sbuild (Debian sbuild) 0.85.10 (30 May 2024) on carme.larted.org.uk +==============================================================================+ | jellyfish 2.3.1-3 (amd64) Tue, 15 Oct 2024 04:23:42 +0000 | +==============================================================================+ Package: jellyfish Version: 2.3.1-3 Source Version: 2.3.1-3 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: NOTICE: Log filtering will replace 'var/run/schroot/mount/perl-5.40-amd64-debomatic-5bb4a942-5ad6-44b0-b066-8a9eae3a7588' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup jellyfish_2.3.1-3 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------ I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup jellyfish_2.3.1-3 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/jellyfish-7e53CU/resolver-vjtHy8' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:2 http://deb.debian.org/debian unstable InRelease Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Get:3 file:/srv/reprepro perl-5.40/main amd64 Packages [634 kB] Hit:4 http://localhost:3142/debian sid InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ 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-7e53CU/jellyfish-2.3.1' with '<>' I: NOTICE: Log filtering will replace 'build/jellyfish-7e53CU' 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 (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: architecture-properties autoconf autoconf-archive automake autopoint autotools-dev bc bsdextrautils ca-certificates chrpath 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 libnsl2 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 libtirpc-common libtirpc3t64 libtool libuchardet0 libunbound8 libxml2 libyaml-0-2 libzstd-dev m4 man-db media-types netbase nettle-dev openssl pkgconf pkgconf-bin po-debconf procps python3 python3-all python3-all-dev python3-autocommand python3-dev python3-inflect python3-jaraco.context python3-jaraco.functools python3-minimal python3-more-itertools python3-pkg-resources python3-setuptools python3-typeguard python3-typing-extensions python3-zipp 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 libnsl2 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 libtirpc-common libtirpc3t64 libtool libuchardet0 libunbound8 libxml2 libyaml-0-2 libzstd-dev m4 man-db media-types netbase nettle-dev openssl pkgconf pkgconf-bin po-debconf procps python3 python3-all python3-all-dev python3-autocommand python3-dev python3-inflect python3-jaraco.context python3-jaraco.functools python3-minimal python3-more-itertools python3-pkg-resources python3-setuptools python3-typeguard python3-typing-extensions python3-zipp 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, 144 newly installed, 0 to remove and 0 not upgraded. Need to get 65.0 MB of archives. After this operation, 255 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [1008 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 3.12.7-1 [814 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.3-1 [105 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.7-1 [2162 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.6-1 [26.7 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 2024b-3 [255 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:14 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b2 [40.3 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.7-1 [1965 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.7-1 [671 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get:22 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.3.2-1 [1381 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-9 [97.2 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 architecture-properties amd64 0.2.3 [2184 B] Get:38 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 bc amd64 1.07.1-4 [103 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 chrpath amd64 0.16-2+b1 [17.1 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 d-shlibs all 0.107 [11.0 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:52 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.1 [699 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.3.0-1 [36.5 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get:66 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 74.1.2-2 [213 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.20.2-1 [10.3 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 74.1.2-2 [736 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20240824 [109 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 dos2unix amd64 7.5.2-1 [518 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libfakeroot amd64 1.36-1 [29.1 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 fakeroot amd64 1.36-1 [75.1 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b4 [300 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b4 [313 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.63.0-1 [74.8 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.4.0-1 [63.1 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-7 [216 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.10.1-2 [360 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10 [181 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.21.1-1 [591 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.6-2 [439 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.6-2 [439 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.7-2 [123 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-2 [208 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.19.0-3+b2 [98.0 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-2+b1 [329 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-2+b1 [640 kB] Get:93 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10-1 [1316 kB] Get:94 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.6-2 [1381 kB] Get:95 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-3 [36.2 kB] Get:96 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-3 [29.9 kB] Get:97 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-3 [26.1 kB] Get:98 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.63.0-1 [115 kB] Get:99 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.4.0-1 [86.5 kB] Get:100 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.6.0-1 [23.8 kB] Get:101 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.6.0-1 [170 kB] Get:102 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1 [77.4 kB] Get:103 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get:104 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b4 [67.7 kB] Get:105 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.3.2-1 [2742 kB] Get:106 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.0-7 [357 kB] Get:107 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.6+dfsg-1 [368 kB] Get:108 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.10.1-2 [471 kB] Get:109 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get:110 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.22-1 [55.8 kB] Get:111 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get:112 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.3-1 [157 kB] Get:113 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get:114 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.20+ds-1 [452 kB] Get:115 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.2-2 [299 kB] Get:116 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.20+ds-1 [1684 kB] Get:117 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:118 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get:119 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 7.4.7-3 [158 kB] Get:120 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2 [104 kB] Get:121 http://deb.debian.org/debian unstable/main amd64 libpython3.12t64 amd64 3.12.7-1 [2149 kB] Get:122 http://deb.debian.org/debian unstable/main amd64 libpython3.12-dev amd64 3.12.7-1 [5122 kB] Get:123 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.12.6-1 [9952 B] Get:124 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.12.6-1 [1064 B] Get:125 http://deb.debian.org/debian unstable/main amd64 rubygems-integration all 1.18 [6704 B] Get:126 http://deb.debian.org/debian unstable/main amd64 ruby3.1 amd64 3.1.2-8.4 [664 kB] Get:127 http://deb.debian.org/debian unstable/main amd64 ruby-rubygems all 3.4.20-1 [309 kB] Get:128 http://deb.debian.org/debian unstable/main amd64 ruby amd64 1:3.1+nmu1 [5584 B] Get:129 http://deb.debian.org/debian unstable/main amd64 rake all 13.2.1-1 [65.2 kB] Get:130 http://deb.debian.org/debian unstable/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get:131 http://deb.debian.org/debian unstable/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB] Get:132 http://deb.debian.org/debian unstable/main amd64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get:133 http://deb.debian.org/debian unstable/main amd64 ruby-sdbm amd64 1.0.0-5+b4 [15.4 kB] Get:134 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-1+b1 [52.6 kB] Get:135 http://deb.debian.org/debian unstable/main amd64 libruby3.1t64 amd64 3.1.2-8.4 [5411 kB] Get:136 http://deb.debian.org/debian unstable/main amd64 libruby amd64 1:3.1+nmu1 [4664 B] Get:137 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.12.6-1 [1040 B] Get:138 http://deb.debian.org/debian unstable/main amd64 python3.12-dev amd64 3.12.7-1 [505 kB] Get:139 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.12.6-1 [26.1 kB] Get:140 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.12.6-1 [1068 B] Get:141 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.20-3 [653 kB] Get:142 http://deb.debian.org/debian unstable/main amd64 swig amd64 4.2.1-1 [1437 kB] Get:143 http://deb.debian.org/debian unstable/main amd64 time amd64 1.9-0.2 [50.8 kB] Get:144 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 65.0 MB in 5s (14.1 MB/s) Selecting previously unselected package autoconf-archive. (Reading database ... 22991 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_3.12.7-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.7-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-1_amd64.deb ... Unpacking python3.12-minimal (3.12.7-1) ... Setting up libpython3.12-minimal:amd64 (3.12.7-1) ... Setting up libexpat1:amd64 (2.6.3-1) ... Setting up python3.12-minimal (3.12.7-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 24493 files and directories currently installed.) 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Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b2) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../13-libpython3.12-stdlib_3.12.7-1_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.7-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../14-python3.12_3.12.7-1_amd64.deb ... Unpacking python3.12 (3.12.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../15-libpython3-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.6-1) ... 