub_commands/merge_main.o sub_commands/bc_main.o sub_commands/query_main.o sub_commands/cite_main.o sub_commands/mem_main.o jellyfish/merge_files.o libjellyfish-2.0.la libtool: link: g++ -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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/jellyfish sub_commands/jellyfish.o sub_commands/count_main.o sub_commands/info_main.o sub_commands/dump_main.o sub_commands/histo_main.o sub_commands/stats_main.o sub_commands/merge_main.o sub_commands/bc_main.o sub_commands/query_main.o sub_commands/cite_main.o sub_commands/mem_main.o jellyfish/merge_files.o -L/<>/debian/tmp/usr/lib/x86_64-linux-gnu -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/<>/debian/tmp/usr/lib/x86_64-linux-gnu /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo `test -f 'swig/perl5/swig_wrap.cpp' || echo './'`swig/perl5/swig_wrap.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c swig/perl5/swig_wrap.cpp -fPIC -DPIC -o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c swig/perl5/swig_wrap.cpp -o swig/perl5/swig_perl5_jellyfish_la-swig_wrap.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -I/<>/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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 libtool: link: 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 -Wl,-rpath -Wl,/<>/.libs -lpthread ./.libs/libjellyfish-2.0.so -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/x86_64-linux-gnu -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 -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 libtool: link: (cd "swig/perl5/.libs" && rm -f "jellyfish.so.0" && ln -s "jellyfish.so.0.0.0" "jellyfish.so.0") libtool: link: (cd "swig/perl5/.libs" && rm -f "jellyfish.so" && ln -s "jellyfish.so.0.0.0" "jellyfish.so") libtool: link: ar cr swig/perl5/.libs/jellyfish.a swig/perl5/swig_perl5_jellyfish_la-swig_wrap.o libtool: link: ranlib swig/perl5/.libs/jellyfish.a libtool: link: ( cd "swig/perl5/.libs" && rm -f "jellyfish.la" && ln -s "../jellyfish.la" "jellyfish.la" ) /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I/usr/include/python3.12 -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo `test -f 'swig/python/swig_wrap.cpp' || echo './'`swig/python/swig_wrap.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/include/python3.12 -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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/python3.12 -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c swig/python/swig_wrap.cpp -o swig/python/swig_python__dna_jellyfish_la-swig_wrap.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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/python3.12/site-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/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 -Wl,-rpath -Wl,/<>/.libs -lpthread ./.libs/libjellyfish-2.0.so -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/x86_64-linux-gnu -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 -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,_dna_jellyfish.so.0 -o swig/python/.libs/_dna_jellyfish.so.0.0.0 libtool: link: (cd "swig/python/.libs" && rm -f "_dna_jellyfish.so.0" && ln -s "_dna_jellyfish.so.0.0.0" "_dna_jellyfish.so.0") libtool: link: (cd "swig/python/.libs" && rm -f "_dna_jellyfish.so" && ln -s "_dna_jellyfish.so.0.0.0" "_dna_jellyfish.so") libtool: link: ar cr swig/python/.libs/_dna_jellyfish.a swig/python/swig_python__dna_jellyfish_la-swig_wrap.o libtool: link: ranlib swig/python/.libs/_dna_jellyfish.a libtool: link: ( cd "swig/python/.libs" && rm -f "_dna_jellyfish.la" && ln -s "../_dna_jellyfish.la" "_dna_jellyfish.la" ) /usr/bin/python3 -c 'import py_compile, sys; py_compile.compile(sys.argv[1], sys.argv[2])' swig/python/dna_jellyfish.py swig/python/__init__.pyc make[3]: Leaving directory '/<>' g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o jellyfish/mersenne.o jellyfish/mersenne.cpp g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o jellyfish/backtrace.o jellyfish/backtrace.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o jellyfish/dbg.o jellyfish/dbg.cc /bin/bash ./libtool --tag=CXX --mode=link g++ -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -pthread -L/<>/debian/tmp/usr/lib/x86_64-linux-gnu -lhts -R/<>/debian/tmp/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o bin/generate_sequence jellyfish/generate_sequence.o jellyfish/mersenne.o jellyfish/backtrace.o jellyfish/dbg.o libjellyfish-2.0.la libtool: link: g++ -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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/generate_sequence jellyfish/generate_sequence.o jellyfish/mersenne.o jellyfish/backtrace.o jellyfish/dbg.o -L/<>/debian/tmp/usr/lib/x86_64-linux-gnu -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/<>/debian/tmp/usr/lib/x86_64-linux-gnu g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_main.o `test -f 'unit_tests/test_main.cc' || echo './'`unit_tests/test_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/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=/<>=. -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/<>/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=/<>=. -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/<>/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=/<>=. -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/<>/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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_rectangular_binary_matrix.o `test -f 'unit_tests/test_rectangular_binary_matrix.cc' || echo './'`unit_tests/test_rectangular_binary_matrix.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_mer_dna.o `test -f 'unit_tests/test_mer_dna.cc' || echo './'`unit_tests/test_mer_dna.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/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=/<>=. -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/<>/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=/<>=. -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/<>/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=/<>=. -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/<>/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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_mer_iterator.o `test -f 'unit_tests/test_mer_iterator.cc' || echo './'`unit_tests/test_mer_iterator.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_hash_counter.o `test -f 'unit_tests/test_hash_counter.cc' || echo './'`unit_tests/test_hash_counter.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_mer_heap.o `test -f 'unit_tests/test_mer_heap.cc' || echo './'`unit_tests/test_mer_heap.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_stream_iterator.o `test -f 'unit_tests/test_stream_iterator.cc' || echo './'`unit_tests/test_stream_iterator.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_token_ring.o `test -f 'unit_tests/test_token_ring.cc' || echo './'`unit_tests/test_token_ring.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_text_dumper.o `test -f 'unit_tests/test_text_dumper.cc' || echo './'`unit_tests/test_text_dumper.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_dumpers.o `test -f 'unit_tests/test_dumpers.cc' || echo './'`unit_tests/test_dumpers.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_mapped_file.o `test -f 'unit_tests/test_mapped_file.cc' || echo './'`unit_tests/test_mapped_file.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_int128.o `test -f 'unit_tests/test_int128.cc' || echo './'`unit_tests/test_int128.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_mer_dna_bloom_counter.o `test -f 'unit_tests/test_mer_dna_bloom_counter.cc' || echo './'`unit_tests/test_mer_dna_bloom_counter.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_whole_sequence_parser.o `test -f 'unit_tests/test_whole_sequence_parser.cc' || echo './'`unit_tests/test_whole_sequence_parser.