sbuild (Debian sbuild) 0.85.9 (29 May 2024) on carme.larted.org.uk +==============================================================================+ | gbrowse 2.56+dfsg-12 (amd64) Mon, 03 Jun 2024 06:28:54 +0000 | +==============================================================================+ Package: gbrowse Version: 2.56+dfsg-12 Source Version: 2.56+dfsg-12 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-92ee69de-3492-452d-9dc8-8f5ef019f6cd' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup gbrowse_2.56+dfsg-12 perl-5.40-throwaway amd64 --------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup gbrowse_2.56+dfsg-12 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/gbrowse-VzDf4G/resolver-3SjsnA' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3039 B] Get:1 file:/srv/reprepro perl-5.40 InRelease [3039 B] Get:2 file:/srv/reprepro perl-5.40/main amd64 Packages [598 kB] Get:3 http://localhost:3142/debian unstable InRelease [198 kB] Get:4 http://localhost:3142/debian sid InRelease [198 kB] Get:5 http://localhost:3142/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:6 http://localhost:3142/debian unstable/main amd64 Packages T-2024-06-03-0205.12-F-2024-06-03-0205.12.pdiff [9885 B] Get:6 http://localhost:3142/debian unstable/main amd64 Packages T-2024-06-03-0205.12-F-2024-06-03-0205.12.pdiff [9885 B] Get:7 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:8 http://localhost:3142/debian sid/main Sources T-2024-06-03-0205.12-F-2024-06-03-0205.12.pdiff [7265 B] Get:8 http://localhost:3142/debian sid/main Sources T-2024-06-03-0205.12-F-2024-06-03-0205.12.pdiff [7265 B] Fetched 541 kB in 6s (90.3 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: login passwd 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1564 kB of archives. After this operation, 57.3 kB disk space will be freed. Get:1 http://localhost:3142/debian unstable/main amd64 login amd64 1:4.13+dfsg1-5 [590 kB] Get:2 http://localhost:3142/debian unstable/main amd64 passwd amd64 1:4.13+dfsg1-5 [974 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1564 kB in 0s (73.3 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21779 files and directories currently installed.) Preparing to unpack .../login_1%3a4.13+dfsg1-5_amd64.deb ... Unpacking login (1:4.13+dfsg1-5) over (1:4.13+dfsg1-4) ... Setting up login (1:4.13+dfsg1-5) ... Installing new version of config file /etc/pam.d/login ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21765 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.13+dfsg1-5_amd64.deb ... Unpacking passwd (1:4.13+dfsg1-5) over (1:4.13+dfsg1-4) ... Setting up passwd (1:4.13+dfsg1-5) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/gbrowse_2.56+dfsg-12.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/gbrowse-VzDf4G/gbrowse-2.56+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/gbrowse-VzDf4G' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: bioperl, debhelper-compat (= 13), dh-apache2, dh-exec, apache2-dev, libbio-graphics-perl, libbio-coordinate-perl, libbio-db-seqfeature-perl, libcapture-tiny-perl, libcgi-session-perl, libgd-gd2-perl | libgd-gd2-noxpm-perl, libio-string-perl, libjson-perl, libstatistics-descriptive-perl, libwww-perl, libhttp-daemon-perl, perl, sqlite3, libdbd-sqlite3-perl, libterm-readkey-perl, libjs-prototype, libjs-scriptaculous, libvm-ec2-perl, libmodule-build-perl, libcgi-pm-perl, rename, build-essential, fakeroot Filtered Build-Depends: bioperl, debhelper-compat (= 13), dh-apache2, dh-exec, apache2-dev, libbio-graphics-perl, libbio-coordinate-perl, libbio-db-seqfeature-perl, libcapture-tiny-perl, libcgi-session-perl, libgd-gd2-perl, libio-string-perl, libjson-perl, libstatistics-descriptive-perl, libwww-perl, libhttp-daemon-perl, perl, sqlite3, libdbd-sqlite3-perl, libterm-readkey-perl, libjs-prototype, libjs-scriptaculous, libvm-ec2-perl, libmodule-build-perl, libcgi-pm-perl, rename, 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 [615 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [1072 B] Get:5 copy:/<>/apt_archive ./ Packages [1082 B] Fetched 2769 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: apache2-bin apache2-dev autoconf automake autopoint autotools-dev bioperl bsdextrautils ca-certificates debhelper dh-autoreconf dh-exec dh-strip-nondeterminism dwz fakeroot file fontconfig-config fonts-dejavu-core fonts-dejavu-mono gettext gettext-base groff-base intltool-debian libabsl20230802 libalgorithm-diff-perl libanyevent-cachedns-perl libanyevent-http-perl libanyevent-perl libaom3 libapache-dbi-perl libapache2-mod-perl2 libapr1-dev libapr1t64 libaprutil1-dbd-sqlite3 libaprutil1-dev libaprutil1-ldap libaprutil1t64 libarchive-zip-perl libavif16 libbio-coordinate-perl libbio-db-biofetch-perl libbio-db-gff-perl libbio-db-seqfeature-perl libbio-graphics-perl libbio-perl-perl libbrotli1 libbsd0 libcapture-tiny-perl libcgi-pm-perl libcgi-session-perl libclass-data-inheritable-perl libclone-perl libcom-err2 libcommon-sense-perl libcurl4t64 libdata-stag-perl libdav1d7 libdbd-pg-perl libdbd-sqlite3-perl libdbi-perl libde265-0 libdebhelper-perl libdeflate0 libdevel-stacktrace-perl libdevel-symdump-perl libelf1t64 libencode-locale-perl libexception-class-perl libexpat1 libexpat1-dev libexporter-tiny-perl libfakeroot libfile-listing-perl libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgav1-1 libgd-perl libgd3 libgssapi-krb5-2 libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-daemon-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libicu72 libio-html-perl libio-socket-ssl-perl libio-string-perl libjbig0 libjpeg62-turbo libjs-prototype libjs-scriptaculous libjson-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-dev libldap2-dev liblerc4 liblist-moreutils-perl liblist-moreutils-xs-perl liblua5.3-0 liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1t64 libmodule-build-perl libnet-http-perl libnet-ssleay-perl libnghttp2-14 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpipeline1 libpng16-16t64 libpq5 libpsl5t64 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib librav1e0 librtmp1 libsctp-dev libsctp1 libsharpyuv0 libssh2-1t64 libstatistics-descriptive-perl libstring-approx-perl libsub-uplevel-perl libsvtav1enc1d1 libterm-readkey-perl libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl libtiff6 libtimedate-perl libtool libtry-tiny-perl libuchardet0 liburi-perl libvm-ec2-perl libwebp7 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libxpm4 libyuv0 m4 man-db media-types netbase openssl perl-openssl-defaults po-debconf python3 python3-minimal python3.11 python3.11-minimal rename sensible-utils sqlite3 tzdata ucf uuid-dev Suggested packages: apache2-doc apache2-suexec-pristine | apache2-suexec-custom www-browser autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libev-perl libevent-perl libio-async-perl libpoe-perl libtask-weaken-perl libxml-sax-expatxs-perl libmldbm-perl libnet-daemon-perl libsql-statement-perl libgd-tools krb5-doc krb5-user libheif-plugin-ffmpegdec libheif-plugin-jpegdec libheif-plugin-jpegenc libheif-plugin-j2kdec libheif-plugin-j2kenc libheif-plugin-rav1e libheif-plugin-svtenc libdata-dump-perl libcrypt-ssleay-perl lksctp-tools libtool-doc gfortran | fortran95-compiler gcj-jdk libsub-name-perl libbusiness-isbn-perl libregexp-ipv6-perl libauthen-ntlm-perl m4-doc apparmor less libmail-box-perl python3-doc python3-tk python3-venv python3.11-venv python3.11-doc binfmt-support sqlite3-doc Recommended packages: bioperl-run perl-doc libcache-cache-perl libbio-perl-run-perl libyaml-perl libace-perl libxml-twig-perl libset-scalar-perl curl | wget | lynx libalgorithm-diff-xs-perl libasync-interrupt-perl libev-perl | libevent-perl libguard-perl libapache2-reload-perl libbsd-resource-perl libbio-scf-perl libberkeleydb-perl libgd-svg-perl bioperl-run | libbio-perl-run-perl libalgorithm-munkres-perl libarray-compare-perl libbio-asn1-entrezgene-perl libconvert-binary-c-perl libdbd-mysql-perl libgraph-perl libgraphviz-perl libhtml-tableextract-perl libpostscript-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-perl libsvg-graph-perl libxml-dom-xpath-perl libxml-parser-perl libxml-sax-writer-perl libxml-writer-perl libcgi-fast-perl libfreezethaw-perl perl-tk libxml-libxslt-perl libmldbm-perl libxml-perl libarchive-cpio-perl libheif-plugin-aomenc libheif-plugin-x265 libhtml-format-perl libio-compress-brotli-perl javascript-common libjson-xs-perl krb5-locales libmodule-signature-perl libpod-readme-perl libsoftware-license-perl publicsuffix libltdl-dev libdata-dump-perl libhtml-form-perl libmailtools-perl libxml-sax-expat-perl libmail-sendmail-perl The following NEW packages will be installed: apache2-bin apache2-dev autoconf automake autopoint autotools-dev bioperl bsdextrautils ca-certificates debhelper dh-autoreconf dh-exec dh-strip-nondeterminism dwz fakeroot file fontconfig-config fonts-dejavu-core fonts-dejavu-mono gettext gettext-base groff-base intltool-debian libabsl20230802 libalgorithm-diff-perl libanyevent-cachedns-perl libanyevent-http-perl libanyevent-perl libaom3 libapache-dbi-perl libapache2-mod-perl2 libapr1-dev libapr1t64 libaprutil1-dbd-sqlite3 libaprutil1-dev libaprutil1-ldap libaprutil1t64 libarchive-zip-perl libavif16 libbio-coordinate-perl libbio-db-biofetch-perl libbio-db-gff-perl libbio-db-seqfeature-perl libbio-graphics-perl libbio-perl-perl libbrotli1 libbsd0 libcapture-tiny-perl libcgi-pm-perl libcgi-session-perl libclass-data-inheritable-perl libclone-perl libcom-err2 libcommon-sense-perl libcurl4t64 libdata-stag-perl libdav1d7 libdbd-pg-perl libdbd-sqlite3-perl libdbi-perl libde265-0 libdebhelper-perl libdeflate0 libdevel-stacktrace-perl libdevel-symdump-perl libelf1t64 libencode-locale-perl libexception-class-perl libexpat1 libexpat1-dev libexporter-tiny-perl libfakeroot libfile-listing-perl libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgav1-1 libgd-perl libgd3 libgssapi-krb5-2 libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-daemon-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libicu72 libio-html-perl libio-socket-ssl-perl libio-string-perl libjbig0 libjpeg62-turbo libjs-prototype libjs-scriptaculous libjson-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-dev libldap2-dev liblerc4 liblist-moreutils-perl liblist-moreutils-xs-perl liblua5.3-0 liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1t64 libmodule-build-perl libnet-http-perl libnet-ssleay-perl libnghttp2-14 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpipeline1 libpng16-16t64 libpq5 libpsl5t64 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib librav1e0 librtmp1 libsctp-dev libsctp1 libsharpyuv0 libssh2-1t64 libstatistics-descriptive-perl libstring-approx-perl libsub-uplevel-perl libsvtav1enc1d1 libterm-readkey-perl libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl libtiff6 libtimedate-perl libtool libtry-tiny-perl libuchardet0 liburi-perl libvm-ec2-perl libwebp7 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libxpm4 libyuv0 m4 man-db media-types netbase openssl perl-openssl-defaults po-debconf python3 python3-minimal python3.11 python3.11-minimal rename sbuild-build-depends-main-dummy sensible-utils sqlite3 tzdata ucf uuid-dev 0 upgraded, 187 newly installed, 0 to remove and 0 not upgraded. Need to get 53.7 MB/57.6 MB of archives. After this operation, 208 MB of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.40/main amd64 libldap-dev amd64 2.5.17+dfsg-1+b1 [301 kB] Get:2 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [1068 B] Get:3 http://localhost:3142/debian unstable/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get:4 file:/srv/reprepro perl-5.40/main amd64 libanyevent-perl amd64 7.170-2+b6 [384 kB] Get:5 file:/srv/reprepro perl-5.40/main amd64 libcommon-sense-perl amd64 3.75-3+b3 [22.9 kB] Get:6 file:/srv/reprepro perl-5.40/main amd64 libhtml-parser-perl amd64 3.82-1+b1 [99.2 kB] Get:7 file:/srv/reprepro perl-5.40/main amd64 libclone-perl amd64 0.46-1+b3 [13.7 kB] Get:8 file:/srv/reprepro perl-5.40/main amd64 libnet-ssleay-perl amd64 1.94-1+b2 [339 kB] Get:9 http://localhost:3142/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get:10 http://localhost:3142/debian unstable/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get:11 file:/srv/reprepro perl-5.40/main amd64 libapache2-mod-perl2 amd64 2.0.13-1+b4 [810 kB] Get:12 file:/srv/reprepro perl-5.40/main amd64 libdbi-perl amd64 1.643-4+b3 [755 kB] Get:13 http://localhost:3142/debian unstable/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get:14 http://localhost:3142/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get:15 