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Unpacking libhts3t64:amd64 (1.20+ds-1) ... Selecting previously unselected package liblzma-dev:amd64. Preparing to unpack .../093-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 .../094-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 .../095-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 .../096-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 .../097-libjs-sphinxdoc_7.4.7-3_all.deb ... Unpacking libjs-sphinxdoc (7.4.7-3) ... Selecting previously unselected package libncurses6:amd64. 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Preparing to unpack .../123-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libhtscodecs2:amd64 (1.6.1-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... 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 (2.40.2-9) ... 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 (0.2.3) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:amd64 (1.1.0-2+b4) ... Setting up libedit2:amd64 (3.1-20240808-1) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.63.0-1) ... Setting up libdeflate0:amd64 (1.22-1) ... 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 (1.36-1) ... 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 (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Oct 15 04:24:03 UTC 2024. Universal Time is now: Tue Oct 15 04:24:03 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.36-1) ... 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 (1.21.1-1) ... Setting up libpkgconf3:amd64 (1.8.1-3) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-2+b1) ... Setting up libexpat1-dev:amd64 (2.6.3-1) ... 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 (2:4.0.4-6) ... Setting up libssl-dev:amd64 (3.3.2-1) ... Setting up autopoint (0.22.5-2) ... Setting up d-shlibs (0.107) ... 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 (2.72-3) ... 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 (2:4.0.4-6) ... 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 (3.3.2-1) ... Setting up libdeflate-dev:amd64 (1.22-1) ... Setting up ruby-xmlrpc (0.3.3-2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... 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 nettle-dev:amd64 (3.10-1) ... Setting up libtool (2.4.7-7) ... 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 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 (7.4.7-3) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libgnutls28-dev:amd64 (3.8.6-2) ... Setting up libnghttp2-dev:amd64 (1.63.0-1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.10.1-2) ... Setting up rubygems-integration (1.18) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libnsl2:amd64 (1.3.0-3+b2) ... Setting up libhts3t64:amd64 (1.20+ds-1) ... Setting up libpython3.12-stdlib:amd64 (3.12.7-1) ... Setting up python3.12 (3.12.7-1) ... Setting up debhelper (13.20) ... Setting up libcurl4-gnutls-dev:amd64 (8.10.1-2) ... Setting up samtools (1.20-3) ... Setting up libpython3.12t64:amd64 (3.12.7-1) ... Setting up libpython3-stdlib:amd64 (3.12.6-1) ... Setting up libhts-dev:amd64 (1.20+ds-1) ... Setting up python3 (3.12.6-1) ... Setting up libpython3.12-dev:amd64 (3.12.7-1) ... Setting up python3-zipp (3.20.2-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3.12-dev (3.12.7-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up libpython3-dev:amd64 (3.12.6-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-typeguard (4.3.0-1) ... Setting up python3-all (3.12.6-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up libpython3-all-dev:amd64 (3.12.6-1) ... Setting up python3-dev (3.12.6-1) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-all-dev (3.12.6-1) ... Setting up python3-setuptools (74.1.2-2) ... Setting up dh-python (6.20240824) ... 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 (3.1.2-8.4) ... Setting up ruby3.1 (3.1.2-8.4) ... 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 (2.40-3) ... 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_2.43.1-5 dpkg-dev_1.22.11 g++-13_13.3.0-8 g++-14_14.2.0-6 gcc-13_13.3.0-8 gcc-14_14.2.0-6 libc6-dev_2.40-3 libstdc++-13-dev_13.3.0-8 libstdc++-14-dev_14.2.0-6 libstdc++6_14.2.0-6 linux-libc-dev_6.11.2-1 Package versions: adduser_3.137 apt_2.9.8 architecture-properties_0.2.3 autoconf_2.72-3 autoconf-archive_20220903-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.5 base-passwd_3.6.4 bash_5.2.32-1+b1 bc_1.07.1-4 binutils_2.43.1-5 binutils-common_2.43.1-5 binutils-x86-64-linux-gnu_2.43.1-5 bsdextrautils_2.40.2-9 bsdutils_1:2.40.2-9 build-essential_12.12 bzip2_1.0.8-6 ca-certificates_20240203 chrpath_0.16-2+b1 coreutils_9.4-3.1 cpp_4:14.2.0-1 cpp-13_13.3.0-8 cpp-13-x86-64-linux-gnu_13.3.0-8 cpp-14_14.2.0-6 cpp-14-x86-64-linux-gnu_14.2.0-6 cpp-x86-64-linux-gnu_4:14.2.0-1 d-shlibs_0.107 dash_0.5.12-9 debconf_1.5.87 debhelper_13.20 debian-archive-keyring_2023.4 debianutils_5.20 dh-autoreconf_20 dh-python_6.20240824 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.44-1 dos2unix_7.5.2-1 dpkg_1.22.11 dpkg-dev_1.22.11 dwz_0.15-1+b1 eatmydata_131-2 fakeroot_1.36-1 file_1:5.45-3 findutils_4.10.0-3 g++_4:14.2.0-1 g++-13_13.3.0-8 g++-13-x86-64-linux-gnu_13.3.0-8 g++-14_14.2.0-6 g++-14-x86-64-linux-gnu_14.2.0-6 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-13_13.3.0-8 gcc-13-base_13.3.0-8 gcc-13-x86-64-linux-gnu_13.3.0-8 gcc-14_14.2.0-6 gcc-14-base_14.2.0-6 gcc-14-x86-64-linux-gnu_14.2.0-6 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.22.5-2 gettext-base_0.22.5-2 