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_allocators_mmap.o `test -f 'unit_tests/test_allocators_mmap.cc' || echo './'`unit_tests/test_allocators_mmap.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_cooperative_pool2.o `test -f 'unit_tests/test_cooperative_pool2.cc' || echo './'`unit_tests/test_cooperative_pool2.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_generator_manager.o `test -f 'unit_tests/test_generator_manager.cc' || echo './'`unit_tests/test_generator_manager.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_atomic_bits_array.o `test -f 'unit_tests/test_atomic_bits_array.cc' || echo './'`unit_tests/test_atomic_bits_array.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/bin_test_all-test_stdio_filebuf.o `test -f 'unit_tests/test_stdio_filebuf.cc' || echo './'`unit_tests/test_stdio_filebuf.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o jellyfish/bin_test_all-backtrace.o `test -f 'jellyfish/backtrace.cc' || echo './'`jellyfish/backtrace.cc /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -I./unit_tests/gtest -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o unit_tests/gtest/src/libgtest_la-gtest-all.lo `test -f 'unit_tests/gtest/src/gtest-all.cc' || echo './'`unit_tests/gtest/src/gtest-all.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -I./unit_tests/gtest -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c unit_tests/gtest/src/gtest-all.cc -fPIC -DPIC -o unit_tests/gtest/src/.libs/libgtest_la-gtest-all.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -I./unit_tests/gtest -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c unit_tests/gtest/src/gtest-all.cc -o unit_tests/gtest/src/libgtest_la-gtest-all.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -I./unit_tests -I./unit_tests/gtest -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -pthread -L/<>/debian/tmp/usr/lib/x86_64-linux-gnu -lhts -R/<>/debian/tmp/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o libgtest.la unit_tests/gtest/src/libgtest_la-gtest-all.lo libtool: link: ar cr .libs/libgtest.a unit_tests/gtest/src/.libs/libgtest_la-gtest-all.o libtool: link: ranlib .libs/libgtest.a libtool: link: ( cd ".libs" && rm -f "libgtest.la" && ln -s "../libgtest.la" "libgtest.la" ) /bin/bash ./libtool --tag=CXX --mode=link g++ -I/<>/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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -pthread -L/<>/debian/tmp/usr/lib/x86_64-linux-gnu -lhts -R/<>/debian/tmp/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o bin/test_all unit_tests/bin_test_all-test_main.o unit_tests/bin_test_all-test_misc.o unit_tests/bin_test_all-test_offsets_key_value.o unit_tests/bin_test_all-test_simple_circular_buffer.o unit_tests/bin_test_all-test_rectangular_binary_matrix.o unit_tests/bin_test_all-test_mer_dna.o unit_tests/bin_test_all-test_large_hash_array.o unit_tests/bin_test_all-test_mer_overlap_sequence_parser.o unit_tests/bin_test_all-test_file_header.o unit_tests/bin_test_all-test_mer_iterator.o unit_tests/bin_test_all-test_hash_counter.o unit_tests/bin_test_all-test_mer_heap.o unit_tests/bin_test_all-test_stream_iterator.o unit_tests/bin_test_all-test_token_ring.o unit_tests/bin_test_all-test_text_dumper.o unit_tests/bin_test_all-test_dumpers.o unit_tests/bin_test_all-test_mapped_file.o unit_tests/bin_test_all-test_int128.o unit_tests/bin_test_all-test_mer_dna_bloom_counter.o unit_tests/bin_test_all-test_whole_sequence_parser.o unit_tests/bin_test_all-test_allocators_mmap.o unit_tests/bin_test_all-test_cooperative_pool2.o unit_tests/bin_test_all-test_generator_manager.o unit_tests/bin_test_all-test_atomic_bits_array.o unit_tests/bin_test_all-test_stdio_filebuf.o jellyfish/bin_test_all-backtrace.o libgtest.la libjellyfish-2.0.la libtool: link: g++ -I/<>/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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/test_all unit_tests/bin_test_all-test_main.o unit_tests/bin_test_all-test_misc.o unit_tests/bin_test_all-test_offsets_key_value.o unit_tests/bin_test_all-test_simple_circular_buffer.o unit_tests/bin_test_all-test_rectangular_binary_matrix.o unit_tests/bin_test_all-test_mer_dna.o unit_tests/bin_test_all-test_large_hash_array.o unit_tests/bin_test_all-test_mer_overlap_sequence_parser.o unit_tests/bin_test_all-test_file_header.o unit_tests/bin_test_all-test_mer_iterator.o unit_tests/bin_test_all-test_hash_counter.o unit_tests/bin_test_all-test_mer_heap.o unit_tests/bin_test_all-test_stream_iterator.o unit_tests/bin_test_all-test_token_ring.o unit_tests/bin_test_all-test_text_dumper.o unit_tests/bin_test_all-test_dumpers.o unit_tests/bin_test_all-test_mapped_file.o unit_tests/bin_test_all-test_int128.o unit_tests/bin_test_all-test_mer_dna_bloom_counter.o unit_tests/bin_test_all-test_whole_sequence_parser.o unit_tests/bin_test_all-test_allocators_mmap.o unit_tests/bin_test_all-test_cooperative_pool2.o unit_tests/bin_test_all-test_generator_manager.o unit_tests/bin_test_all-test_atomic_bits_array.o unit_tests/bin_test_all-test_stdio_filebuf.o jellyfish/bin_test_all-backtrace.o -L/<>/debian/tmp/usr/lib/x86_64-linux-gnu ./.libs/libgtest.a -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/<>/debian/tmp/usr/lib/x86_64-linux-gnu g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -pthread -L/<>/debian/tmp/usr/lib/x86_64-linux-gnu -lhts -R/<>/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/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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/<>/debian/tmp/usr/lib/x86_64-linux-gnu -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/<>/debian/tmp/usr/lib/x86_64-linux-gnu make[2]: Leaving directory '/<>' dh_auto_install -- install-data make -j1 install DESTDIR=/<>/debian/tmp AM_UPDATE_INFO_DIR=no install-data make[2]: Entering directory '/<>' make install-am make[3]: Entering directory '/<>' make[4]: Entering directory '/<>' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/<>/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /<>/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 /<>/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 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /<>/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 '/<>/debian/tmp/usr/bin' /bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/<>/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 /<>/debian/tmp/usr/bin/jellyfish /usr/bin/mkdir -p '/<>/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 '/<>/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 '/<>/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/mkdir -p '/<>/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/<>/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/perl/5.40.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/<>/debian/tmp/usr/lib/perl/5.40.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /<>; /bin/bash "/<>/libtool" --tag CXX --mode=relink g++ -I/<>/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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 /<>/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/<>/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 -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.so.0.0.0T /<>/debian/tmp/usr/lib/perl/5.40.0/jellyfish.so.0.0.0 libtool: install: (cd /<>/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 /<>/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 /<>/debian/tmp/usr/lib/perl/5.40.