http://localhost:3142/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get:16 http://localhost:3142/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get:17 file:/srv/reprepro perl-5.40/main amd64 libpq5 amd64 16.3-1+b1 [219 kB] Get:18 http://localhost:3142/debian unstable/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get:19 file:/srv/reprepro perl-5.40/main amd64 libdbd-pg-perl amd64 3.18.0-1+b3 [211 kB] Get:20 file:/srv/reprepro perl-5.40/main amd64 libdbd-sqlite3-perl amd64 1.74-1+b3 [175 kB] Get:21 file:/srv/reprepro perl-5.40/main amd64 libgd-perl amd64 2.78-1+b3 [131 kB] Get:22 file:/srv/reprepro perl-5.40/main amd64 liblist-moreutils-xs-perl amd64 0.430-4+b2 [41.7 kB] Get:23 file:/srv/reprepro perl-5.40/main amd64 libstring-approx-perl amd64 3.28-2+b4 [39.0 kB] Get:24 file:/srv/reprepro perl-5.40/main amd64 libterm-readkey-perl amd64 2.38-2+b4 [24.7 kB] Get:25 http://localhost:3142/debian unstable/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get:26 file:/srv/reprepro perl-5.40/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-3+b1 [313 kB] Get:27 http://localhost:3142/debian unstable/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get:28 http://localhost:3142/debian unstable/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get:29 http://localhost:3142/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get:30 http://localhost:3142/debian unstable/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get:31 http://localhost:3142/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get:32 http://localhost:3142/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get:33 http://localhost:3142/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get:34 http://localhost:3142/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get:35 http://localhost:3142/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get:36 http://localhost:3142/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get:37 http://localhost:3142/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get:38 http://localhost:3142/debian unstable/main amd64 bsdextrautils amd64 2.40.1-7 [95.9 kB] Get:39 http://localhost:3142/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get:40 http://localhost:3142/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get:41 http://localhost:3142/debian unstable/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:42 http://localhost:3142/debian unstable/main amd64 libapr1t64 amd64 1.7.2-3.2 [102 kB] Get:43 http://localhost:3142/debian unstable/main amd64 libaprutil1t64 amd64 1.6.3-2 [88.3 kB] Get:44 http://localhost:3142/debian unstable/main amd64 libaprutil1-dbd-sqlite3 amd64 1.6.3-2 [13.8 kB] Get:45 http://localhost:3142/debian unstable/main amd64 libaprutil1-ldap amd64 1.6.3-2 [12.0 kB] Get:46 http://localhost:3142/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get:47 http://localhost:3142/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get:48 http://localhost:3142/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get:49 http://localhost:3142/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get:50 http://localhost:3142/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:51 http://localhost:3142/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get:52 http://localhost:3142/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get:53 http://localhost:3142/debian unstable/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get:54 http://localhost:3142/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:55 http://localhost:3142/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get:56 http://localhost:3142/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-5 [215 kB] Get:57 http://localhost:3142/debian unstable/main amd64 libcurl4t64 amd64 8.8.0-1 [441 kB] Get:58 http://localhost:3142/debian unstable/main amd64 liblua5.3-0 amd64 5.3.6-2+b2 [129 kB] Get:59 http://localhost:3142/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get:60 http://localhost:3142/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-2 [670 kB] Get:61 http://localhost:3142/debian unstable/main amd64 apache2-bin amd64 2.4.59-2 [1382 kB] Get:62 http://localhost:3142/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:63 http://localhost:3142/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:64 http://localhost:3142/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get:65 http://localhost:3142/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:66 http://localhost:3142/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get:67 http://localhost:3142/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get:68 http://localhost:3142/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get:69 http://localhost:3142/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:70 http://localhost:3142/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:71 http://localhost:3142/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:72 http://localhost:3142/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:73 http://localhost:3142/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get:74 http://localhost:3142/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:75 http://localhost:3142/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get:76 http://localhost:3142/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:77 http://localhost:3142/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:78 http://localhost:3142/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get:79 http://localhost:3142/debian unstable/main amd64 uuid-dev amd64 2.40.1-7 [45.9 kB] Get:80 http://localhost:3142/debian unstable/main amd64 libsctp1 amd64 1.0.19+dfsg-2+b1 [26.1 kB] Get:81 http://localhost:3142/debian unstable/main amd64 libsctp-dev amd64 1.0.19+dfsg-2+b1 [68.6 kB] Get:82 http://localhost:3142/debian unstable/main amd64 libapr1-dev amd64 1.7.2-3.2 [771 kB] Get:83 http://localhost:3142/debian unstable/main amd64 libldap2-dev all 2.5.17+dfsg-1 [24.8 kB] Get:84 http://localhost:3142/debian unstable/main amd64 libexpat1-dev amd64 2.6.2-1 [155 kB] Get:85 http://localhost:3142/debian unstable/main amd64 libaprutil1-dev amd64 1.6.3-2 [414 kB] Get:86 http://localhost:3142/debian unstable/main amd64 libpcre2-16-0 amd64 10.42-4+b1 [246 kB] Get:87 http://localhost:3142/debian unstable/main amd64 libpcre2-32-0 amd64 10.42-4+b1 [234 kB] Get:88 http://localhost:3142/debian unstable/main amd64 libpcre2-posix3 amd64 10.42-4+b1 [55.8 kB] Get:89 http://localhost:3142/debian unstable/main amd64 libpcre2-dev amd64 10.42-4+b1 [755 kB] Get:90 http://localhost:3142/debian unstable/main amd64 apache2-dev amd64 2.4.59-2 [311 kB] Get:91 http://localhost:3142/debian unstable/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:92 http://localhost:3142/debian unstable/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get:93 http://localhost:3142/debian unstable/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get:94 http://localhost:3142/debian unstable/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:95 http://localhost:3142/debian unstable/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get:96 http://localhost:3142/debian unstable/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get:97 http://localhost:3142/debian unstable/main amd64 libtest-deep-perl all 1.204-1 [52.9 kB] Get:98 http://localhost:3142/debian unstable/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get:99 http://localhost:3142/debian unstable/main amd64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get:100 http://localhost:3142/debian unstable/main amd64 libtext-diff-perl all 1.45-2 [27.2 kB] Get:101 http://localhost:3142/debian unstable/main amd64 libtest-differences-perl all 0.71-1 [17.9 kB] Get:102 http://localhost:3142/debian unstable/main amd64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get:103 http://localhost:3142/debian unstable/main amd64 libtest-exception-perl all 0.43-3 [16.9 kB] Get:104 http://localhost:3142/debian unstable/main amd64 libtest-warn-perl all 0.37-2 [14.5 kB] Get:105 http://localhost:3142/debian unstable/main amd64 libtest-most-perl all 0.38-1 [25.1 kB] Get:106 http://localhost:3142/debian unstable/main amd64 bioperl all 1.7.8-1 [246 kB] Get:107 http://localhost:3142/debian unstable/main amd64 dh-exec amd64 0.30 [25.6 kB] Get:108 http://localhost:3142/debian unstable/main amd64 libfakeroot amd64 1.34-1 [28.9 kB] Get:109 http://localhost:3142/debian unstable/main amd64 fakeroot amd64 1.34-1 [74.0 kB] Get:110 http://localhost:3142/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:111 http://localhost:3142/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:112 http://localhost:3142/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get:113 http://localhost:3142/debian unstable/main amd64 libabsl20230802 amd64 20230802.1-4 [464 kB] Get:114 http://localhost:3142/debian unstable/main amd64 libanyevent-cachedns-perl all 0.08-3 [7708 B] Get:115 http://localhost:3142/debian unstable/main amd64 libanyevent-http-perl all 2.25-2 [35.2 kB] Get:116 http://localhost:3142/debian unstable/main amd64 libaom3 amd64 3.8.2-2 [1869 kB] Get:117 http://localhost:3142/debian unstable/main amd64 libdevel-symdump-perl all 2.18-5 [15.8 kB] Get:118 http://localhost:3142/debian unstable/main amd64 liburi-perl all 5.28-1 [98.6 kB] Get:119 http://localhost:3142/debian unstable/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:120 http://localhost:3142/debian unstable/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:121 http://localhost:3142/debian unstable/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get:122 http://localhost:3142/debian unstable/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get:123 http://localhost:3142/debian unstable/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get:124 http://localhost:3142/debian unstable/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get:125 http://localhost:3142/debian unstable/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get:126 http://localhost:3142/debian unstable/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:127 http://localhost:3142/debian unstable/main amd64 libhttp-message-perl all 6.46-1 [79.7 kB] Get:128 http://localhost:3142/debian unstable/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get:129 http://localhost:3142/debian unstable/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:130 http://localhost:3142/debian unstable/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get:131 http://localhost:3142/debian unstable/main amd64 libio-socket-ssl-perl all 2.085-1 [218 kB] Get:132 http://localhost:3142/debian unstable/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get:133 http://localhost:3142/debian unstable/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get:134 http://localhost:3142/debian unstable/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get:135 http://localhost:3142/debian unstable/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:136 http://localhost:3142/debian unstable/main amd64 libwww-perl all 6.77-1 [183 kB] Get:137 http://localhost:3142/debian unstable/main amd64 libapache-dbi-perl all 1.12-3 [48.5 kB] Get:138 http://localhost:3142/debian unstable/main amd64 libdav1d7 amd64 1.4.2-1 [551 kB] Get:139 http://localhost:3142/debian unstable/main amd64 libgav1-1 amd64 0.19.0-2+b1 [351 kB] Get:140 http://localhost:3142/debian unstable/main amd64 librav1e0 amd64 0.7.1-2 [900 kB] Get:141 http://localhost:3142/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB] Get:142 http://localhost:3142/debian unstable/main amd64 libsvtav1enc1d1 amd64 1.7.0+dfsg-2+b1 [2169 kB] Get:143 http://localhost:3142/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get:144 http://localhost:3142/debian unstable/main amd64 libyuv0 amd64 0.0.1888.20240509-4 [170 kB] Get:145 http://localhost:3142/debian unstable/main amd64 libavif16 amd64 1.0.4-3 [106 kB] Get:146 http://localhost:3142/debian unstable/main amd64 libbio-coordinate-perl all 1.7.1-4 [56.7 kB] Get:147 http://localhost:3142/debian unstable/main amd64 libbio-db-biofetch-perl all 1.7.3-4 [17.5 kB] Get:148 http://localhost:3142/debian unstable/main amd64 libcgi-pm-perl all 4.64-1 [217 kB] Get:149 http://localhost:3142/debian unstable/main amd64 libbio-db-gff-perl all 1.7.4-1 [273 kB] Get:150 http://localhost:3142/debian unstable/main amd64 libbio-db-seqfeature-perl all 1.7.4-2 [169 kB] Get:151 http://localhost:3142/debian unstable/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get:152 http://localhost:3142/debian unstable/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get:153 