gnupg_2.2.44-1 gnupg-l10n_2.2.44-1 gnupg-utils_2.2.44-1 gpg_2.2.44-1 gpg-agent_2.2.44-1 gpg-wks-client_2.2.44-1 gpgconf_2.2.44-1 gpgsm_2.2.44-1 gpgv_2.2.44-1 grep_3.11-4 groff-base_1.23.0-5 gzip_1.12-1.1 hostname_3.25 init-system-helpers_1.67 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2 libapt-pkg6.0t64_2.9.8 libarchive-zip-perl_1.68-1 libasan8_14.2.0-6 libassuan0_2.5.6-1+b1 libassuan9_3.0.1-2 libatomic1_14.2.0-6 libattr1_1:2.5.2-2 libaudit-common_1:4.0.1-1 libaudit1_1:4.0.1-1 libbinutils_2.43.1-5 libblkid1_2.40.2-9 libbrotli-dev_1.1.0-2+b4 libbrotli1_1.1.0-2+b4 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libc-bin_2.40-3 libc-dev-bin_2.40-3 libc-l10n_2.40-3 libc6_2.40-3 libc6-dev_2.40-3 libcap-ng0_0.8.5-2 libcap2_1:2.66-5 libcc1-0_14.2.0-6 libcom-err2_1.47.1-1 libcrypt-dev_1:4.4.36-5 libcrypt1_1:4.4.36-5 libctf-nobfd0_2.43.1-5 libctf0_2.43.1-5 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python3-minimal_3.12.6-1 python3-more-itertools_10.5.0-1 python3-pkg-resources_74.1.2-2 python3-setuptools_74.1.2-2 python3-typeguard_4.3.0-1 python3-typing-extensions_4.12.2-2 python3-zipp_3.20.2-1 python3.12_3.12.7-1 python3.12-dev_3.12.7-1 python3.12-minimal_3.12.7-1 rake_13.2.1-1 readline-common_8.2-5 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_3.1.2-8.4 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_3.10-2 tar_1.35+dfsg-3 time_1.9-0.2 tzdata_2024b-3 usr-is-merged_39 util-linux_2.40.2-9 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 +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network jellyfish_2.3.1-3 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------ I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network jellyfish_2.3.1-3 perl-5.40-throwaway 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-throwaway-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-5bb4a942-5ad6-44b0-b066-8a9eae3a7588 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -Zxz dpkg-buildpackage: info: source package jellyfish dpkg-buildpackage: info: source version 2.3.1-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe 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 '/<>' dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building jellyfish using existing ./jellyfish_2.3.1.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: warning: ignoring deletion of file swig/python/jellyfish.py, use --include-removal to override dpkg-source: info: building jellyfish in jellyfish_2.3.1-3.debian.tar.xz dpkg-source: info: building jellyfish in jellyfish_2.3.1-3.dsc debian/rules binary dh binary 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 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 egrep -e... (cached) /usr/bin/grep -E checking for ELF binary format... yes checking for the common suffixes of directories in the library search path... lib,lib,lib64 checking for htslib... yes checking for samtools... /usr/bin/samtools checking for unix2dos... /usr/bin/unix2dos checking for md5sum... md5sum checking for yaggo... /usr/bin/yaggo checking for x86 cpuid output... unknown checking for x86-AVX xgetbv output... unknown checking for x86 cpuid 0x00000000 output... d:756e6547:6c65746e:49656e69 checking for x86 cpuid 0x80000000 output... 80000008:756e6547:6c65746e:49656e69 checking for x86 cpuid 0x00000001 output... 506e3:800:fffa3223:f8bfbff checking for x86 cpuid 0x00000007 output... 0:9c0fbb: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 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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=/<>=. 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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 () 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++ chmod 644 "jellyfish.bs" "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- jellyfish.bs blib/arch/auto/jellyfish/jellyfish.bs 644 rm -f blib/arch/auto/jellyfish/jellyfish.so x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -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 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -lpthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-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 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 1143632 Oct 15 04:27 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 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 dh_installchangelogs dh_installexamples dh_installman dh_python3 dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms debian/rules override_dh_missing make[1]: Entering directory '/<>' # 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 dh_gencontrol dpkg-gencontrol: warning: Depends field of package jellyfish-examples: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'jellyfish' in '../jellyfish_2.3.1-3_amd64.deb'. dpkg-deb: building package 'python3-dna-jellyfish' in '../python3-dna-jellyfish_2.3.1-3_amd64.deb'. dpkg-deb: building package 'python3-dna-jellyfish-dbgsym' in '../python3-dna-jellyfish-dbgsym_2.3.1-3_amd64.deb'. dpkg-deb: building package 'libjellyfish-perl' in '../libjellyfish-perl_2.3.1-3_amd64.deb'. dpkg-deb: building package 'libjellyfish-perl-dbgsym' in '../libjellyfish-perl-dbgsym_2.3.1-3_amd64.deb'. dpkg-deb: building package 'jellyfish-examples' in '../jellyfish-examples_2.3.1-3_all.deb'. dpkg-deb: building package 'jellyfish-dbgsym' in '../jellyfish-dbgsym_2.3.1-3_amd64.deb'. dpkg-deb: building package 'libjellyfish-2.0-2' in '../libjellyfish-2.0-2_2.3.1-3_amd64.deb'. dpkg-deb: building package 'libjellyfish-2.0-2-dbgsym' in '../libjellyfish-2.0-2-dbgsym_2.3.1-3_amd64.deb'. dpkg-deb: building package 'libjellyfish-2.0-dev' in '../libjellyfish-2.0-dev_2.3.1-3_amd64.deb'. dpkg-genbuildinfo -O../jellyfish_2.3.1-3_amd64.buildinfo dpkg-genchanges -O../jellyfish_2.3.1-3_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2024-10-15T04:29:23Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ jellyfish_2.3.1-3_amd64.changes: -------------------------------- Format: 1.8 Date: Tue, 19 Mar 2024 18:21:25 +0100 Source: jellyfish Binary: jellyfish jellyfish-dbgsym jellyfish-examples libjellyfish-2.0-2 libjellyfish-2.0-2-dbgsym libjellyfish-2.0-dev libjellyfish-perl libjellyfish-perl-dbgsym python3-dna-jellyfish python3-dna-jellyfish-dbgsym Architecture: source amd64 all Version: 2.3.1-3 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: jellyfish - count k-mers in DNA sequences jellyfish-examples - count k-mers in DNA sequences (examples for testing) libjellyfish-2.0-2 - count k-mers in DNA sequences (dynamic library of jellyfish) libjellyfish-2.0-dev - count k-mers in DNA sequences (development files of jellyfish) libjellyfish-perl - count k-mers in DNA sequences (Perl bindings of jellyfish) python3-dna-jellyfish - count k-mers in DNA sequences (Python bindings of jellyfish) Changes: jellyfish (2.3.1-3) unstable; urgency=medium . * Forwarded several patches upstream. * debian/patches/fix_catch.patch is no longer used, remove it. * Point to the Jellyfish 2.0 homepage * d/control: simplify architecture specifications by build-dep'ing on architecture-is-little-endian. * d/patches/drop_distutils: upgrade to setuptools. * d/control: s/pkg-config/pkgconf/g * d/control: stop building on 32-bit architectures, as per upstream's wishes: https://github.com/gmarcais/Jellyfish/pull/202#issuecomment- 2007544485 * d/control: undo the t64 migration, no longer needed. Checksums-Sha1: 6a290eb3769ff4185ef38562d2ce33c1e17f741d 1804 jellyfish_2.3.1-3.dsc 32f49f1dd8cebe75a863a9b20b29e4a41223e1cc 13340 jellyfish_2.3.1-3.debian.tar.xz 97685d564369ab4e6acef8d82eb9f9eeb217b424 7598308 jellyfish-dbgsym_2.3.1-3_amd64.deb 777d94b0448a8451d49b809b79062c203fca5132 13856 jellyfish-examples_2.3.1-3_all.deb 79d6d0be88b1b26e68141b5a6161ed3a47c4fe89 11824 jellyfish_2.3.1-3_amd64.buildinfo 42db338ba2149c2d92feb74b6ace315e53b54a23 807404 jellyfish_2.3.1-3_amd64.deb fd89fbcc7929bb09a44de9e2084d4e1f239cb870 544612 libjellyfish-2.0-2-dbgsym_2.3.1-3_amd64.deb 3c1341f288a4c2f3dd74632906c2efcfc0658c01 66988 libjellyfish-2.0-2_2.3.1-3_amd64.deb 304eadab0bf20d4ce78b7a429b6b40bc618a2fb0 138100 libjellyfish-2.0-dev_2.3.1-3_amd64.deb 105cf95f6fcd3e89c3e55d6d57bf32f7e9665043 353368 libjellyfish-perl-dbgsym_2.3.1-3_amd64.deb 8c6090bb591a4f656972ca68065452a0a06a61c5 56812 libjellyfish-perl_2.3.1-3_amd64.deb 603ec85e3a6fd895358b225b396e3490b6e24f7f 342344 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0efb50c5ba682fb553b44fb1dd15d395d462817a 56636 python3-dna-jellyfish_2.3.1-3_amd64.deb Checksums-Sha256: 9ec3490ec5c48e295f7450382487aff27ff8b339f076ea346358a89ae2fa9f36 1804 jellyfish_2.3.1-3.dsc b1c17d2e079721ec46f5cc69d6c3f50051072279067674cb3203886b316fe35c 7598308 jellyfish-dbgsym_2.3.1-3_amd64.deb 3661dd788ed852773050643c0f4ace988b7b384d58569a3855c71852867cad6e 13856 jellyfish-examples_2.3.1-3_all.deb 00d883ec92dc7ad95dde25400f55868181ac2292f8891611c802bc3fbd0f410a 807404 jellyfish_2.3.1-3_amd64.deb f12ed32955c70bc7a7080ef7bf4c5776415d6756e50e5e3e470762d5968c6250 544612 libjellyfish-2.0-2-dbgsym_2.3.1-3_amd64.deb 4a69d181a3c2342515ac365c44c5654106ca1e2e8398206260dc3992721ca294 66988 libjellyfish-2.0-2_2.3.1-3_amd64.deb 6a7e55648117c0f8096e0bc9463ddd667cd51daff923095ca734c2b5f0cc6536 138100 libjellyfish-2.0-dev_2.3.1-3_amd64.deb 865d2bf83afa75a5b06517e9d41ba53b757d6731fc22fe364f736356d2d661ae 353368 libjellyfish-perl-dbgsym_2.3.1-3_amd64.deb 318691d4503d5a9d8d23813c4cd41af5f22680739d3b3f614c03e610ad0ab07c 56812 libjellyfish-perl_2.3.1-3_amd64.deb 96c9cc35c5d5f824a2d461d5edefb2eebc35d2b8b97f09a7a51bdb4a59f0e9d1 342344 python3-dna-jellyfish-dbgsym_2.3.1-3_amd64.deb 96fce1d7121533b767f6c04df180085b8c234dc157b2baa35f98d1f97eb1a620 56636 python3-dna-jellyfish_2.3.1-3_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Tue, 15 Oct 2024 04:29:23 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: adduser (= 3.137), apt (= 2.9.8), architecture-properties (= 0.2.3), autoconf (= 2.72-3), autoconf-archive (= 20220903-3), automake (= 1:1.16.5-1.3), autopoint (= 0.22.5-2), autotools-dev (= 20220109.1), base-files (= 13.5), base-passwd (= 3.6.4), bash (= 5.2.32-1+b1), bc (= 1.07.1-4), binutils (= 2.43.1-5), binutils-common (= 2.43.1-5), binutils-x86-64-linux-gnu (= 2.43.1-5), bsdextrautils (= 2.40.2-9), bsdutils (= 1:2.40.2-9), build-essential (= 12.12), bzip2 (= 1.0.8-6), ca-certificates (= 20240203), chrpath (= 0.16-2+b1), coreutils (= 9.4-3.1), cpp (= 4:14.2.0-1), cpp-13 (= 13.3.0-8), cpp-13-x86-64-linux-gnu (= 13.3.0-8), cpp-14 (= 14.2.0-6), cpp-14-x86-64-linux-gnu (= 14.2.0-6), cpp-x86-64-linux-gnu (= 4:14.2.0-1), d-shlibs (= 0.107), dash (= 0.5.12-9), debconf (= 1.5.87), debhelper (= 13.20), debian-archive-keyring (= 2023.4), debianutils (= 5.20), dh-autoreconf (= 20), dh-python (= 6.20240824), 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 (= 4.10.0-3), g++ (= 4:14.2.0-1), g++-14 (= 14.2.0-6), g++-14-x86-64-linux-gnu (= 14.2.0-6), g++-x86-64-linux-gnu (= 4:14.2.0-1), gcc (= 4:14.2.0-1), gcc-13 (= 13.3.0-8), gcc-13-base (= 13.3.0-8), gcc-13-x86-64-linux-gnu (= 13.3.0-8), gcc-14 (= 14.2.0-6), gcc-14-base (= 14.2.0-6), gcc-14-x86-64-linux-gnu (= 14.2.0-6), gcc-x86-64-linux-gnu (= 4:14.2.0-1), gettext (= 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Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 8335 Depends: jellyfish (= 2.3.1-3) Section: debug Priority: optional Description: debug symbols for jellyfish Build-Ids: 2353b111a1e464b4a94d3809086936945890c1c0 cd6a757f3764da206539baccdd0d85cab0c5a78d d1d611c1d8fa220bef7c62b07b20cafb462708d2 e457b370cac9185f0eb7f2c6e0f7e9b206801f78 drwxr-xr-x root/root 0 2024-03-19 17:21 ./ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/debug/.build-id/23/ -rw-r--r-- root/root 6857664 2024-03-19 17:21 ./usr/lib/debug/.build-id/23/53b111a1e464b4a94d3809086936945890c1c0.debug drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/debug/.build-id/cd/ -rw-r--r-- root/root 76960 2024-03-19 17:21 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bytes: control archive=1840 bytes. 1173 bytes, 27 lines control 3133 bytes, 34 lines md5sums Package: jellyfish-examples Source: jellyfish Version: 2.3.1-3 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 60 Recommends: jellyfish Section: science Priority: optional Multi-Arch: foreign Homepage: https://www.genome.umd.edu/jellyfish.html Description: count k-mers in DNA sequences (examples for testing) JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. . JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish dump" command. . This package contains examples to test the package drwxr-xr-x root/root 0 2024-03-19 17:21 ./ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/jellyfish/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/jellyfish/bin/ lrwxrwxrwx root/root 0 2024-03-19 17:21 ./usr/lib/jellyfish/bin/jellyfish -> ../../../bin/jellyfish drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/share/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/share/doc/jellyfish-examples/ -rw-r--r-- root/root 2778 2024-03-19 17:21 ./usr/share/doc/jellyfish-examples/changelog.Debian.gz -rw-r--r-- root/root 284 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/changelog.gz -rw-r--r-- root/root 6395 2024-03-19 17:20 ./usr/share/doc/jellyfish-examples/copyright drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/share/doc/jellyfish-examples/examples/ -rw-r--r-- root/root 809 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/big.sh -rw-r--r-- root/root 1535 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/bloom_counter.sh -rw-r--r-- root/root 931 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/bloom_filter.sh -rw-r--r-- root/root 695 2024-03-19 17:21 ./usr/share/doc/jellyfish-examples/examples/compat.sh -rw-r--r-- root/root 755 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/from_stream.sh -rw-r--r-- root/root 567 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/from_stream_fastq.sh -rw-r--r-- root/root 227 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/generate_fastq_sequence.sh -rwxr-xr-x root/root 620 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/generate_sequence.sh -rw-r--r-- root/root 837 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/large_key.sh -rw-r--r-- root/root 1954 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/merge.sh -rw-r--r-- root/root 454 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/min_qual.sh -rw-r--r-- root/root 1286 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/multi_file.sh -rw-r--r-- root/root 544 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/multi_file_fastq.sh -rwxr-xr-x root/root 891 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/parallel_direct_indexing.sh -rw-r--r-- root/root 798 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/parallel_fastq_direct_indexing.sh -rw-r--r-- root/root 629 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/parallel_fastq_hashing.sh -rw-r--r-- root/root 541 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/parallel_fastq_sequence_hashing.sh -rwxr-xr-x root/root 3795 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/parallel_hashing.sh -rw-r--r-- root/root 309 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/parsers.sh -rw-r--r-- root/root 881 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/quality_filter.sh -rw-r--r-- root/root 863 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/raw_hash.sh -rw-r--r-- root/root 1242 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/sam.sh -rwxr-xr-x root/root 427 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/serial_direct_indexing.sh -rwxr-xr-x root/root 541 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/serial_hashing.sh -rwxr-xr-x root/root 540 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/small.sh -rw-r--r-- root/root 455 2024-03-19 17:21 ./usr/share/doc/jellyfish-examples/examples/small_mers.sh -rw-r--r-- root/root 696 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/subset_hashing.sh -rw-r--r-- root/root 536 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/swig_perl.sh -rw-r--r-- root/root 595 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/swig_python.sh -rw-r--r-- root/root 490 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/swig_ruby.sh -rw-r--r-- root/root 132 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/unit_tests.sh jellyfish_2.3.1-3_amd64.deb --------------------------- new Debian package, version 2.0. size 807404 bytes: control archive=1324 bytes. 