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /<>/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: ranlib /<>/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 '/<>/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/<>/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/<>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' libtool: warning: relinking 'swig/python/_dna_jellyfish.la' libtool: install: (cd /<>; /bin/bash "/<>/libtool" --tag CXX --mode=relink g++ -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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/python3.12/site-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /<>/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/<>/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 -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,_dna_jellyfish.so.0 -o swig/python/.libs/_dna_jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.so.0.0.0T /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /<>/debian/tmp/usr/lib/python3.12/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 /<>/debian/tmp/usr/lib/python3.12/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 /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.la libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3.12/site-packages/dna_jellyfish' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' make[4]: Leaving directory '/<>' make[3]: Leaving directory '/<>' /usr/bin/mkdir -p '/<>/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 '/<>/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 '/<>/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/mkdir -p '/<>/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/<>/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/<>/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /<>/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 /<>/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 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /<>/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 '/<>/debian/tmp/usr/lib/perl/5.40.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/<>/debian/tmp/usr/lib/perl/5.40.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /<>; /bin/bash "/<>/libtool" --tag CXX --mode=relink g++ -I/<>/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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 /<>/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/<>/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 -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.so.0.0.0T /<>/debian/tmp/usr/lib/perl/5.40.0/jellyfish.so.0.0.0 libtool: install: (cd /<>/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 /<>/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 /<>/debian/tmp/usr/lib/perl/5.40.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /<>/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: ranlib /<>/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 '/<>/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/<>/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/<>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' libtool: warning: relinking 'swig/python/_dna_jellyfish.la' libtool: install: (cd /<>; /bin/bash "/<>/libtool" --tag CXX --mode=relink g++ -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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/python3.12/site-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /<>/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/<>/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 -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,_dna_jellyfish.so.0 -o swig/python/.libs/_dna_jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.so.0.0.0T /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /<>/debian/tmp/usr/lib/python3.12/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 /<>/debian/tmp/usr/lib/python3.12/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 /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.la libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3.12/site-packages/dna_jellyfish' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' make[2]: Leaving directory '/<>' dh_auto_build --sourcedirectory=swig/perl5 cd swig/perl5 && make -j2 make[2]: Entering directory '/<>/swig/perl5' Running Mkbootstrap for jellyfish () chmod 644 "jellyfish.bs" g++ -c -std=c++0x -I/<>/debian/tmp/usr/include/jellyfish-2.3.1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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++ "/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=/<>=. -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 '/<>/swig/perl5' dh_auto_build --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build build_ext -L/<>/.libs running build running build_py copying dna_jellyfish.py -> /<>/.pybuild/cpython3_3.12_dna_jellyfish/build running build_ext building '_dna_jellyfish' extension creating build creating build/temp.linux-x86_64-cpython-312 x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/debian/tmp/usr/include/jellyfish-2.3.1 -I/usr/include/python3.12 -c swig_wrap.cpp -o build/temp.linux-x86_64-cpython-312/swig_wrap.o -std=c++0x cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -lpthread -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/swig_wrap.o -L-L/<>/debian/tmp/usr/lib/x86_64-linux-gnu -L/<>/.libs -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -lpthread -o /<>/.pybuild/cpython3_3.12_dna_jellyfish/build/_dna_jellyfish.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,-L/<>/debian/tmp/usr/lib/x86_64-linux-gnu make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' 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 '/<>' make check-am make[3]: Entering directory '/<>' make bin/generate_sequence bin/fastq2sam bin/test_all libgtest.la libgtest_main.la make[4]: Entering directory '/<>' 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=/<>=. -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=/<>=. -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=/<>=. -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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -pthread -L/<>/debian/tmp/usr/lib/x86_64-linux-gnu -lhts -R/<>/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 "/<>/./.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 '/<>' make check-TESTS make[4]: Entering directory '/<>' make[5]: Entering directory '/<>' SKIP: tests/big.sh PASS: tests/generate_sequence.sh PASS: tests/parallel_hashing.sh PASS: tests/merge.sh PASS: tests/bloom_filter.sh PASS: unit_tests/unit_tests.sh PASS: tests/subset_hashing.sh PASS: tests/bloom_counter.sh PASS: tests/large_key.sh PASS: tests/multi_file.sh PASS: tests/sam.sh PASS: tests/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 '/<>' make[4]: Leaving directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/<>' chrpath --delete bin/.libs/* dh_auto_install -- install-data make -j1 install DESTDIR=/<>/debian/tmp AM_UPDATE_INFO_DIR=no install-data make[2]: Entering directory '/<>' make install-am make[3]: Entering directory '/<>' make[4]: Entering directory '/<>' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/<>/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /<>/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 /<>/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 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /<>/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 '/<>/debian/tmp/usr/bin' /bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/<>/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 /<>/debian/tmp/usr/bin/jellyfish /usr/bin/mkdir -p '/<>/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 '/<>/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 '/<>/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/mkdir -p '/<>/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/<>/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/perl/5.40.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/<>/debian/tmp/usr/lib/perl/5.40.