http://localhost:3142/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get:154 http://localhost:3142/debian unstable/main amd64 libheif-plugin-dav1d amd64 1.17.6-1+b2 [9856 B] Get:155 http://localhost:3142/debian unstable/main amd64 libde265-0 amd64 1.0.15-1+b1 [187 kB] Get:156 http://localhost:3142/debian unstable/main amd64 libheif-plugin-libde265 amd64 1.17.6-1+b2 [13.1 kB] Get:157 http://localhost:3142/debian unstable/main amd64 libheif1 amd64 1.17.6-1+b2 [284 kB] Get:158 http://localhost:3142/debian unstable/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get:159 http://localhost:3142/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get:160 http://localhost:3142/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get:161 http://localhost:3142/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB] Get:162 http://localhost:3142/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get:163 http://localhost:3142/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get:164 http://localhost:3142/debian unstable/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get:165 http://localhost:3142/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get:166 http://localhost:3142/debian unstable/main amd64 libxcb1 amd64 1.17.0-2 [144 kB] Get:167 http://localhost:3142/debian unstable/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:168 http://localhost:3142/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get:169 http://localhost:3142/debian unstable/main amd64 libxpm4 amd64 1:3.5.17-1+b1 [56.1 kB] Get:170 http://localhost:3142/debian unstable/main amd64 libgd3 amd64 2.3.3-9+b3 [125 kB] Get:171 http://localhost:3142/debian unstable/main amd64 libbio-graphics-perl all 2.40-6 [610 kB] Get:172 http://localhost:3142/debian unstable/main amd64 libcgi-session-perl all 4.48-4 [118 kB] Get:173 http://localhost:3142/debian unstable/main amd64 libexporter-tiny-perl all 1.006002-1 [38.7 kB] Get:174 http://localhost:3142/debian unstable/main amd64 libhttp-daemon-perl all 6.16-1 [23.5 kB] Get:175 http://localhost:3142/debian unstable/main amd64 libjs-prototype all 1.7.3-1 [44.3 kB] Get:176 http://localhost:3142/debian unstable/main amd64 libjs-scriptaculous all 1.9.0-3 [110 kB] Get:177 http://localhost:3142/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get:178 http://localhost:3142/debian unstable/main amd64 liblist-moreutils-perl all 0.430-2 [46.9 kB] Get:179 http://localhost:3142/debian unstable/main amd64 libmodule-build-perl all 0.423400-2 [252 kB] Get:180 http://localhost:3142/debian unstable/main amd64 libstatistics-descriptive-perl all 3.0801-1 [62.8 kB] Get:181 http://localhost:3142/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:182 http://localhost:3142/debian unstable/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:183 http://localhost:3142/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:184 http://localhost:3142/debian unstable/main amd64 libxml-simple-perl all 2.25-2 [69.8 kB] Get:185 http://localhost:3142/debian unstable/main amd64 libvm-ec2-perl all 1.28-4 [760 kB] Get:186 http://localhost:3142/debian unstable/main amd64 rename all 2.02-1 [21.8 kB] Get:187 http://localhost:3142/debian unstable/main amd64 sqlite3 amd64 3.46.0-1 [383 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 53.7 MB in 0s (142 MB/s) Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... 21765 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 22081 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. 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(Reading database ... 23041 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package openssl. Preparing to unpack .../002-openssl_3.2.1-3_amd64.deb ... Unpacking openssl (3.2.1-3) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../003-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../005-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. 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Unpacking libjson-perl (4.10000-1) ... Selecting previously unselected package liblist-moreutils-xs-perl. Preparing to unpack .../162-liblist-moreutils-xs-perl_0.430-4+b2_amd64.deb ... Unpacking liblist-moreutils-xs-perl (0.430-4+b2) ... Selecting previously unselected package liblist-moreutils-perl. Preparing to unpack .../163-liblist-moreutils-perl_0.430-2_all.deb ... Unpacking liblist-moreutils-perl (0.430-2) ... Selecting previously unselected package libmodule-build-perl. Preparing to unpack .../164-libmodule-build-perl_0.423400-2_all.deb ... Adding 'diversion of /usr/bin/config_data to /usr/bin/config_data.diverted by libmodule-build-perl' Adding 'diversion of /usr/share/man/man1/config_data.1.gz to /usr/share/man/man1/config_data.diverted.1.gz by libmodule-build-perl' Unpacking libmodule-build-perl (0.423400-2) ... Selecting previously unselected package libstatistics-descriptive-perl. Preparing to unpack .../165-libstatistics-descriptive-perl_3.0801-1_all.deb ... 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Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up media-types (10.1.0) ... Setting up libanyevent-perl (7.170-2+b6) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up libstring-approx-perl (3.28-2+b4) ... Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... Setting up libaom3:amd64 (3.8.2-2) ... Setting up libxau6:amd64 (1:1.0.9-1+b1) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-4+b1) ... Setting up bsdextrautils (2.40.1-7) ... Setting up libtest-deep-perl (1.204-1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libclone-perl:amd64 (0.46-1+b3) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:amd64 (1.1.0-2+b3) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.61.0-1+b1) ... Setting up libdeflate0:amd64 (1.20-1) ... Setting up perl-openssl-defaults:amd64 (7+b2) ... Setting up libcommon-sense-perl:amd64 (3.75-3+b3) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up gettext-base (0.21-14+b1) ... Setting up libanyevent-http-perl (2.25-2) ... Setting up m4 (1.4.19-4) ... Setting up libencode-locale-perl (1.05-3) ... Setting up rename (2.02-1) ... update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode Setting up libsvtav1enc1d1:amd64 (1.7.0+dfsg-2+b1) ... Setting up libcom-err2:amd64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libjbig0:amd64 (2.1-6.1+b1) ... Setting up librav1e0:amd64 (0.7.1-2) ... Setting up libpcre2-16-0:amd64 (10.42-4+b1) ... Setting up libfakeroot:amd64 (1.34-1) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up libmodule-build-perl (0.423400-2) ... Setting up libkrb5support0:amd64 (1.20.1-6+b1) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Jun 3 06:29:14 UTC 2024. Universal Time is now: Mon Jun 3 06:29:14 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.34-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up libxml-sax-base-perl (1.09-3) ... Setting up libio-string-perl (1.08-4) ... Setting up autotools-dev (20220109.1) ... Setting up libpcre2-32-0:amd64 (10.42-4+b1) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libexpat1-dev:amd64 (2.6.2-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libtext-diff-perl (1.45-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libldap-dev:amd64 (2.5.17+dfsg-1+b1) ... Setting up uuid-dev:amd64 (2.40.1-7) ... Setting up libanyevent-cachedns-perl (0.08-3) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.43-5) ... Setting up libio-html-perl (1.004-3) ... Setting up autopoint (0.21-14) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up liblist-moreutils-xs-perl (0.430-4+b2) ... Setting up libk5crypto3:amd64 (1.20.1-6+b1) ... Setting up libjs-prototype (1.7.3-1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:amd64 (1.4.0-0.1) ... Setting up libcapture-tiny-perl (0.48-2) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libpcre2-posix3:amd64 (10.42-4+b1) ... Setting up dwz (0.15-1+b1) ... Setting up libsctp1:amd64 (1.0.19+dfsg-2+b1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up libdav1d7:amd64 (1.4.2-1) ... Setting up sensible-utils (0.0.22) ... Setting up libtiff6:amd64 (4.5.1+git230720-4) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up liblua5.3-0:amd64 (5.3.6-2+b2) ... Setting up libapr1t64:amd64 (1.7.2-3.2) ... Setting up libjson-perl (4.10000-1) ... Setting up libsub-uplevel-perl (0.2800-3) ... 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 libabsl20230802:amd64 (20230802.1-4) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libkrb5-3:amd64 (1.20.1-6+b1) ... Setting up libdevel-symdump-perl (2.18-5) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libssh2-1t64:amd64 (1.11.0-5) ... Setting up libexporter-tiny-perl (1.006002-1) ... Setting up libterm-readkey-perl (2.38-2+b4) ... Setting up libde265-0:amd64 (1.0.15-1+b1) ... Setting up openssl (3.2.1-3) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up libyuv0:amd64 (0.0.1888.20240509-4) ... Setting up libxml2:amd64 (2.12.7+dfsg-2) ... Setting up liburi-perl (5.28-1) ... Setting up sqlite3 (3.46.0-1) ... Setting up libdbi-perl:amd64 (1.643-4+b3) ... Setting up libnet-ssleay-perl:amd64 (1.94-1+b2) ... 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 libaprutil1t64:amd64 (1.6.3-2) ... Setting up libhttp-date-perl (6.06-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up libxcb1:amd64 (1.17.0-2) ... Setting up gettext (0.21-14+b1) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libpcre2-dev:amd64 (10.42-4+b1) ... Setting up libtool (2.4.7-7) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libjs-scriptaculous (1.9.0-3) ... Setting up liblist-moreutils-perl (0.430-2) ... Setting up libtest-warn-perl (0.37-2) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up libtest-differences-perl (0.71-1) ... Setting up libnet-http-perl (6.23-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libaprutil1-ldap:amd64 (1.6.3-2) ... Setting up libaprutil1-dbd-sqlite3:amd64 (1.6.3-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libldap2-dev (2.5.17+dfsg-1) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libtest-exception-perl (0.43-3) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up libsctp-dev:amd64 (1.0.19+dfsg-2+b1) ... Setting up libgav1-1:amd64 (0.19.0-2+b1) ... Setting up ucf (3.0043+nmu1) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up groff-base (1.23.0-4) ... Setting up libhtml-parser-perl:amd64 (3.82-1+b1) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libdbd-sqlite3-perl:amd64 (1.74-1+b3) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up libio-socket-ssl-perl (2.085-1) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up libhttp-message-perl (6.46-1) ... Setting up python3.11 (3.11.9-1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up libavif16:amd64 (1.0.4-3) ... Setting up libstatistics-descriptive-perl (3.0801-1) ... Setting up libxpm4:amd64 (1:3.5.17-1+b1) ... Setting up libcurl4t64:amd64 (8.8.0-1) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up libtest-most-perl (0.38-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libcgi-pm-perl (4.64-1) ... Setting up libpq5:amd64 (16.3-1+b1) ... Setting up libdbd-pg-perl (3.18.0-1+b3) ... Setting up python3 (3.11.8-1) ... Setting up apache2-bin (2.4.59-2) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-3) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libcgi-session-perl (4.48-4) ... Setting up libapr1-dev (1.7.2-3.2) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-3+b1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libhttp-daemon-perl (6.16-1) ... Setting up libaprutil1-dev (1.6.3-2) ... Setting up bioperl (1.7.8-1) ... Setting up debhelper (13.15.3) ... Setting up dh-exec (0.30) ... Setting up libbio-coordinate-perl (1.7.1-4) ... Setting up libxml-simple-perl (2.25-2) ... Setting up apache2-dev (2.4.59-2) ... Setting up libwww-perl (6.77-1) ... Setting up libapache2-mod-perl2 (2.0.13-1+b4) ... Setting up libbio-db-biofetch-perl (1.7.3-4) ... Setting up libheif-plugin-dav1d:amd64 (1.17.6-1+b2) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libheif-plugin-libde265:amd64 (1.17.6-1+b2) ... Setting up libvm-ec2-perl (1.28-4) ... Setting up libheif1:amd64 (1.17.6-1+b2) ... Setting up libapache-dbi-perl (1.12-3) ... Setting up libgd3:amd64 (2.3.3-9+b3) ... Setting up libbio-db-gff-perl (1.7.4-1) ... Setting up libbio-db-seqfeature-perl (1.7.4-2) ... Setting up libgd-perl (2.78-1+b3) ... Setting up libbio-graphics-perl (2.40-6) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.38-12) ... 