1149 bytes, 23 lines control 904 bytes, 13 lines md5sums Package: jellyfish Version: 2.3.1-3 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 2526 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libhts3t64 (>= 1.17), libjellyfish-2.0-2 (= 2.3.1-3), 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 2024-03-19 17:21 ./ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/bin/ -rwxr-xr-x root/root 347640 2024-03-19 17:21 ./usr/bin/jellyfish drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/jellyfish/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/jellyfish/bin/ -rwxr-xr-x root/root 27168 2024-03-19 17:21 ./usr/lib/jellyfish/bin/fastq2sam -rwxr-xr-x root/root 35560 2024-03-19 17:21 ./usr/lib/jellyfish/bin/generate_sequence -rwxr-xr-x root/root 1915584 2024-03-19 17:21 ./usr/lib/jellyfish/bin/test_all drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/share/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./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 2024-03-19 17:21 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./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 2778 2024-03-19 17:21 ./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 2024-03-19 17:21 ./usr/share/lintian/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./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 2024-03-19 17:21 ./usr/share/man/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/share/man/man1/ -rw-r--r-- root/root 4554 2024-03-19 17:21 ./usr/share/man/man1/jellyfish.1.gz libjellyfish-2.0-2-dbgsym_2.3.1-3_amd64.deb ------------------------------------------- new Debian package, version 2.0. size 544612 bytes: control archive=560 bytes. 422 bytes, 13 lines control 106 bytes, 1 lines md5sums Package: libjellyfish-2.0-2-dbgsym Source: jellyfish Version: 2.3.1-3 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 577 Depends: libjellyfish-2.0-2 (= 2.3.1-3) Section: debug Priority: optional Multi-Arch: same Description: debug symbols for libjellyfish-2.0-2 Build-Ids: f38b38b6b118c726f96e674bdaaef96bcd414c82 drwxr-xr-x root/root 0 2024-03-19 17:21 ./ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/debug/.build-id/f3/ -rw-r--r-- root/root 580488 2024-03-19 17:21 ./usr/lib/debug/.build-id/f3/8b38b6b118c726f96e674bdaaef96bcd414c82.debug drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/share/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-03-19 17:21 ./usr/share/doc/libjellyfish-2.0-2-dbgsym -> libjellyfish-2.0-2 libjellyfish-2.0-2_2.3.1-3_amd64.deb ------------------------------------ new Debian package, version 2.0. size 66988 bytes: control archive=1292 bytes. 1370 bytes, 31 lines control 410 bytes, 5 lines md5sums 49 bytes, 1 lines shlibs 66 bytes, 2 lines triggers Package: libjellyfish-2.0-2 Source: jellyfish Version: 2.3.1-3 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 204 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) 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 2024-03-19 17:21 ./ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/x86_64-linux-gnu/ lrwxrwxrwx root/root 0 2024-03-19 17:21 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2 -> libjellyfish-2.0.so.2.0.0 -rw-r--r-- root/root 182296 2024-03-19 17:21 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/share/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/share/doc/libjellyfish-2.0-2/ -rw-r--r-- root/root 2779 2024-03-19 17:21 ./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 2024-03-19 17:21 ./usr/share/lintian/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./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_amd64.deb -------------------------------------- new Debian package, version 2.0. size 138100 bytes: control archive=2516 bytes. 1215 bytes, 27 lines control 4183 bytes, 56 lines md5sums Package: libjellyfish-2.0-dev Source: jellyfish Version: 2.3.1-3 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 690 Depends: libjellyfish-2.0-2 (= 2.3.1-3) 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 2024-03-19 17:21 ./ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/include/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/include/jellyfish/ -rw-r--r-- root/root 1596 2024-03-19 17:21 ./usr/include/jellyfish/allocators_mmap.hpp -rw-r--r-- root/root 5898 2024-03-19 17:21 ./usr/include/jellyfish/atomic_bits_array.hpp -rw-r--r-- root/root 4770 2024-03-19 17:21 ./usr/include/jellyfish/atomic_field.hpp -rw-r--r-- root/root 1392 2024-03-19 17:21 ./usr/include/jellyfish/atomic_gcc.hpp -rw-r--r-- root/root 272 2024-03-19 17:21 ./usr/include/jellyfish/backtrace.hpp -rw-r--r-- root/root 6829 2024-03-19 17:21 ./usr/include/jellyfish/binary_dumper.hpp -rw-r--r-- root/root 3480 2024-03-19 17:21 ./usr/include/jellyfish/bloom_common.hpp -rw-r--r-- root/root 6778 2024-03-19 17:21 ./usr/include/jellyfish/bloom_counter2.hpp -rw-r--r-- root/root 5447 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17:21 ./usr/include/jellyfish/stream_iterator.hpp -rw-r--r-- root/root 6318 2024-03-19 17:21 ./usr/include/jellyfish/stream_manager.hpp -rw-r--r-- root/root 2063 2024-03-19 17:21 ./usr/include/jellyfish/text_dumper.hpp -rw-r--r-- root/root 994 2024-03-19 17:21 ./usr/include/jellyfish/thread_exec.hpp -rw-r--r-- root/root 1884 2024-03-19 17:21 ./usr/include/jellyfish/time.hpp -rw-r--r-- root/root 1599 2024-03-19 17:21 ./usr/include/jellyfish/token_ring.hpp -rw-r--r-- root/root 