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /<>; /bin/bash "/<>/libtool" --tag CXX --mode=relink g++ -I/<>/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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 /<>/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/<>/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 -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.so.0.0.0T /<>/debian/tmp/usr/lib/perl/5.40.0/jellyfish.so.0.0.0 libtool: install: (cd /<>/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 /<>/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 /<>/debian/tmp/usr/lib/perl/5.40.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /<>/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: ranlib /<>/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 '/<>/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/<>/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/<>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' libtool: warning: relinking 'swig/python/_dna_jellyfish.la' libtool: install: (cd /<>; /bin/bash "/<>/libtool" --tag CXX --mode=relink g++ -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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/python3.12/site-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /<>/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/<>/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 -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,_dna_jellyfish.so.0 -o swig/python/.libs/_dna_jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.so.0.0.0T /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /<>/debian/tmp/usr/lib/python3.12/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 /<>/debian/tmp/usr/lib/python3.12/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 /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.la libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3.12/site-packages/dna_jellyfish' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' make[4]: Leaving directory '/<>' make[3]: Leaving directory '/<>' /usr/bin/mkdir -p '/<>/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 '/<>/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 '/<>/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/mkdir -p '/<>/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/<>/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/<>/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /<>/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 /<>/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 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /<>/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 '/<>/debian/tmp/usr/lib/perl/5.40.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/<>/debian/tmp/usr/lib/perl/5.40.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /<>; /bin/bash "/<>/libtool" --tag CXX --mode=relink g++ -I/<>/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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 /<>/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/<>/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 -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.so.0.0.0T /<>/debian/tmp/usr/lib/perl/5.40.0/jellyfish.so.0.0.0 libtool: install: (cd /<>/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 /<>/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 /<>/debian/tmp/usr/lib/perl/5.40.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /<>/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: ranlib /<>/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 '/<>/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/<>/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/<>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' libtool: warning: relinking 'swig/python/_dna_jellyfish.la' libtool: install: (cd /<>; /bin/bash "/<>/libtool" --tag CXX --mode=relink g++ -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -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/python3.12/site-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /<>/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/<>/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 -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,_dna_jellyfish.so.0 -o swig/python/.libs/_dna_jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.so.0.0.0T /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /<>/debian/tmp/usr/lib/python3.12/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 /<>/debian/tmp/usr/lib/python3.12/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 /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.la libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3.12/site-packages/dna_jellyfish' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' make[2]: Leaving directory '/<>' dh_auto_install --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /<>/debian/python3-dna-jellyfish running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: 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 -> /<>/.pybuild/cpython3_3.12_dna_jellyfish/build running build_ext running install_lib creating /<>/debian/python3-dna-jellyfish creating /<>/debian/python3-dna-jellyfish/usr creating /<>/debian/python3-dna-jellyfish/usr/lib creating /<>/debian/python3-dna-jellyfish/usr/lib/python3.12 creating /<>/debian/python3-dna-jellyfish/usr/lib/python3.12/dist-packages copying /<>/.pybuild/cpython3_3.12_dna_jellyfish/build/dna_jellyfish.py -> /<>/debian/python3-dna-jellyfish/usr/lib/python3.12/dist-packages copying /<>/.pybuild/cpython3_3.12_dna_jellyfish/build/_dna_jellyfish.cpython-312-x86_64-linux-gnu.so -> /<>/debian/python3-dna-jellyfish/usr/lib/python3.12/dist-packages byte-compiling /<>/debian/python3-dna-jellyfish/usr/lib/python3.12/dist-packages/dna_jellyfish.py to dna_jellyfish.cpython-312.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 /<>/debian/python3-dna-jellyfish/usr/lib/python3.12/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=/<>/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr make[2]: Entering directory '/<>/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 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/jellyfish/jellyfish.so make[2]: Leaving directory '/<>/swig/perl5' ls -l debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so -r-xr-xr-x 1 debomatic sbuild 1143560 Aug 3 11:37 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 /<>/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 /<>/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 '/<>' dh_install -a debian/rules execute_after_dh_install make[1]: Entering directory '/<>' # 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 '/<>' 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 '/<>' # 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 '/<>' 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_2.3.1-3+b6_amd64.deb'. dpkg-deb: building package 'python3-dna-jellyfish' in '../python3-dna-jellyfish_2.3.1-3+b6_amd64.deb'. dpkg-deb: building package 'python3-dna-jellyfish-dbgsym' in '../python3-dna-jellyfish-dbgsym_2.3.1-3+b6_amd64.deb'. dpkg-deb: building package 'libjellyfish-perl' in '../libjellyfish-perl_2.3.1-3+b6_amd64.deb'. dpkg-deb: building package 'libjellyfish-perl-dbgsym' in '../libjellyfish-perl-dbgsym_2.3.1-3+b6_amd64.deb'. dpkg-deb: building package 'jellyfish-dbgsym' in '../jellyfish-dbgsym_2.3.1-3+b6_amd64.deb'. dpkg-deb: building package 'libjellyfish-2.0-2' in '../libjellyfish-2.0-2_2.3.1-3+b6_amd64.deb'. dpkg-deb: building package 'libjellyfish-2.0-2-dbgsym' in '../libjellyfish-2.0-2-dbgsym_2.3.1-3+b6_amd64.deb'. dpkg-deb: building package 'libjellyfish-2.0-dev' in '../libjellyfish-2.0-dev_2.3.1-3+b6_amd64.deb'. dpkg-genbuildinfo --build=any -O../jellyfish_2.3.1-3+b6_amd64.buildinfo dpkg-genchanges --build=any -mDebian Perl autobuilder -O../jellyfish_2.3.1-3+b6_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 