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 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) amd64 (x86_64) Toolchain package versions: binutils_2.42-4 dpkg-dev_1.22.6 g++-13_13.2.0-25 gcc-13_13.2.0-25 libc6-dev_2.38-12 libstdc++-13-dev_13.2.0-25 libstdc++6_14.1.0-1 linux-libc-dev_6.8.12-1 Package versions: adduser_3.137 apache2-bin_2.4.59-2 apache2-dev_2.4.59-2 apt_2.9.4 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13.2 base-passwd_3.6.3 bash_5.2.21-2+b1 binutils_2.42-4 binutils-common_2.42-4 binutils-x86-64-linux-gnu_2.42-4 bioperl_1.7.8-1 bsdextrautils_2.40.1-7 bsdutils_1:2.40.1-7 build-essential_12.10 bzip2_1.0.8-5.1 ca-certificates_20240203 coreutils_9.4-3.1 cpp_4:13.2.0-7 cpp-13_13.2.0-25 cpp-13-x86-64-linux-gnu_13.2.0-25 cpp-x86-64-linux-gnu_4:13.2.0-7 dash_0.5.12-8 debconf_1.5.86 debhelper_13.15.3 debian-archive-keyring_2023.4 debianutils_5.17 dh-autoreconf_20 dh-exec_0.30 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.43-7 dpkg_1.22.6 dpkg-dev_1.22.6 dwz_0.15-1+b1 eatmydata_131-2 fakeroot_1.34-1 file_1:5.45-3 findutils_4.9.0-6 fontconfig-config_2.15.0-1.1 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 g++_4:13.2.0-7 g++-13_13.2.0-25 g++-13-x86-64-linux-gnu_13.2.0-25 g++-x86-64-linux-gnu_4:13.2.0-7 gcc_4:13.2.0-7 gcc-13_13.2.0-25 gcc-13-base_13.2.0-25 gcc-13-x86-64-linux-gnu_13.2.0-25 gcc-14-base_14.1.0-1 gcc-x86-64-linux-gnu_4:13.2.0-7 gettext_0.21-14+b1 gettext-base_0.21-14+b1 gnupg_2.2.43-7 gnupg-l10n_2.2.43-7 gnupg-utils_2.2.43-7 gpg_2.2.43-7 gpg-agent_2.2.43-7 gpg-wks-client_2.2.43-7 gpgconf_2.2.43-7 gpgsm_2.2.43-7 gpgv_2.2.43-7 grep_3.11-4 groff-base_1.23.0-4 gzip_1.12-1.1 hostname_3.23+nmu2 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libabsl20230802_20230802.1-4 libacl1_2.3.2-2 libalgorithm-diff-perl_1.201-1 libanyevent-cachedns-perl_0.08-3 libanyevent-http-perl_2.25-2 libanyevent-perl_7.170-2+b6 libaom3_3.8.2-2 libapache-dbi-perl_1.12-3 libapache2-mod-perl2_2.0.13-1+b4 libapr1-dev_1.7.2-3.2 libapr1t64_1.7.2-3.2 libaprutil1-dbd-sqlite3_1.6.3-2 libaprutil1-dev_1.6.3-2 libaprutil1-ldap_1.6.3-2 libaprutil1t64_1.6.3-2 libapt-pkg6.0t64_2.9.4 libarchive-zip-perl_1.68-1 libasan8_14.1.0-1 libassuan0_2.5.6-1+b1 libatomic1_14.1.0-1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-2.1 libaudit1_1:3.1.2-2.1 libavif16_1.0.4-3 libbinutils_2.42-4 libbio-coordinate-perl_1.7.1-4 libbio-db-biofetch-perl_1.7.3-4 libbio-db-gff-perl_1.7.4-1 libbio-db-seqfeature-perl_1.7.4-2 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libsub-uplevel-perl_0.2800-3 libsvtav1enc1d1_1.7.0+dfsg-2+b1 libsystemd0_256~rc3-7 libtasn1-6_4.19.0-3+b2 libterm-readkey-perl_2.38-2+b4 libtest-deep-perl_1.204-1 libtest-differences-perl_0.71-1 libtest-exception-perl_0.43-3 libtest-most-perl_0.38-1 libtest-warn-perl_0.37-2 libtext-diff-perl_1.45-2 libtiff6_4.5.1+git230720-4 libtimedate-perl_2.3300-2 libtinfo6_6.5-2 libtool_2.4.7-7 libtry-tiny-perl_0.31-2 libtsan2_14.1.0-1 libubsan1_14.1.0-1 libuchardet0_0.0.8-1+b1 libudev1_256~rc3-7 libunistring5_1.2-1 liburi-perl_5.28-1 libuuid1_2.40.1-7 libvm-ec2-perl_1.28-4 libwebp7_1.4.0-0.1 libwww-perl_6.77-1 libwww-robotrules-perl_6.02-1 libx11-6_2:1.8.7-1+b1 libx11-data_2:1.8.7-1 libxau6_1:1.0.9-1+b1 libxcb1_1.17.0-2 libxdmcp6_1:1.1.2-3+b1 libxml-libxml-perl_2.0207+dfsg+really+2.0134-3+b1 libxml-namespacesupport-perl_1.12-2 libxml-sax-base-perl_1.09-3 libxml-sax-perl_1.02+dfsg-3 libxml-simple-perl_2.25-2 libxml2_2.12.7+dfsg-2 libxpm4_1:3.5.17-1+b1 libxxhash0_0.8.2-2+b1 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+------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: gbrowse Binary: gbrowse, gbrowse-data, gbrowse-calign Architecture: any all Version: 2.56+dfsg-12 Maintainer: Debian Med Packaging Team Uploaders: Olivier Sallou , Charles Plessy , Aaron M. Ucko , Andreas Tille Homepage: http://gmod.org/wiki/GBrowse Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/gbrowse Vcs-Git: https://salsa.debian.org/med-team/gbrowse.git Testsuite: autopkgtest-pkg-perl Build-Depends: bioperl, debhelper-compat (= 13), dh-apache2, dh-exec, apache2-dev, libbio-graphics-perl, libbio-coordinate-perl, libbio-db-seqfeature-perl, libcapture-tiny-perl, libcgi-session-perl, libgd-gd2-perl | libgd-gd2-noxpm-perl, libio-string-perl, libjson-perl, libstatistics-descriptive-perl, libwww-perl, libhttp-daemon-perl, perl, sqlite3, libdbd-sqlite3-perl, libterm-readkey-perl, libjs-prototype, libjs-scriptaculous, libvm-ec2-perl, libmodule-build-perl, libcgi-pm-perl, rename Package-List: gbrowse deb science optional arch=all gbrowse-calign deb science optional arch=any gbrowse-data deb science optional arch=all Checksums-Sha1: 269fba6b75112b0a2037350308914f05d4747697 4355977 gbrowse_2.56+dfsg.orig.tar.gz 5e72e89de1c1adf2ac189a41ad2611a8775c30a5 24584 gbrowse_2.56+dfsg-12.debian.tar.xz Checksums-Sha256: f6da1ff315b17ec260810cf439a54ae7ddd66728015be03f7fbb6ba795676f81 4355977 gbrowse_2.56+dfsg.orig.tar.gz 4e104a986d7f79ba9d3381909dec5defb4dae011e36b01636de911d92287fed1 24584 gbrowse_2.56+dfsg-12.debian.tar.xz Files: 9638dd3e43897548172911706277f177 4355977 gbrowse_2.56+dfsg.orig.tar.gz cabc4b9cf63c022b8b95e0e73b935951 24584 gbrowse_2.56+dfsg-12.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmVyLnURHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFjtxAAldyMVFMO0Yfrf2gKXYfzw5Ttbo4YYiXs BTpOBU0Vdek1XqLM93YbmwJ9LUCgZT6gLjkVbT6SnWvusH/TtIOPPaoDyo3BSHf4 GdR9xQXUXbbTZ8rSVMFfixiOd2tBZ/R+xeNQcppmtm/STOv4RT9TFu1A+lLkFhHz wpbKMleGT7DOr6sddWD0SUqIIArNA77ngd5KNajWB8FGunqrMWem/E58mUGTX7gS YnM6aea0k9A/VikqXLlu+NMmALM0rgQp9VKKpnpyCR6cDV2bw7wQh0M40wbU7PJg C1/HuWckRSAjgt+IzXRpTVnO+5uWl2hqkk6/+B15Oawj17YiVTepKYSagDPPtlZo 7Gl/CebucsQzeA0wmRIkU/qY10vjo68p8XZqRw10KnIeiaMsCXe3vw//D3DtGt6F +5SJLfUknMixkBLg43NwLkEDhHc3OXz2GYVKMwrQ2zTsekBW+4nPQwa4aNMECxVD IHplhzQD9O3aU+9ibTx1TQGz2UZuQY8CEqaNyHnxe9CLp91wTgIEdRYNKQia78yY P4BBlT0/nXo7pwALa/J44ZPcK7LtvDmVknLaSGAxwJ1jouLtlvdILIRrYN8DHNbD lFW8YiWzmuUT/H4MjbLOYjJiYTSnn2QxGdxcUBdxQuk2Fpsc7xUw7WMXmSYWQvd6 jujaKKQHYio= =SHf0 -----END PGP SIGNATURE----- gpgv: Signature made Thu Dec 7 20:43:33 2023 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./gbrowse_2.56+dfsg-12.dsc: no acceptable signature found dpkg-source: info: extracting gbrowse in /<> dpkg-source: info: unpacking gbrowse_2.56+dfsg.orig.tar.gz dpkg-source: info: unpacking gbrowse_2.56+dfsg-12.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying debian-packaging-patch dpkg-source: info: applying gbrowse-slave-fix_defaults_path dpkg-source: info: applying manpages.patch dpkg-source: info: applying fix_pop_url dpkg-source: info: applying skip_check_installed_test.patch dpkg-source: info: applying source_init_functions dpkg-source: info: applying init_script_dependency.patch dpkg-source: info: applying fix_runlevel.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying fix_whatis_entry.patch dpkg-source: info: applying remove_copy_of_LoadHelper.pm.patch dpkg-source: info: applying fix_gd2_deprecation dpkg-source: info: applying 0001-Build.PL-Seed-random-number-generator-with-SOURCE_DA.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network gbrowse_2.56+dfsg-12 perl-5.40-throwaway amd64 --------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network gbrowse_2.56+dfsg-12 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-92ee69de-3492-452d-9dc8-8f5ef019f6cd 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 gbrowse dpkg-buildpackage: info: source version 2.56+dfsg-12 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with apache2 dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building gbrowse using existing ./gbrowse_2.56+dfsg.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building gbrowse in gbrowse_2.56+dfsg-12.debian.tar.xz dpkg-source: info: building gbrowse in gbrowse_2.56+dfsg-12.dsc debian/rules binary dh binary --with apache2 dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- --conf=/etc/gbrowse --htdocs=/usr/share/gbrowse/htdocs --tmp=/var/cache/gbrowse --databases=/var/lib/gbrowse/databases --cgibin=/usr/lib/cgi-bin/gbrowse --www-user=www-data --registration_done=1 --persistent=/var/lib/gbrowse /usr/bin/perl Build.PL --installdirs vendor --config "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" --config "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" --conf=/etc/gbrowse --htdocs=/usr/share/gbrowse/htdocs --tmp=/var/cache/gbrowse --databases=/var/lib/gbrowse/databases --cgibin=/usr/lib/cgi-bin/gbrowse --www-user=www-data --registration_done=1 --persistent=/var/lib/gbrowse WARNING: the following files are missing in your kit: contrib/ace2gff.pl contrib/AxtPairwise_convert/axt2phy.pl contrib/blast2gff.pl contrib/conf_files/01.yeast.conf contrib/conf_files/02.wormbase.conf contrib/conf_files/03.fly.conf contrib/conf_files/04.human.conf contrib/conf_files/05.embl_proxy.conf contrib/conf_files/06.biosql.conf contrib/conf_files/07.chado.conf contrib/conf_files/08.genbank.conf contrib/conf_files/09.human_karyotype.conf contrib/conf_files/index.html contrib/conf_files/wormbase.syn contrib/Coverage/INSTALL contrib/Coverage/plugin/Coverage.pm contrib/Coverage/README contrib/gdump.pl contrib/GeneFinder/genefinder/gfcode.c contrib/GeneFinder/genefinder/README contrib/GeneFinder/genefinder/readseq.c contrib/GeneFinder/genefinder/readseq.h contrib/GeneFinder/nematode_gftables/cds.hex contrib/GeneFinder/nematode_gftables/gftables contrib/GeneFinder/nematode_gftables/newnem.atg contrib/GeneFinder/nematode_gftables/newnem.codon contrib/GeneFinder/nematode_gftables/newnem.gene contrib/GeneFinder/nematode_gftables/newnem.intron3 contrib/GeneFinder/nematode_gftables/newnem.intron5 contrib/GeneFinder/nematode_gftables/ref.hist contrib/GeneFinder/nematode_gftables/zk637.atg contrib/GeneFinder/nematode_gftables/zk637.intron3 contrib/GeneFinder/nematode_gftables/zk637.intron5 contrib/GeneFinder/nematode_gftables/zk637.trinuc contrib/import_ncbi_mv_hs.pl contrib/install_macosx/BuildConfig.pm contrib/install_macosx/README.html contrib/install_macosx/README.pod contrib/install_macosx/scripts/build-gbrowse.pl contrib/install_macosx/scripts/build-libraries.pl contrib/README contrib/SynView/cgi-lib/DAS/GUS.pm contrib/SynView/cgi-lib/DAS/GUS/Segment.pm contrib/SynView/cgi-lib/DAS/GUS/Segment/Feature.pm contrib/SynView/cgi-lib/DAS/Util/SqlParser.pm contrib/SynView/gbrowse.conf/plasmodb.conf contrib/SynView/gbrowse.conf/plasmodb.xml contrib/SynView/MAL11/MAL11.conf contrib/SynView/MAL11/MAL11.fa contrib/SynView/MAL11/MAL11.gff3 contrib/SynView/README contrib/TextDumper/README contrib/TextDumper/TextDumper.pm lib/Bio/DB/SeqFeature/Store/LoadHelper.pm Please inform the author. Checking prerequisites... recommends: * Bio::DB::BigFile is not installed * Bio::DB::Sam is not installed * Bio::Das is not installed * Crypt::SSLeay is not installed * DBD::mysql is not installed * DB_File::Lock is not installed * FCGI is not installed * File::NFSLock is not installed * GD::SVG is not installed * Net::OpenID::Consumer is not installed * Net::SMTP::SSL is not installed * Parse::Apache::ServerStatus is not installed * Template is not installed * Do not worry if some "recommended" prerequisites are missing. You can install * * them later if you need the features they provide. Do not proceed with the * * install if any of "REQUIRED" prerequisites are missing. * * * * The optional Safe::World module does not currently run on Perl 5.10 or * * higher, and so cannot be installed. * ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation Run 'Build installdeps' to install missing prerequisites. **** WARNING ***************************************************************************************** If you are upgrading from an earlier version of GBrowse and wish to use named user accounts, please set "user_accounts" to 1 in /etc/gbrowse2/GBrowse.conf and run bin/gbrowse_metadb_config.pl to create/update your user account database. See /etc/gbrowse2/GBrowse.conf.new for suggested settings. ****************************************************************************************************** Now run: ./Build test ./Build demo (optional) ./Build install (as superuser/administrator) -or- ./Build install_slave (optional, for slave installations) Other useful targets: ./Build register (to register your copy of GBrowse) ./Build reconfig (to reconfigure install locations) ./Build demostop (to stop the demo) Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'GBrowse' version '2.56' make[1]: Leaving directory '/<>' dh_auto_build /usr/bin/perl Build NOTE: Run ./Build reconfig to change existing configuration. Building GBrowse x86_64-linux-gnu-gcc -I/<>/libalign -I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE '-DVERSION="2.56"' '-DXS_VERSION="2.56"' -fPIC -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE '-D_FILE_OFFSET_BITS=64' -g -O2 '-Werror=implicit-function-declaration' '-ffile-prefix-map=/<>=.' -fstack-protector-strong -fstack-clash-protection -Wformat '-Werror=format-security' -fcf-protection -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' -o lib/Bio/Graphics/Browser2/CAlign.o lib/Bio/Graphics/Browser2/CAlign.c ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/Graphics/Browser2/CAlign/CAlign.bs') 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 -shared -L/usr/local/lib -fstack-protector-strong -o blib/arch/auto/Bio/Graphics/Browser2/CAlign/CAlign.so lib/Bio/Graphics/Browser2/CAlign.o Performing variable substitutions in blib/conf/aws_balancer.conf Performing variable substitutions in blib/conf/detail_select_menu.conf Performing variable substitutions in blib/conf/enzymes.txt Performing variable substitutions in blib/conf/GBrowse.conf Performing variable substitutions in blib/conf/log4perl.conf Performing variable substitutions in blib/conf/MobyServices/moby.conf Performing variable substitutions in blib/conf/pop_demo.conf Performing variable substitutions in blib/conf/renderfarm.conf Performing variable substitutions in blib/conf/slave_preload.conf Performing variable substitutions in blib/conf/submitter_plugin.conf Performing variable substitutions in blib/conf/synteny/oryza.synconf.disabled.conf Performing variable substitutions in blib/conf/synteny/rice_synteny.conf Performing variable substitutions in blib/conf/synteny/wild_rice_synteny.conf Performing variable substitutions in blib/conf/themes/solid_gray_colors Performing variable substitutions in blib/conf/themes/transparent_colors Performing variable substitutions in blib/conf/themes/warm_colors Performing variable substitutions in blib/conf/volvox.conf Performing variable substitutions in blib/conf/yeast_chr1+2.conf Performing variable substitutions in blib/conf/yeast_renderfarm.conf Performing variable substitutions in blib/conf/yeast_simple.conf Performing variable substitutions in blib/htdocs/annotation_help.html Performing variable substitutions in blib/htdocs/cloud_index.html Performing variable substitutions in blib/htdocs/example_scripts/index.html Performing variable substitutions in blib/htdocs/example_scripts/README Performing variable substitutions in blib/htdocs/gbrowse_karyotype_help.html Performing variable substitutions in blib/htdocs/gbrowse_syn_help.html Performing variable substitutions in blib/htdocs/general_help.html Performing variable substitutions in blib/htdocs/index.html Performing variable substitutions in blib/htdocs/tutorial/conf_files/elegans_core.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/elegans_extra.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/HEADER.html Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_final.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_final_withPhylo.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_halfway.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_Phylo.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_quarter.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_refactored.conf Performing variable substitutions in blib/htdocs/tutorial/data_files/HEADER.html Performing variable substitutions in blib/htdocs/tutorial/tutorial.html Performing variable substitutions in blib/htdocs/tutorial/tutorial.phyTreeEdit.html Performing variable substitutions in blib/htdocs/vbox_index.html Use of uninitialized value in pattern match (m//) at /<>/install_util/GBrowseInstall.pm line 778. debian/rules override_dh_auto_test make[1]: Entering directory '/<>' dh_auto_test -- TEST_FILES="t/00.compile.t t/01.yeast.t t/02.rearchitecture.t t/05.deferredrendering.t t/07.balancer.t t/08.calign.t" /usr/bin/perl Build test --verbose 1 "TEST_FILES=t/00.compile.t t/01.yeast.t t/02.rearchitecture.t t/05.deferredrendering.t t/07.balancer.t t/08.calign.t" NOTE: Run ./Build reconfig to change existing configuration. Use of uninitialized value in pattern match (m//) at /<>/install_util/GBrowseInstall.pm line 778. t/00.compile.t ............ ok 1 - cgi-bin/das compiled ok ok 2 - cgi-bin/das stderr said "syntax OK" ok 3 - cgi-bin/das nothing on stdout ok 4 - cgi-bin/gbgff compiled ok ok 5 - cgi-bin/gbgff stderr said "syntax OK" ok 6 - cgi-bin/gbgff nothing on stdout ok 7 - cgi-bin/gbrowse compiled ok ok 8 - cgi-bin/gbrowse stderr said "syntax OK" ok 9 - cgi-bin/gbrowse nothing on stdout ok 10 - cgi-bin/gbrowse_details compiled ok ok 11 - cgi-bin/gbrowse_details stderr said "syntax OK" ok 12 - cgi-bin/gbrowse_details nothing on stdout ok 13 # skip explicitly skipping cgi-bin/gbrowse_gmap ok 14 - cgi-bin/gbrowse_img compiled ok ok 15 - cgi-bin/gbrowse_img stderr said "syntax OK" ok 16 - cgi-bin/gbrowse_img nothing on stdout ok 17 - cgi-bin/gbrowse_key_img compiled ok ok 18 - cgi-bin/gbrowse_key_img stderr said "syntax OK" ok 19 - cgi-bin/gbrowse_key_img nothing on stdout ok 20 - cgi-bin/gbrowse_login compiled ok ok 21 - cgi-bin/gbrowse_login stderr said "syntax OK" ok 22 - cgi-bin/gbrowse_login nothing on stdout ok 23 - cgi-bin/gbrowse_syn compiled ok ok 24 - cgi-bin/gbrowse_syn stderr said "syntax OK" ok 25 - cgi-bin/gbrowse_syn nothing on stdout ok 26 - bin/auto_install_databases.pl compiled ok ok 27 - bin/auto_install_databases.pl stderr said "syntax OK" ok 28 - bin/auto_install_databases.pl nothing on stdout ok 29 - bin/bed2gff3.pl compiled ok ok 30 - bin/bed2gff3.pl stderr said "syntax OK" ok 31 - bin/bed2gff3.pl nothing on stdout ok 32 - bin/bp_load_gff.pl compiled ok ok 33 - bin/bp_load_gff.pl stderr said "syntax OK" ok 34 - bin/bp_load_gff.pl nothing on stdout ok 35 # skip explicitly skipping bin/gbrowse_aws_balancer.pl ok 36 - bin/gbrowse_change_passwd.pl compiled ok ok 37 - bin/gbrowse_change_passwd.pl stderr said "syntax OK" ok 38 - bin/gbrowse_change_passwd.pl nothing on stdout ok 39 - bin/gbrowse_clean.pl compiled ok ok 40 - bin/gbrowse_clean.pl stderr said "syntax OK" ok 41 - bin/gbrowse_clean.pl nothing on stdout ok 42 - bin/gbrowse_configure_slaves.pl compiled ok ok 43 - bin/gbrowse_configure_slaves.pl stderr said "syntax OK" ok 44 - bin/gbrowse_configure_slaves.pl nothing on stdout ok 45 - bin/gbrowse_create_account.pl compiled ok ok 46 - bin/gbrowse_create_account.pl stderr said "syntax OK" ok 47 - bin/gbrowse_create_account.pl nothing on stdout ok 48 # skip explicitly skipping bin/gbrowse_grow_cloud_vol.pl ok 49 - bin/gbrowse_import_ucsc_db.pl compiled ok ok 50 - bin/gbrowse_import_ucsc_db.pl stderr said "syntax OK" ok 51 - bin/gbrowse_import_ucsc_db.pl nothing on stdout ok 52 - bin/gbrowse_metadb_config.pl compiled ok ok 53 - bin/gbrowse_metadb_config.pl stderr said "syntax OK" ok 54 - bin/gbrowse_metadb_config.pl nothing on stdout ok 55 # skip explicitly skipping bin/gbrowse_netinstall.pl ok 56 # skip explicitly skipping bin/gbrowse_netinstall2.pl ok 57 - bin/gbrowse_set_admin_passwd.pl compiled ok ok 58 - bin/gbrowse_set_admin_passwd.pl stderr said "syntax OK" ok 59 - bin/gbrowse_set_admin_passwd.pl nothing on stdout ok 60 - bin/gbrowse_slave compiled ok ok 61 - bin/gbrowse_slave stderr said "syntax OK" ok 62 - bin/gbrowse_slave nothing on stdout ok 63 # skip explicitly skipping bin/gbrowse_slave_start_aws.sh ok 64 - bin/gbrowse_syn_load_alignment_database.pl compiled ok ok 65 - bin/gbrowse_syn_load_alignment_database.pl stderr said "syntax OK" ok 66 - bin/gbrowse_syn_load_alignment_database.pl nothing on stdout ok 67 - bin/gbrowse_syn_load_alignments_msa.pl compiled ok ok 68 - bin/gbrowse_syn_load_alignments_msa.pl stderr said "syntax OK" ok 69 - bin/gbrowse_syn_load_alignments_msa.pl nothing on stdout ok 70 # skip explicitly skipping bin/gbrowse_sync_aws_slave.pl ok 71 - bin/gtf2gff3.pl compiled ok ok 72 - bin/gtf2gff3.pl stderr said "syntax OK" ok 73 - bin/gtf2gff3.pl nothing on stdout ok 74 - bin/load_genbank.pl compiled ok ok 75 - bin/load_genbank.pl stderr said "syntax OK" ok 76 - bin/load_genbank.pl nothing on stdout ok 77 # skip explicitly skipping bin/make_das_conf.pl ok 78 - bin/process_bamfiles.pl compiled ok ok 79 - bin/process_bamfiles.pl stderr said "syntax OK" ok 80 - bin/process_bamfiles.pl nothing on stdout ok 81 - bin/process_gadfly.pl compiled ok ok 82 - bin/process_gadfly.pl stderr said "syntax OK" ok 83 - bin/process_gadfly.pl nothing on stdout ok 84 - bin/process_ncbi_human.pl compiled ok ok 85 - bin/process_ncbi_human.pl stderr said "syntax OK" ok 86 - bin/process_ncbi_human.pl nothing on stdout ok 87 - bin/process_sgd.pl compiled ok ok 88 - bin/process_sgd.pl stderr said "syntax OK" ok 89 - bin/process_sgd.pl nothing on stdout ok 90 - bin/report_missing_language_tags.pl compiled ok ok 91 - bin/report_missing_language_tags.pl stderr said "syntax OK" ok 92 - bin/report_missing_language_tags.pl nothing on stdout ok 93 - bin/scan_gbrowse.pl compiled ok ok 94 - bin/scan_gbrowse.pl stderr said "syntax OK" ok 95 - bin/scan_gbrowse.pl nothing on stdout ok 96 - bin/split_wig.pl compiled ok ok 97 - bin/split_wig.pl stderr said "syntax OK" ok 98 - bin/split_wig.pl nothing on stdout ok 99 - bin/ucsc_genes2gff.pl compiled ok ok 100 - bin/ucsc_genes2gff.pl stderr said "syntax OK" ok 101 - bin/ucsc_genes2gff.pl nothing on stdout ok 102 - bin/wiggle2gff3.pl compiled ok ok 103 - bin/wiggle2gff3.pl stderr said "syntax OK" ok 104 - bin/wiggle2gff3.pl nothing on stdout 1..104 ok Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. t/01.yeast.t .............. 1..7 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok t/02.rearchitecture.t ..... 1..90 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value $_[5] in pack at /usr/share/perl5/Bio/DB/IndexedBase.pm line 1005, line 2. Use of uninitialized value $_[5] in pack at /usr/share/perl5/Bio/DB/IndexedBase.pm line 1005, line 2. t/03.render.t ............. 1..150 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok Sometimes this test gets 'stuck'. If this happens, kill the test and Build test again. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Can't locate object method "png" via package "\x{89}PNG\r\n\32\n\0\0\0\rIHDR\0\0\3z\0\0\0E\4\3\0\0\0î\x{b9}\x{89}\x{ae}\0\0\0\17PLTEõÞ\x{b3}àÿÿ\0ÿÿÓÓÓ\0\0\0(âÐç\0\0\0\tpHYs\0"..."-Iî\35\x{ab}wémô\x{f7}é\x{b8}\37V/É]Õk\x{8d}\x{ab}ê\x{95}\x{ac}U=UOÕ;Ã!ÃåÁY\x{ab}zª\x{9e}ªw\x{86}C\x{86}Ë\x{83}\x{b3}VõT=Uï\f"... (perhaps you forgot to load "\x{89}PNG\r\n\32\n\0\0\0\rIHDR\0\0\3z\0\0\0E\4\3\0\0\0î\x{b9}\x{89}\x{ae}\0\0\0\17PLTEõÞ\x{b3}àÿÿ\0ÿÿÓÓÓ\0\0\0(âÐç\0\0\0\tpHYs\0"..."-Iî\35\x{ab}wémô\x{f7}é\x{b8}\37V/É]Õk\x{8d}\x{ab}ê\x{95}\x{ac}U=UOÕ;Ã!ÃåÁY\x{ab}zª\x{9e}ªw\x{86}C\x{86}Ë\x{83}\x{b3}VõT=Uï\f"...?) at /<>/t/../lib/Bio/Graphics/Browser2/CachedTrack.pm line 154, <> line 45. Can't locate object method "png" via package "\x{89}PNG\r\n\32\n\0\0\0\rIHDR\0\0\3z\0\0\0E\4\3\0\0\0î\x{b9}\x{89}\x{ae}\0\0\0\17PLTEõÞ\x{b3}àÿÿ\0ÿÿ\0\0\0ÓÓÓ|ü3C\0\0\0\tpHYs\0"..."\177ÞÛô>0\x{bd}[\x{bf}\x{8d}þ\x{be}<ï\x{9b}é\25\x{bd}+\x{bd}Þy\x{95}\36W\x{ad}ô\x{94}\x{9e}Ò\x{bb}â!áÕEU+=\x{a5}\x{a7}ô\x{ae}xHx"... (perhaps you forgot to load "\x{89}PNG\r\n\32\n\0\0\0\rIHDR\0\0\3z\0\0\0E\4\3\0\0\0î\x{b9}\x{89}\x{ae}\0\0\0\17PLTEõÞ\x{b3}àÿÿ\0ÿÿ\0\0\0ÓÓÓ|ü3C\0\0\0\tpHYs\0"..."\177ÞÛô>0\x{bd}[\x{bf}\x{8d}þ\x{be}<ï\x{9b}é\25\x{bd}+\x{bd}Þy\x{95}\36W\x{ad}ô\x{94}\x{9e}Ò\x{bb}â!áÕEU+=\x{a5}\x{a7}ô\x{ae}xHx"...?) at /<>/t/../lib/Bio/Graphics/Browser2/CachedTrack.pm line 154, <> line 45. t/04.remoteserver.t ....... 1..43 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Can't locate object method "png" via package "\x{89}PNG\r\n\32\n\0\0\0\rIHDR\0\0\3z\0\0\0E\4\3\0\0\0î\x{b9}\x{89}\x{ae}\0\0\0\17PLTEõÞ\x{b3}àÿÿ\0ÿÿÓÓÓ\0\0\0(âÐç\0\0\0\tpHYs\0"..."-Iî\35\x{ab}wémô\x{f7}é\x{b8}\37V/É]Õk\x{8d}\x{ab}ê\x{95}\x{ac}U=UOÕ;Ã!ÃåÁY\x{ab}zª\x{9e}ªw\x{86}C\x{86}Ë\x{83}\x{b3}VõT=Uï\f"... (perhaps you forgot to load "\x{89}PNG\r\n\32\n\0\0\0\rIHDR\0\0\3z\0\0\0E\4\3\0\0\0î\x{b9}\x{89}\x{ae}\0\0\0\17PLTEõÞ\x{b3}àÿÿ\0ÿÿÓÓÓ\0\0\0(âÐç\0\0\0\tpHYs\0"..."-Iî\35\x{ab}wémô\x{f7}é\x{b8}\37V/É]Õk\x{8d}\x{ab}ê\x{95}\x{ac}U=UOÕ;Ã!ÃåÁY\x{ab}zª\x{9e}ªw\x{86}C\x{86}Ë\x{83}\x{b3}VõT=Uï\f"...?) at /<>/t/../lib/Bio/Graphics/Browser2/CachedTrack.pm line 154, <> line 45. Can't locate object method "png" via package "\x{89}PNG\r\n\32\n\0\0\0\rIHDR\0\0\3z\0\0\0E\4\3\0\0\0î\x{b9}\x{89}\x{ae}\0\0\0\17PLTEõÞ\x{b3}àÿÿ\0ÿÿ\0\0\0ÓÓÓ|ü3C\0\0\0\tpHYs\0"..."\177ÞÛô>0\x{bd}[\x{bf}\x{8d}þ\x{be}<ï\x{9b}é\25\x{bd}+\x{bd}Þy\x{95}\36W\x{ad}ô\x{94}\x{9e}Ò\x{bb}â!áÕEU+=\x{a5}\x{a7}ô\x{ae}xHx"... (perhaps you forgot to load "\x{89}PNG\r\n\32\n\0\0\0\rIHDR\0\0\3z\0\0\0E\4\3\0\0\0î\x{b9}\x{89}\x{ae}\0\0\0\17PLTEõÞ\x{b3}àÿÿ\0ÿÿ\0\0\0ÓÓÓ|ü3C\0\0\0\tpHYs\0"..."