6761 2024-03-19 17:21 ./usr/include/jellyfish/whole_sequence_parser.hpp drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/x86_64-linux-gnu/ -rw-r--r-- root/root 318440 2024-03-19 17:21 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a -rw-r--r-- root/root 1005 2024-03-19 17:21 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.la lrwxrwxrwx root/root 0 2024-03-19 17:21 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so -> libjellyfish-2.0.so.2.0.0 drwxr-xr-x root/root 0 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Team Installed-Size: 373 Depends: libjellyfish-perl (= 2.3.1-3) Section: debug Priority: optional Multi-Arch: same Description: debug symbols for libjellyfish-perl Build-Ids: 4bb9e10add1773dec04194ba836a6419c74113a2 drwxr-xr-x root/root 0 2024-03-19 17:21 ./ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/debug/.build-id/4b/ -rw-r--r-- root/root 371152 2024-03-19 17:21 ./usr/lib/debug/.build-id/4b/b9e10add1773dec04194ba836a6419c74113a2.debug drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/share/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-03-19 17:21 ./usr/share/doc/libjellyfish-perl-dbgsym -> libjellyfish-perl libjellyfish-perl_2.3.1-3_amd64.deb ----------------------------------- new Debian package, version 2.0. size 56812 bytes: control archive=1132 bytes. 1237 bytes, 27 lines control 402 bytes, 5 lines md5sums Package: libjellyfish-perl Source: jellyfish Version: 2.3.1-3 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 176 Depends: perl (>= 5.40.0-6), 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 2024-03-19 17:21 ./ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/x86_64-linux-gnu/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/x86_64-linux-gnu/perl5/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/x86_64-linux-gnu/perl5/5.40/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/x86_64-linux-gnu/perl5/5.40/auto/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/x86_64-linux-gnu/perl5/5.40/auto/jellyfish/ -rw-r--r-- root/root 146664 2024-03-19 17:21 ./usr/lib/x86_64-linux-gnu/perl5/5.40/auto/jellyfish/jellyfish.so drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/share/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/share/doc/libjellyfish-perl/ -rw-r--r-- root/root 2781 2024-03-19 17:21 ./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 2024-03-19 17:21 ./usr/share/perl5/ -rw-r--r-- root/root 7414 2024-03-19 17:21 ./usr/share/perl5/jellyfish.pm python3-dna-jellyfish-dbgsym_2.3.1-3_amd64.deb ---------------------------------------------- new Debian package, version 2.0. size 342344 bytes: control archive=548 bytes. 414 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: python3-dna-jellyfish-dbgsym Source: jellyfish Version: 2.3.1-3 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 367 Depends: python3-dna-jellyfish (= 2.3.1-3) Section: debug Priority: optional Description: debug symbols for python3-dna-jellyfish Build-Ids: 219352060ce69e008b49cc01bf0ad23d85e4b7ce drwxr-xr-x root/root 0 2024-03-19 17:21 ./ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/debug/.build-id/21/ -rw-r--r-- root/root 364712 2024-03-19 17:21 ./usr/lib/debug/.build-id/21/9352060ce69e008b49cc01bf0ad23d85e4b7ce.debug drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/share/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-03-19 17:21 ./usr/share/doc/python3-dna-jellyfish-dbgsym -> python3-dna-jellyfish python3-dna-jellyfish_2.3.1-3_amd64.deb --------------------------------------- new Debian package, version 2.0. size 56636 bytes: control archive=1568 bytes. 1299 bytes, 26 lines control 768 bytes, 8 lines md5sums 289 bytes, 12 lines * postinst #!/bin/sh 402 bytes, 12 lines * prerm #!/bin/sh Package: python3-dna-jellyfish Source: jellyfish Version: 2.3.1-3 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 186 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 2024-03-19 17:21 ./ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/python3/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/python3/dist-packages/ -rw-r--r-- root/root 149784 2024-03-19 17:21 ./usr/lib/python3/dist-packages/_dna_jellyfish.cpython-312-x86_64-linux-gnu.so drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/lib/python3/dist-packages/dna_jellyfish-0.0.1.egg-info/ -rw-r--r-- root/root 127 2024-03-19 17:21 ./usr/lib/python3/dist-packages/dna_jellyfish-0.0.1.egg-info/PKG-INFO -rw-r--r-- root/root 1 2024-03-19 17:21 ./usr/lib/python3/dist-packages/dna_jellyfish-0.0.1.egg-info/dependency_links.txt -rw-r--r-- root/root 29 2024-03-19 17:21 ./usr/lib/python3/dist-packages/dna_jellyfish-0.0.1.egg-info/top_level.txt -rw-r--r-- root/root 12643 2024-03-19 17:21 ./usr/lib/python3/dist-packages/dna_jellyfish.py drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/share/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-19 17:21 ./usr/share/doc/python3-dna-jellyfish/ -rw-r--r-- root/root 2778 2024-03-19 17:21 ./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: full Build-Space: 1825856 Build-Time: 313 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 20 Job: /srv/debomatic/incoming/jellyfish_2.3.1-3.dsc Machine Architecture: amd64 Package: jellyfish Package-Time: 341 Source-Version: 2.3.1-3 Space: 1825856 Status: successful Version: 2.3.1-3 -------------------------------------------------------------------------------- Finished at 2024-10-15T04:29:23Z Build needed 00:05:41, 1825856k disk space