2024-08-03T11:40:19Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ jellyfish_2.3.1-3+b6_amd64.changes: ----------------------------------- Format: 1.8 Date: Sat, 03 Aug 2024 11:34:58 +0000 Source: jellyfish (2.3.1-3) 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: 2.3.1-3+b6 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 (2.3.1-3+b6) 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: af605e75259a9307b772347de0b246bcbfe37eaf 7597052 jellyfish-dbgsym_2.3.1-3+b6_amd64.deb bcd7bca642ddd3bd4c9705ed771e4bedeffe1b3a 11363 jellyfish_2.3.1-3+b6_amd64.buildinfo b374327797718bbdd8ed2dadbc2e36bffcf74250 807228 jellyfish_2.3.1-3+b6_amd64.deb c0111fa89b37015b410f5446abee9f891a2c7d88 544612 libjellyfish-2.0-2-dbgsym_2.3.1-3+b6_amd64.deb 45a622874391b96c650b1e5a27468503445509d0 67320 libjellyfish-2.0-2_2.3.1-3+b6_amd64.deb b637be524a55a0e23efab015408d5051ed444823 138484 libjellyfish-2.0-dev_2.3.1-3+b6_amd64.deb d4fd0ec657119bff4ab89445b0786aae575e4b67 353340 libjellyfish-perl-dbgsym_2.3.1-3+b6_amd64.deb ed8540e7a9ddf5d5e3eb7136583bddd2359a5d9f 57140 libjellyfish-perl_2.3.1-3+b6_amd64.deb 632b195c4e94c11c8a7fe8051ec69b70664c43a7 341196 python3-dna-jellyfish-dbgsym_2.3.1-3+b6_amd64.deb a56b362635227cb737214aa924d5a385f5b2b4ec 56148 python3-dna-jellyfish_2.3.1-3+b6_amd64.deb Checksums-Sha256: e3dd5bdf6e947d5752c6d1301a112d24f1d53194b4729f2efd654f2ed3bfad7c 7597052 jellyfish-dbgsym_2.3.1-3+b6_amd64.deb e91bd31097eb6e52fa62edd087908946974a94a7b0c4d2962f72f38019cc6a9d 11363 jellyfish_2.3.1-3+b6_amd64.buildinfo 15dfc2a0a8789134e8e54754b373bf57f98a8ad1ecd87f166547a35f998fca3c 807228 jellyfish_2.3.1-3+b6_amd64.deb 73b123d7944374bb0daada19c1fd27d0f88e4fde44d74d51f5bfc14802ca6887 544612 libjellyfish-2.0-2-dbgsym_2.3.1-3+b6_amd64.deb d23bd8f66868eaa1993336dc245ed2330a1777cf16089a9d6df598a129fc0ce0 67320 libjellyfish-2.0-2_2.3.1-3+b6_amd64.deb 1c45c50cb69cbb699aa6b4602a0a11e20c269b41c19a244821f92169356994ac 138484 libjellyfish-2.0-dev_2.3.1-3+b6_amd64.deb 92a554089821ef547cfb91a9f4e927f8bc77ead26caebcf7f1070caf474d365b 353340 libjellyfish-perl-dbgsym_2.3.1-3+b6_amd64.deb 304f43ad34d7824c17d6ec42162774dde3a4499e0781df1a9bee72fd78c9f049 57140 libjellyfish-perl_2.3.1-3+b6_amd64.deb 82800983eff53f9cfd0aed126252a62fb3019aa39a9b5c92fac4c2c9c822ecc7 341196 python3-dna-jellyfish-dbgsym_2.3.1-3+b6_amd64.deb 71946da3fdb750c3aca5131aded777d88f35b86a36bbaca8103ac0645252bd54 56148 python3-dna-jellyfish_2.3.1-3+b6_amd64.deb Files: d40d9a9a5cb1f8a1f0093b87ee207177 7597052 debug optional jellyfish-dbgsym_2.3.1-3+b6_amd64.deb a7ae72c7cf498eac9f839ced13ab2e32 11363 science optional jellyfish_2.3.1-3+b6_amd64.buildinfo 9495f4ee7eda88c07ad750a28756ad68 807228 science optional jellyfish_2.3.1-3+b6_amd64.deb 46e4ca6f82c90d055c78766d6ccc60fe 544612 debug optional libjellyfish-2.0-2-dbgsym_2.3.1-3+b6_amd64.deb 7aeb0ecab171bb1d8add9ddb41d4a534 67320 libs optional libjellyfish-2.0-2_2.3.1-3+b6_amd64.deb 1848659456489c4a9428d0a1813a465c 138484 libdevel optional libjellyfish-2.0-dev_2.3.1-3+b6_amd64.deb 135a240b525015340259f9eb63160035 353340 debug optional libjellyfish-perl-dbgsym_2.3.1-3+b6_amd64.deb dabf4060419f2eabfb4664dc65cf9fd5 57140 perl optional libjellyfish-perl_2.3.1-3+b6_amd64.deb a6c9b88e50c195b5ba24b91065c48193 341196 debug optional python3-dna-jellyfish-dbgsym_2.3.1-3+b6_amd64.deb 5408eb6256c4ae588364fc261417c209 56148 python optional python3-dna-jellyfish_2.3.1-3+b6_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: jellyfish (2.3.1-3) 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: 2.3.1-3+b6 Binary-Only-Changes: jellyfish (2.3.1-3+b6) 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 Sat, 03 Aug 2024 11:34:58 +0000 Checksums-Md5: d40d9a9a5cb1f8a1f0093b87ee207177 7597052 jellyfish-dbgsym_2.3.1-3+b6_amd64.deb 9495f4ee7eda88c07ad750a28756ad68 807228 jellyfish_2.3.1-3+b6_amd64.deb 46e4ca6f82c90d055c78766d6ccc60fe 544612 libjellyfish-2.0-2-dbgsym_2.3.1-3+b6_amd64.deb 7aeb0ecab171bb1d8add9ddb41d4a534 67320 libjellyfish-2.0-2_2.3.1-3+b6_amd64.deb 1848659456489c4a9428d0a1813a465c 138484 libjellyfish-2.0-dev_2.3.1-3+b6_amd64.deb 135a240b525015340259f9eb63160035 353340 libjellyfish-perl-dbgsym_2.3.1-3+b6_amd64.deb dabf4060419f2eabfb4664dc65cf9fd5 57140 libjellyfish-perl_2.3.1-3+b6_amd64.deb a6c9b88e50c195b5ba24b91065c48193 341196 python3-dna-jellyfish-dbgsym_2.3.1-3+b6_amd64.deb 5408eb6256c4ae588364fc261417c209 56148 python3-dna-jellyfish_2.3.1-3+b6_amd64.deb Checksums-Sha1: af605e75259a9307b772347de0b246bcbfe37eaf 7597052 jellyfish-dbgsym_2.3.1-3+b6_amd64.deb b374327797718bbdd8ed2dadbc2e36bffcf74250 807228 jellyfish_2.3.1-3+b6_amd64.deb c0111fa89b37015b410f5446abee9f891a2c7d88 544612 libjellyfish-2.0-2-dbgsym_2.3.1-3+b6_amd64.deb 45a622874391b96c650b1e5a27468503445509d0 67320 libjellyfish-2.0-2_2.3.1-3+b6_amd64.deb b637be524a55a0e23efab015408d5051ed444823 138484 libjellyfish-2.0-dev_2.3.1-3+b6_amd64.deb d4fd0ec657119bff4ab89445b0786aae575e4b67 353340 libjellyfish-perl-dbgsym_2.3.1-3+b6_amd64.deb ed8540e7a9ddf5d5e3eb7136583bddd2359a5d9f 57140 libjellyfish-perl_2.3.1-3+b6_amd64.deb 632b195c4e94c11c8a7fe8051ec69b70664c43a7 341196 python3-dna-jellyfish-dbgsym_2.3.1-3+b6_amd64.deb a56b362635227cb737214aa924d5a385f5b2b4ec 56148 python3-dna-jellyfish_2.3.1-3+b6_amd64.deb Checksums-Sha256: e3dd5bdf6e947d5752c6d1301a112d24f1d53194b4729f2efd654f2ed3bfad7c 7597052 jellyfish-dbgsym_2.3.1-3+b6_amd64.deb 15dfc2a0a8789134e8e54754b373bf57f98a8ad1ecd87f166547a35f998fca3c 807228 jellyfish_2.3.1-3+b6_amd64.deb 73b123d7944374bb0daada19c1fd27d0f88e4fde44d74d51f5bfc14802ca6887 544612 libjellyfish-2.0-2-dbgsym_2.3.1-3+b6_amd64.deb d23bd8f66868eaa1993336dc245ed2330a1777cf16089a9d6df598a129fc0ce0 67320 libjellyfish-2.0-2_2.3.1-3+b6_amd64.deb 1c45c50cb69cbb699aa6b4602a0a11e20c269b41c19a244821f92169356994ac 138484 libjellyfish-2.0-dev_2.3.1-3+b6_amd64.deb 92a554089821ef547cfb91a9f4e927f8bc77ead26caebcf7f1070caf474d365b 353340 libjellyfish-perl-dbgsym_2.3.1-3+b6_amd64.deb 304f43ad34d7824c17d6ec42162774dde3a4499e0781df1a9bee72fd78c9f049 57140 libjellyfish-perl_2.3.1-3+b6_amd64.deb 82800983eff53f9cfd0aed126252a62fb3019aa39a9b5c92fac4c2c9c822ecc7 341196 python3-dna-jellyfish-dbgsym_2.3.1-3+b6_amd64.deb 71946da3fdb750c3aca5131aded777d88f35b86a36bbaca8103ac0645252bd54 56148 python3-dna-jellyfish_2.3.1-3+b6_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sat, 03 Aug 2024 11:40:18 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: adduser (= 3.137), apt (= 2.9.7), architecture-properties (= 0.1.1+b1), autoconf (= 2.71-3), autoconf-archive (= 20220903-3), automake (= 1:1.16.5-1.3), autopoint (= 0.22.5-2), autotools-dev (= 20220109.1), base-files (= 13.4), base-passwd (= 3.6.4), bash (= 5.2.21-2.1), bc (= 1.07.1-4), binutils (= 2.42.90.20240720-2), binutils-common (= 2.42.90.20240720-2), binutils-x86-64-linux-gnu (= 2.42.90.20240720-2), bsdextrautils (= 2.40.2-1), bsdutils (= 1:2.40.2-1), build-essential (= 12.10), bzip2 (= 1.0.8-5.1), ca-certificates (= 20240203), chrpath (= 0.16-2+b1), coreutils (= 9.4-3.1), cpp (= 4:14.1.0-2), cpp-13 (= 13.3.0-4), cpp-13-x86-64-linux-gnu (= 13.3.0-4), cpp-14 (= 14.2.0-1), cpp-14-x86-64-linux-gnu (= 14.2.0-1), cpp-x86-64-linux-gnu (= 4:14.1.0-2), d-shlibs (= 0.106), dash (= 0.5.12-9), debconf (= 1.5.87), debhelper (= 13.16), debian-archive-keyring (= 2023.4), debianutils (= 5.20), dh-autoreconf (= 20), dh-python (= 6.20240603), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-1), dos2unix (= 7.5.2-1), dpkg (= 1.22.11), dpkg-dev (= 1.22.11), dwz (= 0.15-1+b1), file (= 1:5.45-3), findutils (= 4.10.0-2), g++ (= 4:14.1.0-2), g++-14 (= 14.2.0-1), g++-14-x86-64-linux-gnu (= 14.2.0-1), g++-x86-64-linux-gnu (= 4:14.1.0-2), gcc (= 4:14.1.0-2), gcc-13 (= 13.3.0-4), gcc-13-base (= 13.3.0-4), gcc-13-x86-64-linux-gnu (= 13.3.0-4), gcc-14 (= 14.2.0-1), gcc-14-base (= 14.2.0-1), gcc-14-x86-64-linux-gnu (= 14.2.0-1), gcc-x86-64-linux-gnu (= 4:14.1.0-2), gettext (= 0.22.5-2), gettext-base (= 0.22.5-2), gpgv (= 2.2.43-8), grep (= 3.11-4), groff-base (= 1.23.0-5), gzip (= 1.12-1.1), hostname (= 3.23+nmu2), init-system-helpers (= 1.66), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2), libapt-pkg6.0t64 (= 2.9.7), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.2.0-1), libatomic1 (= 14.2.0-1), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-4), libaudit1 (= 1:3.1.2-4+b1), libbinutils (= 2.42.90.20240720-2), libblkid1 (= 2.40.2-1), libbrotli-dev (= 1.1.0-2+b4), libbrotli1 (= 1.1.0-2+b4), libbsd0 (= 0.12.2-1), libbz2-1.0 (= 1.0.8-5.1), libc-bin (= 2.39-6), libc-dev-bin (= 2.39-6), libc6 (= 2.39-6), libc6-dev (= 2.39-6), libcap-ng0 (= 0.8.5-1+b1), libcap2 (= 1:2.66-5), libcc1-0 (= 14.2.0-1), libcom-err2 (= 1.47.1-1), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.42.90.20240720-2), libctf0 (= 2.42.90.20240720-2), libcurl3t64-gnutls (= 8.9.1-1), libcurl4-gnutls-dev (= 8.9.1-1), libdb5.3t64 (= 5.3.28+dfsg2-7), libdebconfclient0 (= 0.272), libdebhelper-perl (= 13.16), libdeflate-dev (= 1.20-1), libdeflate0 (= 1.20-1), libdpkg-perl (= 1.22.11), libedit2 (= 3.1-20240517-1), libelf1t64 (= 0.191-2), libevent-2.1-7t64 (= 2.1.12-stable-10), libexpat1 (= 2.6.2-1), libexpat1-dev (= 2.6.2-1), libffi8 (= 3.4.6-1), libfile-stripnondeterminism-perl (= 1.14.0-1), libgcc-13-dev (= 13.3.0-4), libgcc-14-dev (= 14.2.0-1), libgcc-s1 (= 14.2.0-1), libgcrypt20 (= 1.11.0-5), libgdbm-compat4t64 (= 1.23-6), libgdbm6t64 (= 1.23-6), libgmp-dev (= 2:6.3.0+dfsg-2+b1), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgmpxx4ldbl (= 2:6.3.0+dfsg-2+b1), libgnutls-dane0t64 (= 3.8.6-2), libgnutls-openssl27t64 (= 3.8.6-2), libgnutls28-dev (= 3.8.6-2), libgnutls30t64 (= 3.8.6-2), libgomp1 (= 14.2.0-1), libgpg-error0 (= 1.49-2), libgprofng0 (= 2.42.90.20240720-2), libgssapi-krb5-2 (= 1.21.3-3), libhogweed6t64 (= 3.10-1), libhts-dev (= 1.20+ds-1), libhts3t64 (= 1.20+ds-1), libhtscodecs2 (= 1.6.0-1+b1), libhwasan0 (= 14.2.0-1), libicu72 (= 72.1-5), libidn2-0 (= 2.3.7-2), libidn2-dev (= 2.3.7-2), libisl23 (= 0.26-3+b2), libitm1 (= 14.2.0-1), libjansson4 (= 2.14-2+b2), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libjs-sphinxdoc (= 7.3.7-4), libjs-underscore (= 1.13.4~dfsg+~1.11.4-3), libk5crypto3 (= 1.21.3-3), libkeyutils1 (= 1.6.3-3), libkrb5-3 (= 1.21.3-3), libkrb5support0 (= 1.21.3-3), libldap-2.5-0 (= 2.5.18+dfsg-2+b1), liblsan0 (= 14.2.0-1), liblz4-1 (= 1.9.4-3), liblzma-dev (= 5.6.2-2), liblzma5 (= 5.6.2-2), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmd0 (= 1.1.0-2), libmount1 (= 2.40.2-1), libmpc3 (= 1.3.1-1+b2), libmpfr6 (= 4.2.1-1+b1), libncurses6 (= 6.5-2), libncursesw6 (= 6.5-2), libnettle8t64 (= 3.10-1), libnghttp2-14 (= 1.62.1-2), libnghttp2-dev (= 1.62.1-2), libnghttp3-9 (= 1.4.0-1), libnghttp3-dev (= 1.4.0-1), libngtcp2-16 (= 1.6.0-1), libngtcp2-crypto-gnutls-dev (= 1.6.0-1), libngtcp2-crypto-gnutls8 (= 1.6.0-1), libngtcp2-dev (= 1.6.0-1), libp11-kit-dev (= 0.25.5-2), libp11-kit0 (= 0.25.5-2), libpam-modules (= 1.5.3-7), libpam-modules-bin (= 1.5.3-7), libpam-runtime (= 1.5.3-7), libpam0g (= 1.5.3-7), libpcre2-8-0 (= 10.42-4+b1), libperl5.40 (= 5.40.0-1), libpipeline1 (= 1.5.7-2), libpkgconf3 (= 1.8.1-3), libproc2-0 (= 2:4.0.4-5), libpsl-dev (= 0.21.2-1.1), libpsl5t64 (= 0.21.2-1.1), libpython3-all-dev (= 3.12.4-1), libpython3-dev (= 3.12.4-1), libpython3-stdlib (= 3.12.4-1), libpython3.12-dev (= 3.12.4-3), libpython3.12-minimal (= 3.12.4-3), libpython3.12-stdlib (= 3.12.4-3), libpython3.12t64 (= 3.12.4-3), libquadmath0 (= 14.2.0-1), libreadline8t64 (= 8.2-4), librtmp-dev (= 2.4+20151223.gitfa8646d.1-2+b4), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b4), libruby (= 1:3.1+nmu1), libruby3.1t64 (= 3.1.2-8.3), libsasl2-2 (= 2.1.28+dfsg1-6), libsasl2-modules-db (= 2.1.28+dfsg1-6), libseccomp2 (= 2.5.5-1+b1), libselinux1 (= 3.5-2+b3), libsemanage-common (= 3.5-1), libsemanage2 (= 3.5-1+b4), libsepol2 (= 3.5-2+b1), libsframe1 (= 2.42.90.20240720-2), libsmartcols1 (= 2.40.2-1), libsqlite3-0 (= 3.46.0-1), libssh2-1-dev (= 1.11.0-7), libssh2-1t64 (= 1.11.0-7), libssl-dev (= 3.2.2-1), libssl3t64 (= 3.2.2-1), libstdc++-14-dev (= 14.2.0-1), libstdc++6 (= 14.2.0-1), libsystemd0 (= 256.4-2), libtasn1-6 (= 4.19.0-3+b2), libtasn1-6-dev (= 4.19.0-3+b2), libtinfo6 (= 6.5-2), libtool (= 2.4.7-7), libtsan2 (= 14.2.0-1), libubsan1 (= 14.2.0-1), libuchardet0 (= 0.0.8-1+b1), libudev1 (= 256.4-2), libunbound8 (= 1.20.0-1+b1), libunistring5 (= 1.2-1), libuuid1 (= 2.40.2-1), libxml2 (= 2.12.7+dfsg-3+b1), libxxhash0 (= 0.8.2-2+b1), libyaml-0-2 (= 0.2.5-1+b1), libzstd-dev (= 1.5.6+dfsg-1), libzstd1 (= 1.5.6+dfsg-1), linux-libc-dev (= 6.9.12-1), login (= 1:4.15.3-3), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.12.1-2), mawk (= 1.3.4.20240622-2), media-types (= 10.1.0), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2), netbase (= 6.4), nettle-dev (= 3.10-1), openssl (= 3.2.2-1), passwd (= 1:4.15.3-3), patch (= 2.7.6-7), perl (= 5.40.0-1), perl-base (= 5.40.0-1), perl-modules-5.40 (= 5.40.0-1), pkgconf (= 1.8.1-3), pkgconf-bin (= 1.8.1-3), po-debconf (= 1.0.21+nmu1), procps (= 2:4.0.4-5), python3 (= 3.12.4-1), python3-all (= 3.12.4-1), python3-all-dev (= 3.12.4-1), python3-dev (= 3.12.4-1), python3-minimal (= 3.12.4-1), python3-pkg-resources (= 70.3.0-2), python3-setuptools (= 70.3.0-2), python3.12 (= 3.12.4-3), python3.12-dev (= 3.12.4-3), python3.12-minimal (= 3.12.4-3), rake (= 13.2.1-1), readline-common (= 8.2-4), rpcsvc-proto (= 1.4.3-1), ruby (= 1:3.1+nmu1), ruby-net-telnet (= 0.2.0-1), ruby-rubygems (= 3.4.20-1), ruby-sdbm (= 1.0.0-5+b4), ruby-webrick (= 1.8.1-1), ruby-xmlrpc (= 0.3.3-2), ruby3.1 (= 3.1.2-8.3), rubygems-integration (= 1.18), samtools (= 1.20-3), sed (= 4.9-2), sensible-utils (= 0.0.24), swig (= 4.2.1-1), sysvinit-utils (= 3.09-2), tar (= 1.35+dfsg-3), time (= 1.9-0.2), tzdata (= 2024a-4), usr-is-merged (= 39), util-linux (= 2.40.2-1), xz-utils (= 5.6.2-2), yaggo (= 1.5.11-1), zlib1g (= 1:1.3.dfsg+really1.3.1-1), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1) 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="1722684898" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ jellyfish-dbgsym_2.3.1-3+b6_amd64.deb ------------------------------------- new Debian package, version 2.0. size 7597052 bytes: control archive=760 bytes. 518 bytes, 12 lines control 510 bytes, 5 lines md5sums Package: jellyfish-dbgsym Source: jellyfish (2.3.1-3) Version: 2.3.1-3+b6 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 8335 Depends: jellyfish (= 2.3.1-3+b6) Section: debug Priority: optional Description: debug symbols for jellyfish Build-Ids: 1932d30f59781be1895bd0fb315e354179ad32b5 23bc7aef43ecc2e40c220d1a19bb13ca4743a6fc b12d3999e0ebfe42212e1a71ad16655219d785e4 cfb1a703d17d002980e6a35381879bbee4cc5062 drwxr-xr-x root/root 0 2024-08-03 11:34 ./ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/debug/.build-id/19/ -rw-r--r-- root/root 6857440 2024-08-03 11:34 ./usr/lib/debug/.build-id/19/32d30f59781be1895bd0fb315e354179ad32b5.debug drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/debug/.build-id/23/ -rw-r--r-- root/root 61424 2024-08-03 11:34 ./usr/lib/debug/.build-id/23/bc7aef43ecc2e40c220d1a19bb13ca4743a6fc.debug drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/debug/.build-id/b1/ -rw-r--r-- root/root 76936 2024-08-03 11:34 ./usr/lib/debug/.build-id/b1/2d3999e0ebfe42212e1a71ad16655219d785e4.debug drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/debug/.build-id/cf/ -rw-r--r-- root/root 1442392 2024-08-03 11:34 ./usr/lib/debug/.build-id/cf/b1a703d17d002980e6a35381879bbee4cc5062.debug drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 78880 2024-08-03 11:34 ./usr/lib/debug/.dwz/x86_64-linux-gnu/jellyfish.debug drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-08-03 11:34 ./usr/share/doc/jellyfish-dbgsym -> jellyfish jellyfish_2.3.1-3+b6_amd64.deb ------------------------------ new Debian package, version 2.0. size 807228 bytes: control archive=1372 bytes. 