\177ÞÛô>0\x{bd}[\x{bf}\x{8d}þ\x{be}<ï\x{9b}é\25\x{bd}+\x{bd}Þy\x{95}\36W\x{ad}ô\x{94}\x{9e}Ò\x{bb}â!áÕEU+=\x{a5}\x{a7}ô\x{ae}xHx"...?) at /<>/t/../lib/Bio/Graphics/Browser2/CachedTrack.pm line 154, <> line 45. t/05.deferredrendering.t .. 1..19 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781. t/06.featuresearch.t ...... 1..26 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok t/07.balancer.t ........... skipped: Optional module Parse::Apache::ServerStatus not installed t/07.karyotype.t .......... 1..3 ok 1 ok 2 ok 3 ok t/08.calign.t ............. 1..6 # Running under perl version 5.040000 for linux # Current time local: Mon Jun 3 06:29:37 2024 # Current time GMT: Mon Jun 3 06:29:37 2024 # Using Test.pm version 1.31 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok All tests successful. Files=10, Tests=448, 15 wallclock secs ( 0.07 usr 0.01 sys + 8.56 cusr 2.99 csys = 11.63 CPU) Result: PASS make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_installdirs make[1]: Entering directory '/<>' # svn(-buildpackage) seems to ignore the x bit chmod +x debian/gbrowse-calign.dirs dh_installdirs make[1]: Leaving directory '/<>' debian/rules override_dh_auto_install make[1]: Entering directory '/<>' ./Build --install_base=debian/gbrowse debianinstall NOTE: Run ./Build reconfig to change existing configuration. Use of uninitialized value in pattern match (m//) at /<>/install_util/GBrowseInstall.pm line 778. Building GBrowse Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/auto/Bio/Graphics/Browser2/CAlign/CAlign.so Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/auto/Bio/Graphics/Browser2/CAlign/CAlign.bs Installing debian/gbrowse/man/man1/make_das_conf.pl.1p Installing debian/gbrowse/man/man1/load_genbank.pl.1p Installing debian/gbrowse/man/man1/gbrowse_sync_aws_slave.pl.1p Installing debian/gbrowse/man/man1/bed2gff3.pl.1p Installing debian/gbrowse/man/man1/wiggle2gff3.pl.1p Installing debian/gbrowse/man/man1/ucsc_genes2gff.pl.1p Installing debian/gbrowse/man/man1/gbrowse_clean.pl.1p Installing debian/gbrowse/man/man1/gtf2gff3.pl.1p Installing debian/gbrowse/man/man1/gbrowse_aws_balancer.pl.1p Installing debian/gbrowse/man/man1/gbrowse_grow_cloud_vol.pl.1p Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_gmap Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_img Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbgff Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_key_img Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_details Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_syn Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/das Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_login Installing debian/gbrowse/etc/gbrowse/aws_balancer.conf Installing debian/gbrowse/etc/gbrowse/enzymes.txt Installing debian/gbrowse/etc/gbrowse/volvox.conf Installing debian/gbrowse/etc/gbrowse/yeast_chr1+2.conf Installing debian/gbrowse/etc/gbrowse/yeast_simple.conf Installing debian/gbrowse/etc/gbrowse/yeast_renderfarm.conf Installing debian/gbrowse/etc/gbrowse/pop_demo.conf Installing debian/gbrowse/etc/gbrowse/slave_preload.conf Installing debian/gbrowse/etc/gbrowse/GBrowse.conf Installing debian/gbrowse/etc/gbrowse/submitter_plugin.conf Installing debian/gbrowse/etc/gbrowse/detail_select_menu.conf Installing debian/gbrowse/etc/gbrowse/log4perl.conf Installing debian/gbrowse/etc/gbrowse/renderfarm.conf Installing debian/gbrowse/etc/gbrowse/languages/ko.pm Installing debian/gbrowse/etc/gbrowse/languages/POSIX.pm Installing debian/gbrowse/etc/gbrowse/languages/fr.pm Installing debian/gbrowse/etc/gbrowse/languages/de.pm Installing debian/gbrowse/etc/gbrowse/languages/zh.pm Installing debian/gbrowse/etc/gbrowse/languages/pl.pm Installing debian/gbrowse/etc/gbrowse/languages/zh_cn.pm Installing debian/gbrowse/etc/gbrowse/languages/es.pm Installing debian/gbrowse/etc/gbrowse/languages/en.pm Installing debian/gbrowse/etc/gbrowse/languages/it.pm Installing debian/gbrowse/etc/gbrowse/languages/ja.pm Installing debian/gbrowse/etc/gbrowse/languages/nl.pm Installing debian/gbrowse/etc/gbrowse/languages/is.pm Installing debian/gbrowse/etc/gbrowse/languages/ru.pm Installing debian/gbrowse/etc/gbrowse/themes/transparent_colors Installing debian/gbrowse/etc/gbrowse/themes/solid_gray_colors Installing debian/gbrowse/etc/gbrowse/themes/warm_colors Installing debian/gbrowse/etc/gbrowse/synteny/rice_synteny.conf Installing debian/gbrowse/etc/gbrowse/synteny/oryza.synconf.disabled.conf Installing debian/gbrowse/etc/gbrowse/synteny/wild_rice_synteny.conf Installing debian/gbrowse/etc/gbrowse/MobyServices/text_html_renderer.pm Installing debian/gbrowse/etc/gbrowse/MobyServices/b64_encoded_gif_renderer.pm Installing debian/gbrowse/etc/gbrowse/MobyServices/text_xml_renderer.pm Installing debian/gbrowse/etc/gbrowse/MobyServices/GbrowseServices.PMS Installing debian/gbrowse/etc/gbrowse/MobyServices/moby.conf Installing debian/gbrowse/etc/gbrowse/MobyServices/text_plain_renderer.pm Installing debian/gbrowse/etc/gbrowse/MobyServices/b64_encoded_jpeg_renderer.pm Installing debian/gbrowse/etc/gbrowse/MobyServices/text_formatted_renderer.pm Installing debian/gbrowse/etc/gbrowse/MobyServices/GbrowseServices.pm Installing debian/gbrowse/etc/gbrowse/plugins/SequenceDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/AlignTwoSequences.pm Installing debian/gbrowse/etc/gbrowse/plugins/FilterTest.pm Installing debian/gbrowse/etc/gbrowse/plugins/ProteinDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/CMapDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/TestFinder.pm Installing debian/gbrowse/etc/gbrowse/plugins/LDAPAuthenticate.pm Installing debian/gbrowse/etc/gbrowse/plugins/RestrictionAnnotator.pm Installing debian/gbrowse/etc/gbrowse/plugins/TestAuthenticator.pm Installing debian/gbrowse/etc/gbrowse/plugins/BatchDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/Spectrogram.pm Installing debian/gbrowse/etc/gbrowse/plugins/Blat.pm Installing debian/gbrowse/etc/gbrowse/plugins/SourceTrackFinder.pm Installing debian/gbrowse/etc/gbrowse/plugins/RandomGene.pm Installing debian/gbrowse/etc/gbrowse/plugins/GeneFinder.pm Installing debian/gbrowse/etc/gbrowse/plugins/FBTableDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/OligoFinder.pm Installing debian/gbrowse/etc/gbrowse/plugins/PamAuthenticate.pm Installing debian/gbrowse/etc/gbrowse/plugins/AttributeHiliter.pm Installing debian/gbrowse/etc/gbrowse/plugins/test.pm Installing debian/gbrowse/etc/gbrowse/plugins/SinWave.pm Installing debian/gbrowse/etc/gbrowse/plugins/Submitter.pm Installing debian/gbrowse/etc/gbrowse/plugins/SimpleTrackFinder.pm Installing debian/gbrowse/etc/gbrowse/plugins/FastaDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/Aligner.pm Installing debian/gbrowse/etc/gbrowse/plugins/TrackDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/CreateBlastDB.pm Installing debian/gbrowse/etc/gbrowse/plugins/TrackFinder.pm Installing debian/gbrowse/etc/gbrowse/plugins/PrimerDesigner.pm Installing debian/gbrowse/var/lib/gbrowse/databases/ideograms/mouse_cytobands.gff Installing debian/gbrowse/var/lib/gbrowse/databases/ideograms/rat_cytobands.gff Installing debian/gbrowse/var/lib/gbrowse/databases/ideograms/human_cytobands.gff Installing debian/gbrowse/var/lib/gbrowse/databases/pop_demo/pop_demo.gff3 Installing debian/gbrowse/var/lib/gbrowse/databases/admin_uploads/README Installing debian/gbrowse/var/lib/gbrowse/databases/yeast_chr1+2/yeast_chr1+2.gff3 Installing debian/gbrowse/var/lib/gbrowse/databases/yeast_chr1+2/dummy.fa Installing debian/gbrowse/var/lib/gbrowse/databases/gbrowse_syn/alignments/rice.aln.gz Installing debian/gbrowse/var/lib/gbrowse/databases/gbrowse_syn/wild_rice/wild_rice.gff3 Installing debian/gbrowse/var/lib/gbrowse/databases/gbrowse_syn/rice/rice.gff3 Installing debian/gbrowse/var/lib/gbrowse/databases/yeast_scaffolds/chr1.fa Installing debian/gbrowse/var/lib/gbrowse/databases/yeast_scaffolds/chr2.fa Installing debian/gbrowse/var/lib/gbrowse/databases/yeast_scaffolds/chromosomes.gff3 Installing 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debian/gbrowse/man/man3/Bio::Graphics::Browser2::GFFhelper.3pm Installing debian/gbrowse/man/man3/GBrowse::ConfigData.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render::Slave::AWS_Balancer.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::PadAlignment.3pm Installing debian/gbrowse/man/man3/Bio::DB::SeqFeature::Store::Alias.3pm Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RegionSearch.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render::Slave::Status.3pm Installing debian/gbrowse/man/man3/Legacy::Graphics::Browser.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::CAlign.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Markup.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Realign.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::OptionPick.3pm Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Util.3pm Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataLoader::useq.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataBase.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RemoteSet.3pm Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::match_gap.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Plugin.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::PluginSet.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RenderPanels.3pm Installing debian/gbrowse/man/man3/CGI::Toggle.3pm Installing debian/gbrowse/man/man3/Bio::DB::Tagger.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Region.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Plugin::AuthPlugin.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataLoader::archive.3pm Installing debian/gbrowse/bin/scan_gbrowse.pl Installing debian/gbrowse/bin/gbrowse_import_ucsc_db.pl Installing debian/gbrowse/bin/gbrowse_grow_cloud_vol.pl Installing debian/gbrowse/bin/gbrowse_set_admin_passwd.pl Installing debian/gbrowse/bin/wiggle2gff3.pl Installing debian/gbrowse/bin/bed2gff3.pl Installing debian/gbrowse/bin/gbrowse_create_account.pl Installing debian/gbrowse/bin/load_genbank.pl Installing debian/gbrowse/bin/gbrowse_clean.pl Installing debian/gbrowse/bin/gbrowse_aws_balancer.pl Installing debian/gbrowse/bin/gbrowse_change_passwd.pl Installing debian/gbrowse/bin/gbrowse_metadb_config.pl Installing debian/gbrowse/bin/gbrowse_syn_load_alignment_database.pl Installing debian/gbrowse/bin/make_das_conf.pl Installing debian/gbrowse/bin/gbrowse_slave Installing debian/gbrowse/bin/ucsc_genes2gff.pl Installing debian/gbrowse/bin/gtf2gff3.pl Installing debian/gbrowse/bin/gbrowse_sync_aws_slave.pl Installing debian/gbrowse/bin/gbrowse_syn_load_alignments_msa.pl Installing debian/gbrowse/bin/gbrowse_configure_slaves.pl #./Build apache_conf > debian/gbrowse/etc/gbrowse/gbrowse_apache2.conf perl Build.PL --conf=/etc/gbrowse --htdocs=/usr/share/gbrowse/htdocs --tmp=/var/cache/gbrowse --databases=/var/lib/gbrowse/databases --cgibin=/usr/lib/cgi-bin/gbrowse --www-user=www-data --registration_done=1 --persistent=/var/lib/gbrowse --installetc=y WARNING: the following files are missing in your kit: contrib/ace2gff.pl contrib/AxtPairwise_convert/axt2phy.pl contrib/blast2gff.pl contrib/conf_files/01.yeast.conf contrib/conf_files/02.wormbase.conf contrib/conf_files/03.fly.conf contrib/conf_files/04.human.conf contrib/conf_files/05.embl_proxy.conf contrib/conf_files/06.biosql.conf contrib/conf_files/07.chado.conf contrib/conf_files/08.genbank.conf contrib/conf_files/09.human_karyotype.conf contrib/conf_files/index.html contrib/conf_files/wormbase.syn contrib/Coverage/INSTALL contrib/Coverage/plugin/Coverage.pm contrib/Coverage/README contrib/gdump.pl contrib/GeneFinder/genefinder/gfcode.c contrib/GeneFinder/genefinder/README contrib/GeneFinder/genefinder/readseq.c contrib/GeneFinder/genefinder/readseq.h contrib/GeneFinder/nematode_gftables/cds.hex contrib/GeneFinder/nematode_gftables/gftables contrib/GeneFinder/nematode_gftables/newnem.atg contrib/GeneFinder/nematode_gftables/newnem.codon contrib/GeneFinder/nematode_gftables/newnem.gene contrib/GeneFinder/nematode_gftables/newnem.intron3 contrib/GeneFinder/nematode_gftables/newnem.intron5 contrib/GeneFinder/nematode_gftables/ref.hist contrib/GeneFinder/nematode_gftables/zk637.atg contrib/GeneFinder/nematode_gftables/zk637.intron3 contrib/GeneFinder/nematode_gftables/zk637.intron5 contrib/GeneFinder/nematode_gftables/zk637.trinuc contrib/import_ncbi_mv_hs.pl contrib/install_macosx/BuildConfig.pm contrib/install_macosx/README.html contrib/install_macosx/README.pod contrib/install_macosx/scripts/build-gbrowse.pl