1183 bytes, 24 lines control 988 bytes, 14 lines md5sums Package: jellyfish Source: jellyfish (2.3.1-3) Version: 2.3.1-3+b6 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 (= 2.3.1-3+b6), 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 2024-08-03 11:34 ./ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/bin/ -rwxr-xr-x root/root 347640 2024-08-03 11:34 ./usr/bin/jellyfish drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/jellyfish/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/jellyfish/bin/ -rwxr-xr-x root/root 27168 2024-08-03 11:34 ./usr/lib/jellyfish/bin/fastq2sam -rwxr-xr-x root/root 35560 2024-08-03 11:34 ./usr/lib/jellyfish/bin/generate_sequence -rwxr-xr-x root/root 1915584 2024-08-03 11:34 ./usr/lib/jellyfish/bin/test_all drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/doc-base/ -rw-r--r-- root/root 987 2019-09-27 12:56 ./usr/share/doc-base/jellyfish.jellyfish drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/doc/jellyfish/ -rw-r--r-- root/root 321 2019-09-27 12:56 ./usr/share/doc/jellyfish/README.test -rw-r--r-- root/root 207 2024-08-03 11:34 ./usr/share/doc/jellyfish/changelog.Debian.amd64.gz -rw-r--r-- root/root 2778 2024-08-03 11:34 ./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 2024-03-19 17:20 ./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 2024-02-28 13:56 ./usr/share/doc/jellyfish/run-unit-test drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/lintian/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 144 2024-02-28 13:56 ./usr/share/lintian/overrides/jellyfish drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/man/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/man/man1/ -rw-r--r-- root/root 4554 2024-08-03 11:34 ./usr/share/man/man1/jellyfish.1.gz libjellyfish-2.0-2-dbgsym_2.3.1-3+b6_amd64.deb ---------------------------------------------- new Debian package, version 2.0. size 544612 bytes: control archive=568 bytes. 438 bytes, 13 lines control 106 bytes, 1 lines md5sums Package: libjellyfish-2.0-2-dbgsym Source: jellyfish (2.3.1-3) Version: 2.3.1-3+b6 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 577 Depends: libjellyfish-2.0-2 (= 2.3.1-3+b6) Section: debug Priority: optional Multi-Arch: same Description: debug symbols for libjellyfish-2.0-2 Build-Ids: 3980feb9db13ac3614e2eac8e324bd325d426ad9 drwxr-xr-x root/root 0 2024-08-03 11:34 ./ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/debug/.build-id/39/ -rw-r--r-- root/root 580472 2024-08-03 11:34 ./usr/lib/debug/.build-id/39/80feb9db13ac3614e2eac8e324bd325d426ad9.debug drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-08-03 11:34 ./usr/share/doc/libjellyfish-2.0-2-dbgsym -> libjellyfish-2.0-2 libjellyfish-2.0-2_2.3.1-3+b6_amd64.deb --------------------------------------- new Debian package, version 2.0. size 67320 bytes: control archive=1332 bytes. 1386 bytes, 31 lines control 503 bytes, 6 lines md5sums 49 bytes, 1 lines shlibs 66 bytes, 2 lines triggers Package: libjellyfish-2.0-2 Source: jellyfish (2.3.1-3) Version: 2.3.1-3+b6 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 (= 2.3.1-3+b6) 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 2024-08-03 11:34 ./ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/x86_64-linux-gnu/ lrwxrwxrwx root/root 0 2024-08-03 11:34 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2 -> libjellyfish-2.0.so.2.0.0 -rw-r--r-- root/root 182296 2024-08-03 11:34 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/doc/libjellyfish-2.0-2/ -rw-r--r-- root/root 207 2024-08-03 11:34 ./usr/share/doc/libjellyfish-2.0-2/changelog.Debian.amd64.gz -rw-r--r-- root/root 2779 2024-08-03 11:34 ./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 2024-03-19 17:20 ./usr/share/doc/libjellyfish-2.0-2/copyright drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/lintian/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 178 2024-03-19 17:17 ./usr/share/lintian/overrides/libjellyfish-2.0-2 libjellyfish-2.0-dev_2.3.1-3+b6_amd64.deb ----------------------------------------- new Debian package, version 2.0. size 138484 bytes: control archive=2544 bytes. 1231 bytes, 27 lines control 4278 bytes, 57 lines md5sums Package: libjellyfish-2.0-dev Source: jellyfish (2.3.1-3) Version: 2.3.1-3+b6 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 691 Depends: libjellyfish-2.0-2 (= 2.3.1-3+b6) 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 2024-08-03 11:34 ./ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/include/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/include/jellyfish/ -rw-r--r-- root/root 1596 2024-08-03 11:34 ./usr/include/jellyfish/allocators_mmap.hpp -rw-r--r-- root/root 5898 2024-08-03 11:34 ./usr/include/jellyfish/atomic_bits_array.hpp -rw-r--r-- root/root 4770 2024-08-03 11:34 ./usr/include/jellyfish/atomic_field.hpp -rw-r--r-- root/root 1392 2024-08-03 11:34 ./usr/include/jellyfish/atomic_gcc.hpp -rw-r--r-- root/root 272 2024-08-03 11:34 ./usr/include/jellyfish/backtrace.hpp -rw-r--r-- root/root 6829 2024-08-03 11:34 ./usr/include/jellyfish/binary_dumper.hpp -rw-r--r-- root/root 3480 2024-08-03 11:34 ./usr/include/jellyfish/bloom_common.hpp -rw-r--r-- root/root 6778 2024-08-03 11:34 ./usr/include/jellyfish/bloom_counter2.hpp -rw-r--r-- root/root 5447 2024-08-03 11:34 ./usr/include/jellyfish/bloom_filter.hpp -rw-r--r-- root/root 5211 2024-08-03 11:34 ./usr/include/jellyfish/circular_buffer.hpp -rw-r--r-- root/root 2408 2024-08-03 11:34 ./usr/include/jellyfish/compare_and_swap.hpp -rw-r--r-- root/root 7472 2024-08-03 11:34 ./usr/include/jellyfish/cooperative_pool.hpp -rw-r--r-- root/root 8494 2024-08-03 11:34 ./usr/include/jellyfish/cooperative_pool2.hpp -rw-r--r-- root/root 4125 2024-08-03 11:34 ./usr/include/jellyfish/cpp_array.hpp -rw-r--r-- root/root 2742 2024-08-03 11:34 ./usr/include/jellyfish/divisor.hpp -rw-r--r-- root/root 2710 2024-08-03 11:34 ./usr/include/jellyfish/dumper.hpp -rw-r--r-- root/root 2257 2024-08-03 11:34 ./usr/include/jellyfish/err.hpp -rw-r--r-- root/root 4033 2024-08-03 11:34 ./usr/include/jellyfish/file_header.hpp -rw-r--r-- root/root 4637 2024-08-03 11:34 ./usr/include/jellyfish/generator_manager.hpp -rw-r--r-- root/root 6814 2024-08-03 11:34 ./usr/include/jellyfish/generic_file_header.hpp -rw-r--r-- root/root 8326 2024-08-03 11:34 ./usr/include/jellyfish/hash_counter.hpp -rw-r--r-- root/root 7025 2024-08-03 11:34 ./usr/include/jellyfish/int128.hpp -rw-r--r-- root/root 1118 2024-08-03 11:34 ./usr/include/jellyfish/jellyfish.hpp -rw-r--r-- root/root 61697 2024-08-03 11:34 ./usr/include/jellyfish/json.h -rw-r--r-- root/root 40578 2024-08-03 11:34 ./usr/include/jellyfish/large_hash_array.hpp -rw-r--r-- root/root 7564 2024-08-03 11:34 ./usr/include/jellyfish/large_hash_iterator.hpp -rw-r--r-- root/root 4328 2024-08-03 11:34 ./usr/include/jellyfish/locks_pthread.hpp -rw-r--r-- root/root 5181 2024-08-03 11:34 ./usr/include/jellyfish/mapped_file.hpp -rw-r--r-- root/root 23839 2024-08-03 11:34 ./usr/include/jellyfish/mer_dna.hpp -rw-r--r-- root/root 1296 2024-08-03 11:34 ./usr/include/jellyfish/mer_dna_bloom_counter.hpp -rw-r--r-- root/root 3076 2024-08-03 11:34 ./usr/include/jellyfish/mer_heap.hpp -rw-r--r-- root/root 2588 2024-08-03 11:34 ./usr/include/jellyfish/mer_iterator.hpp -rw-r--r-- root/root 9371 2024-08-03 11:34 ./usr/include/jellyfish/mer_overlap_sequence_parser.hpp -rw-r--r-- root/root 3247 2024-08-03 11:34 ./usr/include/jellyfish/mer_qual_iterator.hpp -rw-r--r-- root/root 8066 2024-08-03 11:34 ./usr/include/jellyfish/misc.hpp -rw-r--r-- root/root 10025 2024-08-03 11:34 ./usr/include/jellyfish/offsets_key_value.hpp -rw-r--r-- root/root 960 