contrib/install_macosx/scripts/build-libraries.pl contrib/README contrib/SynView/cgi-lib/DAS/GUS.pm contrib/SynView/cgi-lib/DAS/GUS/Segment.pm contrib/SynView/cgi-lib/DAS/GUS/Segment/Feature.pm contrib/SynView/cgi-lib/DAS/Util/SqlParser.pm contrib/SynView/gbrowse.conf/plasmodb.conf contrib/SynView/gbrowse.conf/plasmodb.xml contrib/SynView/MAL11/MAL11.conf contrib/SynView/MAL11/MAL11.fa contrib/SynView/MAL11/MAL11.gff3 contrib/SynView/README contrib/TextDumper/README contrib/TextDumper/TextDumper.pm lib/Bio/DB/SeqFeature/Store/LoadHelper.pm Please inform the author. Checking prerequisites... recommends: * Bio::DB::BigFile is not installed * Bio::DB::Sam is not installed * Bio::Das is not installed * Crypt::SSLeay is not installed * DBD::mysql is not installed * DB_File::Lock is not installed * FCGI is not installed * File::NFSLock is not installed * GD::SVG is not installed * Net::OpenID::Consumer is not installed * Net::SMTP::SSL is not installed * Parse::Apache::ServerStatus is not installed * Template is not installed * Do not worry if some "recommended" prerequisites are missing. You can install * * them later if you need the features they provide. Do not proceed with the * * install if any of "REQUIRED" prerequisites are missing. * * * * The optional Safe::World module does not currently run on Perl 5.10 or * * higher, and so cannot be installed. * ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation Run 'Build installdeps' to install missing prerequisites. **** WARNING ***************************************************************************************** If you are upgrading from an earlier version of GBrowse and wish to use named user accounts, please set "user_accounts" to 1 in /etc/gbrowse2/GBrowse.conf and run bin/gbrowse_metadb_config.pl to create/update your user account database. See /etc/gbrowse2/GBrowse.conf.new for suggested settings. ****************************************************************************************************** NOTE: Run ./Build reconfig to change existing configuration. Now run: ./Build test ./Build demo (optional) ./Build install (as superuser/administrator) -or- ./Build install_slave (optional, for slave installations) Other useful targets: ./Build register (to register your copy of GBrowse) ./Build reconfig (to reconfigure install locations) ./Build demostop (to stop the demo) Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'GBrowse' version '2.56' ./Build --install_base=debian/gbrowse install_slave NOTE: Run ./Build reconfig to change existing configuration. Performing variable substitutions in blib/conf/aws_balancer.conf Performing variable substitutions in blib/conf/detail_select_menu.conf Performing variable substitutions in blib/conf/enzymes.txt Performing variable substitutions in blib/conf/GBrowse.conf Performing variable substitutions in blib/conf/log4perl.conf Performing variable substitutions in blib/conf/MobyServices/moby.conf Performing variable substitutions in blib/conf/pop_demo.conf Performing variable substitutions in blib/conf/renderfarm.conf Performing variable substitutions in blib/conf/slave_preload.conf Performing variable substitutions in blib/conf/submitter_plugin.conf Performing variable substitutions in blib/conf/synteny/oryza.synconf.disabled.conf Performing variable substitutions in blib/conf/synteny/rice_synteny.conf Performing variable substitutions in blib/conf/synteny/wild_rice_synteny.conf Performing variable substitutions in blib/conf/themes/solid_gray_colors Performing variable substitutions in blib/conf/themes/transparent_colors Performing variable substitutions in blib/conf/themes/warm_colors Performing variable substitutions in blib/conf/volvox.conf Performing variable substitutions in blib/conf/yeast_chr1+2.conf Performing variable substitutions in blib/conf/yeast_renderfarm.conf Performing variable substitutions in blib/conf/yeast_simple.conf Performing variable substitutions in blib/htdocs/annotation_help.html Performing variable substitutions in blib/htdocs/cloud_index.html Performing variable substitutions in blib/htdocs/example_scripts/index.html Performing variable substitutions in blib/htdocs/example_scripts/README Performing variable substitutions in blib/htdocs/gbrowse_karyotype_help.html Performing variable substitutions in blib/htdocs/gbrowse_syn_help.html Performing variable substitutions in blib/htdocs/general_help.html Performing variable substitutions in blib/htdocs/index.html Performing variable substitutions in blib/htdocs/tutorial/conf_files/elegans_core.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/elegans_extra.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/HEADER.html Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_final.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_final_withPhylo.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_halfway.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_Phylo.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_quarter.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_refactored.conf Performing variable substitutions in blib/htdocs/tutorial/data_files/HEADER.html Performing variable substitutions in blib/htdocs/tutorial/tutorial.html Performing variable substitutions in blib/htdocs/tutorial/tutorial.phyTreeEdit.html Performing variable substitutions in blib/htdocs/vbox_index.html Performing variable substitutions in blib/etc/default/gbrowse-aws-balancer Use of uninitialized value $wwwuser in substitution (s///) at /<>/install_util/GBrowseInstall.pm line 871, line 10. Performing variable substitutions in blib/etc/default/gbrowse-slave Performing variable substitutions in blib/etc/init.d/gbrowse-aws-balancer Performing variable substitutions in blib/etc/init.d/gbrowse-slave Use of uninitialized value $wwwuser in substitution (s///) at /<>/install_util/GBrowseInstall.pm line 871, line 20. Building GBrowse Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing debian/gbrowse/etc/init.d/gbrowse-slave Installing debian/gbrowse/etc/init.d/gbrowse-aws-balancer Installing debian/gbrowse/etc/default/gbrowse-slave Installing debian/gbrowse/etc/default/gbrowse-aws-balancer Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/GBrowse/ConfigData.pm mv debian/gbrowse/lib/perl5/* debian/gbrowse/usr/share/perl5 # Remove arch dependant data mkdir -p debian/gbrowse-calign/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/Bio/Graphics/Browser2/CAlign/ mkdir -p debian/gbrowse-calign/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Graphics/Browser2/ mv debian/gbrowse/usr/share/perl5/auto/Bio/Graphics/Browser2/CAlign/* debian/gbrowse-calign/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/Bio/Graphics/Browser2/CAlign/ mv debian/gbrowse/usr/share/perl5/Bio/Graphics/Browser2/CAlign.pm debian/gbrowse-calign/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Graphics/Browser2/CAlign.pm rm -rf debian/gbrowse/lib rm -f debian/gbrowse/usr/share/doc/gbrowse/INSTALL rm -f debian/gbrowse/usr/share/perl5/auto/GBrowse/.packlist rm -f debian/gbrowse/usr/share/gbrowse/htdocs/js/prototype.js rm -f debian/gbrowse/usr/share/gbrowse/htdocs/js/scriptaculous.js chmod 644 debian/gbrowse/etc/gbrowse/MobyServices/text_xml_renderer.pm chmod 644 debian/gbrowse/etc/gbrowse/synteny/oryza.synconf.disabled.conf #Remove database (kept as separate package) rm -rf debian/gbrowse/var/lib/gbrowse/databases/* #Rename pl scripts in bin file-rename 's/\.pl//' debian/gbrowse/bin/*.pl mv debian/gbrowse/bin debian/gbrowse/usr/bin # Activate configuration files. find /<>/debian/gbrowse/etc -name '*.new' | xargs file-rename 's/.new//' rm -rf /<>/debian/gbrowse/usr/share/perl5/auto # Update conf files sed -i 's/gbrowse2/gbrowse/g' /<>/debian/gbrowse/etc/gbrowse/yeast*.conf sed -i 's/gbrowse2/gbrowse/g' /<>/debian/gbrowse/etc/gbrowse/slave*.conf # move OpenID constumer secret to /etc/gbrowse to make it system admin configurable mv /<>/debian/gbrowse/usr/share/perl5/GBrowse/ConfigData.pm /<>/debian/gbrowse/etc/gbrowse/ConfigData.pm make[1]: Leaving directory '/<>' dh_install dh_apache2 dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/<>' #Rename due to perl extension seen as polish file-rename 's/\.pl\.1p/\.1p/' debian/gbrowse/man/man1/*.pl.1p mkdir -p debian/gbrowse-calign/man/man3/ mv debian/gbrowse/man/man3/Bio::Graphics::Browser2::CAlign.3pm debian/gbrowse-calign/man/man3/Bio::Graphics::Browser2::CAlign.3pm dh_installman rm -rf debian/gbrowse/man rm -rf debian/gbrowse-calign/man make[1]: Leaving directory '/<>' dh_lintian dh_perl debian/rules override_dh_link make[1]: Entering directory '/<>' dh_link # Fix broken link ... even if I habe no idea what a link to a not existing dir should serve for ln -sf /var/cache/gbrowse/images debian/gbrowse/usr/share/gbrowse/htdocs/i make[1]: Leaving directory '/<>' dh_strip_nondeterminism dh_strip_nondeterminism: warning: Ignoring unwritable file: menulink_active.png dh_strip_nondeterminism: warning: Ignoring unwritable file: menulink.png dh_strip_nondeterminism: warning: Ignoring unwritable file: pattern3.png dh_strip_nondeterminism: warning: Ignoring unwritable file: pattern2.png dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-right-open.png dh_strip_nondeterminism: warning: Ignoring unwritable file: icon.png dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-down-on.png dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-right-on.png dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-left-on.png dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-down.png dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-up.png dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-left-open.png dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-up-on.png dh_strip_nondeterminism: warning: Ignoring unwritable file: pattern1.png dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-left.png dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-down-open.png dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-up-open.png dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-right.png dh_strip_nondeterminism: warning: Ignoring unwritable file: balloon.png dh_strip_nondeterminism: warning: Ignoring unwritable file: balloon_ie.png dh_strip_nondeterminism: warning: Ignoring unwritable file: down_right.png dh_strip_nondeterminism: warning: Ignoring unwritable file: up_right.png dh_strip_nondeterminism: warning: Ignoring unwritable file: up_left.png dh_strip_nondeterminism: warning: Ignoring unwritable file: close.png dh_strip_nondeterminism: warning: Ignoring unwritable file: down_left.png dh_strip_nondeterminism: warning: Ignoring unwritable file: balloon.png dh_strip_nondeterminism: warning: Ignoring unwritable file: down_right.png dh_strip_nondeterminism: warning: Ignoring unwritable file: up_right.png dh_strip_nondeterminism: warning: Ignoring unwritable file: up_left.png dh_strip_nondeterminism: warning: Ignoring unwritable file: close.png dh_strip_nondeterminism: warning: Ignoring unwritable file: down_left.png dh_strip_nondeterminism: warning: Ignoring unwritable file: worm_telomeric_spec.png dh_strip_nondeterminism: warning: Ignoring unwritable file: upload_list.png dh_strip_nondeterminism: warning: Ignoring unwritable file: overview+detail.png dh_strip_nondeterminism: warning: Ignoring unwritable file: detail.png dh_strip_nondeterminism: warning: Ignoring unwritable file: worm_exons_spec.png dh_strip_nondeterminism: warning: Ignoring unwritable file: sugarcane_sorghum_synteny.png dh_strip_nondeterminism: warning: Ignoring unwritable file: navbar.png dh_strip_nondeterminism: warning: Ignoring unwritable file: upload_field.png dh_strip_nondeterminism: warning: Ignoring unwritable file: upload.png dh_strip_nondeterminism: warning: Ignoring unwritable file: multiple_hits.png dh_strip_nondeterminism: warning: Ignoring unwritable file: remote.png dh_strip_nondeterminism: warning: Ignoring unwritable file: landmark.png dh_strip_nondeterminism: warning: Ignoring unwritable file: yeast_I_genes_spec.png dh_strip_nondeterminism: warning: Ignoring unwritable file: detail_scale.png dh_strip_nondeterminism: warning: Ignoring unwritable file: myopenid-logo.png dh_strip_nondeterminism: warning: Ignoring unwritable file: aim-logo.png dh_strip_nondeterminism: warning: Ignoring unwritable file: livejournal-logo.png dh_strip_nondeterminism: warning: Ignoring unwritable file: yahoo-logo.png dh_strip_nondeterminism: warning: Ignoring unwritable file: blogspot-logo.png dh_strip_nondeterminism: warning: Ignoring unwritable file: ruler.png dh_strip_nondeterminism: warning: Ignoring