2024-08-03 11:34 ./usr/include/jellyfish/parser_common.hpp -rw-r--r-- root/root 12859 2024-08-03 11:34 ./usr/include/jellyfish/rectangular_binary_matrix.hpp -rw-r--r-- root/root 2311 2024-08-03 11:34 ./usr/include/jellyfish/sam_format.hpp -rw-r--r-- root/root 3504 2024-08-03 11:34 ./usr/include/jellyfish/simple_circular_buffer.hpp -rw-r--r-- root/root 3346 2024-08-03 11:34 ./usr/include/jellyfish/sorted_dumper.hpp -rw-r--r-- root/root 5069 2024-08-03 11:34 ./usr/include/jellyfish/stdio_filebuf.hpp -rw-r--r-- root/root 602 2024-08-03 11:34 ./usr/include/jellyfish/storage.hpp -rw-r--r-- root/root 2036 2024-08-03 11:34 ./usr/include/jellyfish/stream_iterator.hpp -rw-r--r-- root/root 6318 2024-08-03 11:34 ./usr/include/jellyfish/stream_manager.hpp -rw-r--r-- root/root 2063 2024-08-03 11:34 ./usr/include/jellyfish/text_dumper.hpp -rw-r--r-- root/root 994 2024-08-03 11:34 ./usr/include/jellyfish/thread_exec.hpp -rw-r--r-- root/root 1884 2024-08-03 11:34 ./usr/include/jellyfish/time.hpp -rw-r--r-- root/root 1599 2024-08-03 11:34 ./usr/include/jellyfish/token_ring.hpp -rw-r--r-- root/root 6761 2024-08-03 11:34 ./usr/include/jellyfish/whole_sequence_parser.hpp drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/x86_64-linux-gnu/ -rw-r--r-- root/root 318440 2024-08-03 11:34 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a -rw-r--r-- root/root 1005 2024-08-03 11:34 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.la lrwxrwxrwx root/root 0 2024-08-03 11:34 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so -> libjellyfish-2.0.so.2.0.0 drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/x86_64-linux-gnu/pkgconfig/ -rw-r--r-- root/root 273 2024-08-03 11:34 ./usr/lib/x86_64-linux-gnu/pkgconfig/jellyfish-2.0.pc drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/doc/libjellyfish-2.0-dev/ -rw-r--r-- root/root 207 2024-08-03 11:34 ./usr/share/doc/libjellyfish-2.0-dev/changelog.Debian.amd64.gz -rw-r--r-- root/root 2779 2024-08-03 11:34 ./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 2024-03-19 17:20 ./usr/share/doc/libjellyfish-2.0-dev/copyright libjellyfish-perl-dbgsym_2.3.1-3+b6_amd64.deb --------------------------------------------- new Debian package, version 2.0. size 353340 bytes: control archive=568 bytes. 435 bytes, 13 lines control 106 bytes, 1 lines md5sums Package: libjellyfish-perl-dbgsym Source: jellyfish (2.3.1-3) Version: 2.3.1-3+b6 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 373 Depends: libjellyfish-perl (= 2.3.1-3+b6) Section: debug Priority: optional Multi-Arch: same Description: debug symbols for libjellyfish-perl Build-Ids: fbbed8ee48535a4337cb5e90cf9d1996ec0b893f drwxr-xr-x root/root 0 2024-08-03 11:34 ./ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/debug/.build-id/fb/ -rw-r--r-- root/root 371128 2024-08-03 11:34 ./usr/lib/debug/.build-id/fb/bed8ee48535a4337cb5e90cf9d1996ec0b893f.debug drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-08-03 11:34 ./usr/share/doc/libjellyfish-perl-dbgsym -> libjellyfish-perl libjellyfish-perl_2.3.1-3+b6_amd64.deb -------------------------------------- new Debian package, version 2.0. size 57140 bytes: control archive=1172 bytes. 1250 bytes, 27 lines control 494 bytes, 6 lines md5sums Package: libjellyfish-perl Source: jellyfish (2.3.1-3) Version: 2.3.1-3+b6 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 177 Depends: perl (>= 5.40.0-1), perlapi-5.40.0, libc6 (>= 2.38), libgcc-s1 (>= 3.0) Section: perl Priority: optional Multi-Arch: same Homepage: https://www.genome.umd.edu/jellyfish.html Description: count k-mers in DNA sequences (Perl bindings of jellyfish) JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. . JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish dump" command. . This package contains the Perl bindings of jellyfish. drwxr-xr-x root/root 0 2024-08-03 11:34 ./ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/x86_64-linux-gnu/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/x86_64-linux-gnu/perl5/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/x86_64-linux-gnu/perl5/5.40/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/x86_64-linux-gnu/perl5/5.40/auto/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/x86_64-linux-gnu/perl5/5.40/auto/jellyfish/ -rw-r--r-- root/root 146664 2024-08-03 11:34 ./usr/lib/x86_64-linux-gnu/perl5/5.40/auto/jellyfish/jellyfish.so drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/doc/libjellyfish-perl/ -rw-r--r-- root/root 207 2024-08-03 11:34 ./usr/share/doc/libjellyfish-perl/changelog.Debian.amd64.gz -rw-r--r-- root/root 2781 2024-08-03 11:34 ./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 2024-03-19 17:20 ./usr/share/doc/libjellyfish-perl/copyright drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/perl5/ -rw-r--r-- root/root 7414 2024-08-03 11:34 ./usr/share/perl5/jellyfish.pm python3-dna-jellyfish-dbgsym_2.3.1-3+b6_amd64.deb ------------------------------------------------- new Debian package, version 2.0. size 341196 bytes: control archive=548 bytes. 430 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: python3-dna-jellyfish-dbgsym Source: jellyfish (2.3.1-3) Version: 2.3.1-3+b6 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 365 Depends: python3-dna-jellyfish (= 2.3.1-3+b6) Section: debug Priority: optional Description: debug symbols for python3-dna-jellyfish Build-Ids: 552eb41256a923eb312a46061877e9357a7ce743 drwxr-xr-x root/root 0 2024-08-03 11:34 ./ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/debug/.build-id/55/ -rw-r--r-- root/root 363360 2024-08-03 11:34 ./usr/lib/debug/.build-id/55/2eb41256a923eb312a46061877e9357a7ce743.debug drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-08-03 11:34 ./usr/share/doc/python3-dna-jellyfish-dbgsym -> python3-dna-jellyfish python3-dna-jellyfish_2.3.1-3+b6_amd64.deb ------------------------------------------ new Debian package, version 2.0. size 56148 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 (2.3.1-3) Version: 2.3.1-3+b6 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 187 Depends: python3 (<< 3.13), python3 (>= 3.12~), 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 2024-08-03 11:34 ./ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/python3/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/python3/dist-packages/ -rw-r--r-- root/root 149784 2024-08-03 11:34 ./usr/lib/python3/dist-packages/_dna_jellyfish.cpython-312-x86_64-linux-gnu.so drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/lib/python3/dist-packages/dna_jellyfish-0.0.1.egg-info/ -rw-r--r-- root/root 127 2024-08-03 11:34 ./usr/lib/python3/dist-packages/dna_jellyfish-0.0.1.egg-info/PKG-INFO -rw-r--r-- root/root 1 2024-08-03 11:34 ./usr/lib/python3/dist-packages/dna_jellyfish-0.0.1.egg-info/dependency_links.txt -rw-r--r-- root/root 29 2024-08-03 11:34 ./usr/lib/python3/dist-packages/dna_jellyfish-0.0.1.egg-info/top_level.txt -rw-r--r-- root/root 12643 2024-08-03 11:34 ./usr/lib/python3/dist-packages/dna_jellyfish.py drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-08-03 11:34 ./usr/share/doc/python3-dna-jellyfish/ -rw-r--r-- root/root 207 2024-08-03 11:34 ./usr/share/doc/python3-dna-jellyfish/changelog.Debian.amd64.gz -rw-r--r-- root/root 2778 2024-08-03 11:34 ./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 2024-03-19 17:20 ./usr/share/doc/python3-dna-jellyfish/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 1818636 Build-Time: 321 Distribution: perl-5.40 Host Architecture: amd64 Install-Time: 21 Job: /srv/debomatic/incoming/jellyfish_2.3.1-3.dsc Machine Architecture: amd64 Package: jellyfish Package-Time: 355 Source-Version: 2.3.1-3 Space: 1818636 Status: successful Version: 2.3.1-3+b6 -------------------------------------------------------------------------------- Finished at 2024-08-03T11:40:19Z Build needed 00:05:55, 1818636k disk space