unwritable file: grey_0.4_pixel.png dh_strip_nondeterminism: warning: Ignoring unwritable file: fmini_2.png dh_strip_nondeterminism: warning: Ignoring unwritable file: ficon_2.png dh_strip_nondeterminism: warning: Ignoring unwritable file: empty.png dh_strip_nondeterminism: warning: Ignoring unwritable file: mplus.png dh_strip_nondeterminism: warning: Ignoring unwritable file: panright2.png dh_strip_nondeterminism: warning: Ignoring unwritable file: query.png dh_strip_nondeterminism: warning: Ignoring unwritable file: snap_mail.png dh_strip_nondeterminism: warning: Ignoring unwritable file: snap_ex.png dh_strip_nondeterminism: warning: Ignoring unwritable file: menu.png dh_strip_nondeterminism: warning: Ignoring unwritable file: mminus.png dh_strip_nondeterminism: warning: Ignoring unwritable file: panright.png dh_strip_nondeterminism: warning: Ignoring unwritable file: panleft2.png dh_strip_nondeterminism: warning: Ignoring unwritable file: minus12.png dh_strip_nondeterminism: warning: Ignoring unwritable file: opacity_thumb.png dh_strip_nondeterminism: warning: Ignoring unwritable file: pop_out.png dh_strip_nondeterminism: warning: Ignoring unwritable file: tools.png dh_strip_nondeterminism: warning: Ignoring unwritable file: square.png dh_strip_nondeterminism: warning: Ignoring unwritable file: ex.png dh_strip_nondeterminism: warning: Ignoring unwritable file: blue_peaks.png dh_strip_nondeterminism: warning: Ignoring unwritable file: ruler-icon.png dh_strip_nondeterminism: warning: Ignoring unwritable file: plus.png dh_strip_nondeterminism: warning: Ignoring unwritable file: snap_down.png dh_strip_nondeterminism: warning: Ignoring unwritable file: pop_in.png dh_strip_nondeterminism: warning: Ignoring unwritable file: snap_share.png dh_strip_nondeterminism: warning: Ignoring unwritable file: grey.png dh_strip_nondeterminism: warning: Ignoring unwritable file: ficon.png dh_strip_nondeterminism: warning: Ignoring unwritable file: trash.png dh_strip_nondeterminism: warning: Ignoring unwritable file: share.png dh_strip_nondeterminism: warning: Ignoring unwritable file: dark_0.4_pixel.png dh_strip_nondeterminism: warning: Ignoring unwritable file: snap_check.png dh_strip_nondeterminism: warning: Ignoring unwritable file: panleft.png dh_strip_nondeterminism: warning: Ignoring unwritable file: red_peaks.png dh_strip_nondeterminism: warning: Ignoring unwritable file: check.png dh_strip_nondeterminism: warning: Ignoring unwritable file: download.png dh_strip_nondeterminism: warning: Ignoring unwritable file: minus.png dh_strip_nondeterminism: warning: Ignoring unwritable file: open_open.png dh_strip_nondeterminism: warning: Ignoring unwritable file: dna2.png dh_strip_nondeterminism: warning: Ignoring unwritable file: wiggle_density.png dh_strip_nondeterminism: warning: Ignoring unwritable file: trace1.png dh_strip_nondeterminism: warning: Ignoring unwritable file: categorytable.png dh_strip_nondeterminism: warning: Ignoring unwritable file: dna1.png dh_strip_nondeterminism: warning: Ignoring unwritable file: trace2.png dh_strip_nondeterminism: warning: Ignoring unwritable file: config_editing.png dh_strip_nondeterminism: warning: Ignoring unwritable file: setting_popup.png dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'gbrowse-calign' in '../gbrowse-calign_2.56+dfsg-12_amd64.deb'. dpkg-deb: building package 'gbrowse' in '../gbrowse_2.56+dfsg-12_all.deb'. dpkg-deb: building package 'gbrowse-calign-dbgsym' in '../gbrowse-calign-dbgsym_2.56+dfsg-12_amd64.deb'. dpkg-deb: building package 'gbrowse-data' in '../gbrowse-data_2.56+dfsg-12_all.deb'. dpkg-genbuildinfo -O../gbrowse_2.56+dfsg-12_amd64.buildinfo dpkg-genchanges -O../gbrowse_2.56+dfsg-12_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 2024-06-03T06:29:46Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ gbrowse_2.56+dfsg-12_amd64.changes: ----------------------------------- Format: 1.8 Date: Thu, 07 Dec 2023 21:40:51 +0100 Source: gbrowse Binary: gbrowse gbrowse-calign gbrowse-calign-dbgsym gbrowse-data Architecture: source amd64 all Version: 2.56+dfsg-12 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: gbrowse - GMOD Generic Genome Browser gbrowse-calign - CAlign helper gbrowse-data - Sample data to use GBrowse Closes: 1037272 1044196 Changes: gbrowse (2.56+dfsg-12) unstable; urgency=medium . [ Vagrant Cascadian ] * Build reproducibly Closes: #1037272 . [ Andreas Tille ] * Standards-Version: 4.6.2 (routine-update) * Remove trailing whitespace in debian/changelog (routine-update) * Drop dependency lsb-base * Fix clean target Closes: #1044196 Checksums-Sha1: 192c489b8f464f53d8024b6565679edf2c971e4d 1766 gbrowse_2.56+dfsg-12.dsc 5e72e89de1c1adf2ac189a41ad2611a8775c30a5 24584 gbrowse_2.56+dfsg-12.debian.tar.xz f291be028cf775f25cd7447cd62b80c75a49fcda 31368 gbrowse-calign-dbgsym_2.56+dfsg-12_amd64.deb 309a5419f21f5a3e297264125a3ca10bf271f659 34192 gbrowse-calign_2.56+dfsg-12_amd64.deb 11274cc3b0bf7b22be4c88c45d4f4e3f7e11d57d 1233348 gbrowse-data_2.56+dfsg-12_all.deb 791dba18dfb5c761d474048fa6ef237fae3e8ff5 2334240 gbrowse_2.56+dfsg-12_all.deb 63cd3587d2b4806ffa2fedd26c72d709cd84f063 11109 gbrowse_2.56+dfsg-12_amd64.buildinfo Checksums-Sha256: 2f85ab72094ee13ad87c8310c660ae83751c6abca66ee7bf1dc7f7f29d352a5c 1766 gbrowse_2.56+dfsg-12.dsc 4e104a986d7f79ba9d3381909dec5defb4dae011e36b01636de911d92287fed1 24584 gbrowse_2.56+dfsg-12.debian.tar.xz 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gbrowse_2.56+dfsg-12.dsc f291be028cf775f25cd7447cd62b80c75a49fcda 31368 gbrowse-calign-dbgsym_2.56+dfsg-12_amd64.deb 309a5419f21f5a3e297264125a3ca10bf271f659 34192 gbrowse-calign_2.56+dfsg-12_amd64.deb 11274cc3b0bf7b22be4c88c45d4f4e3f7e11d57d 1233348 gbrowse-data_2.56+dfsg-12_all.deb 791dba18dfb5c761d474048fa6ef237fae3e8ff5 2334240 gbrowse_2.56+dfsg-12_all.deb Checksums-Sha256: 2f85ab72094ee13ad87c8310c660ae83751c6abca66ee7bf1dc7f7f29d352a5c 1766 gbrowse_2.56+dfsg-12.dsc 5c8abd062af2fe4f9c600d0ee521b74f577c13b689489b6bedcce181370759cf 31368 gbrowse-calign-dbgsym_2.56+dfsg-12_amd64.deb ce11d36ce10de3e24c98d6059e39e0d88502053b05d9a5f2c06e54b4a6e852b7 34192 gbrowse-calign_2.56+dfsg-12_amd64.deb f9e972178360a951c392f7a4879dd5c7a1431b5eca87d0a1ce5008287eeb0948 1233348 gbrowse-data_2.56+dfsg-12_all.deb 74b884f7f5264dc6fac6773da085f565496674527c13b73b8d79ab0b9a895378 2334240 gbrowse_2.56+dfsg-12_all.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 03 Jun 2024 06:29:45 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: apache2-bin (= 2.4.59-2), apache2-dev (= 2.4.59-2), autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-14), autotools-dev (= 20220109.1), base-files (= 13.2), base-passwd (= 3.6.3), bash (= 5.2.21-2+b1), binutils (= 2.42-4), binutils-common (= 2.42-4), binutils-x86-64-linux-gnu (= 2.42-4), bioperl (= 1.7.8-1), bsdextrautils (= 2.40.1-7), bsdutils (= 1:2.40.1-7), build-essential (= 12.10), bzip2 (= 1.0.8-5.1), ca-certificates (= 20240203), coreutils (= 9.4-3.1), cpp (= 4:13.2.0-7), cpp-13 (= 13.2.0-25), cpp-13-x86-64-linux-gnu (= 13.2.0-25), cpp-x86-64-linux-gnu (= 4:13.2.0-7), dash (= 0.5.12-8), debconf (= 1.5.86), debhelper (= 13.15.3), debianutils (= 5.17), dh-autoreconf (= 20), dh-exec (= 0.30), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-1), dpkg (= 1.22.6), dpkg-dev (= 1.22.6), dwz (= 0.15-1+b1), file (= 1:5.45-3), findutils (= 4.9.0-6), fontconfig-config (= 2.15.0-1.1), fonts-dejavu-core (= 2.37-8), fonts-dejavu-mono (= 2.37-8), g++ (= 4:13.2.0-7), g++-13 (= 13.2.0-25), g++-13-x86-64-linux-gnu (= 13.2.0-25), g++-x86-64-linux-gnu (= 4:13.2.0-7), gcc (= 4:13.2.0-7), gcc-13 (= 13.2.0-25), gcc-13-base (= 13.2.0-25), gcc-13-x86-64-linux-gnu (= 13.2.0-25), gcc-14-base (= 14.1.0-1), gcc-x86-64-linux-gnu (= 4:13.2.0-7), gettext (= 0.21-14+b1), gettext-base (= 0.21-14+b1), grep (= 3.11-4), groff-base (= 1.23.0-4), gzip (= 1.12-1.1), hostname (= 3.23+nmu2), init-system-helpers (= 1.66), intltool-debian (= 0.35.0+20060710.6), libabsl20230802 (= 20230802.1-4), libacl1 (= 2.3.2-2), libalgorithm-diff-perl (= 1.201-1), libanyevent-cachedns-perl (= 0.08-3), libanyevent-http-perl (= 2.25-2), libanyevent-perl (= 7.170-2+b6), libaom3 (= 3.8.2-2), libapache-dbi-perl (= 1.12-3), libapache2-mod-perl2 (= 2.0.13-1+b4), libapr1-dev (= 1.7.2-3.2), libapr1t64 (= 1.7.2-3.2), libaprutil1-dbd-sqlite3 (= 1.6.3-2), libaprutil1-dev (= 1.6.3-2), libaprutil1-ldap (= 1.6.3-2), libaprutil1t64 (= 1.6.3-2), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.1.0-1), libatomic1 (= 14.1.0-1), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-2.1), libaudit1 (= 1:3.1.2-2.1), libavif16 (= 1.0.4-3), libbinutils (= 2.42-4), libbio-coordinate-perl (= 1.7.1-4), libbio-db-biofetch-perl (= 1.7.3-4), libbio-db-gff-perl (= 1.7.4-1), libbio-db-seqfeature-perl (= 1.7.4-2), libbio-graphics-perl (= 2.40-6), libbio-perl-perl (= 1.7.8-1), libblkid1 (= 2.40.1-7), libbrotli1 (= 1.1.0-2+b3), libbsd0 (= 0.12.2-1), libbz2-1.0 (= 1.0.8-5.1), libc-bin (= 2.38-12), libc-dev-bin (= 2.38-12), libc6 (= 2.38-12), libc6-dev (= 2.38-12), libcap-ng0 (= 0.8.5-1), libcap2 (= 1:2.66-5), libcapture-tiny-perl (= 0.48-2), libcc1-0 (= 14.1.0-1), libcgi-pm-perl (= 4.64-1), libcgi-session-perl (= 4.48-4), libclass-data-inheritable-perl (= 0.08-3), libclone-perl (= 0.46-1+b3), libcom-err2 (= 1.47.1-1), libcommon-sense-perl (= 3.75-3+b3), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.42-4), libctf0 (= 2.42-4), libcurl4t64 (= 8.8.0-1), libdata-stag-perl (= 0.14-3), libdav1d7 (= 1.4.2-1), libdb5.3t64 (= 5.3.28+dfsg2-7), libdbd-pg-perl (= 3.18.0-1+b3), libdbd-sqlite3-perl (= 1.74-1+b3), libdbi-perl (= 1.643-4+b3), libde265-0 (= 1.0.15-1+b1), libdebconfclient0 (= 0.272), libdebhelper-perl (= 13.15.3), libdeflate0 (= 1.20-1), libdevel-stacktrace-perl (= 2.0500-1), libdevel-symdump-perl (= 2.18-5), libdpkg-perl (= 1.22.6), libelf1t64 (= 0.191-1+b1), libencode-locale-perl (= 1.05-3), libexception-class-perl (= 1.45-1), libexpat1 (= 2.6.2-1), libexpat1-dev (= 2.6.2-1), libexporter-tiny-perl (= 1.006002-1), libffi8 (= 3.4.6-1), libfile-listing-perl (= 6.16-1), libfile-stripnondeterminism-perl (= 1.14.0-1), libfontconfig1 (= 2.15.0-1.1), libfreetype6 (= 2.13.2+dfsg-1+b4), libgav1-1 (= 0.19.0-2+b1), libgcc-13-dev (= 13.2.0-25), libgcc-s1 (= 14.1.0-1), libgd-perl (= 2.78-1+b3), libgd3 (= 2.3.3-9+b3), libgdbm-compat4t64 (= 1.23-5.1+b1), libgdbm6t64 (= 1.23-5.1+b1), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgnutls30t64 (= 3.8.5-4), libgomp1 (= 14.1.0-1), libgprofng0 (= 2.42-4), libgssapi-krb5-2 (= 1.20.1-6+b1), libheif-plugin-dav1d (= 1.17.6-1+b2), libheif-plugin-libde265 (= 1.17.6-1+b2), libheif1 (= 1.17.6-1+b2), libhogweed6t64 (= 3.9.1-2.2), libhtml-parser-perl (= 3.82-1+b1), libhtml-tagset-perl (= 3.24-1), libhtml-tree-perl (= 5.07-3), libhttp-cookies-perl (= 6.11-1), libhttp-daemon-perl (= 6.16-1), libhttp-date-perl (= 6.06-1), libhttp-message-perl (= 6.46-1), libhttp-negotiate-perl (= 6.01-2), libhwasan0 (= 14.1.0-1), libicu72 (= 72.1-4+b1), libidn2-0 (= 2.3.7-2), libio-html-perl (= 1.004-3), libio-socket-ssl-perl (= 2.085-1), libio-string-perl (= 1.08-4), libisl23 (= 0.26-3+b2), libitm1 (= 14.1.0-1), libjansson4 (= 2.14-2+b2), libjbig0 (= 2.1-6.1+b1), libjpeg62-turbo (= 1:2.1.5-3), libjs-prototype (= 1.7.3-1), libjs-scriptaculous (= 1.9.0-3), libjson-perl (= 4.10000-1), libk5crypto3 (= 1.20.1-6+b1), libkeyutils1 (= 1.6.3-3), libkrb5-3 (= 1.20.1-6+b1), libkrb5support0 (= 1.20.1-6+b1), libldap-2.5-0 (= 2.5.17+dfsg-1+b1), libldap-dev (= 2.5.17+dfsg-1+b1), libldap2-dev (= 2.5.17+dfsg-1), liblerc4 (= 4.0.0+ds-4+b1), liblist-moreutils-perl (= 0.430-2), liblist-moreutils-xs-perl (= 0.430-4+b2), liblsan0 (= 14.1.0-1), liblua5.3-0 (= 5.3.6-2+b2), liblwp-mediatypes-perl (= 6.04-2), liblwp-protocol-https-perl (= 6.14-1), liblzma5 (= 5.6.1+really5.4.5-1), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmd0 (= 1.1.0-2), libmodule-build-perl (= 0.423400-2), libmount1 (= 2.40.1-7), libmpc3 (= 1.3.1-1+b2), libmpfr6 (= 4.2.1-1+b1), libncursesw6 (= 6.5-2), libnet-http-perl (= 6.23-1), libnet-ssleay-perl (= 1.94-1+b2), libnettle8t64 (= 3.9.1-2.2), libnghttp2-14 (= 1.61.0-1+b1), libp11-kit0 (= 0.25.3-5), libpam-modules (= 1.5.3-7), libpam-modules-bin (= 1.5.3-7), libpam-runtime (= 1.5.3-7), libpam0g (= 1.5.3-7), libpcre2-16-0 (= 10.42-4+b1), libpcre2-32-0 (= 10.42-4+b1), libpcre2-8-0 (= 10.42-4+b1), libpcre2-dev (= 10.42-4+b1), libpcre2-posix3 (= 10.42-4+b1), libperl5.40 (= 5.40.0~rc1-1), libpipeline1 (= 1.5.7-2), libpng16-16t64 (= 1.6.43-5), libpq5 (= 16.3-1+b1), libpsl5t64 (= 0.21.2-1.1), libpython3-stdlib (= 3.11.8-1), libpython3.11-minimal (= 3.11.9-1), libpython3.11-stdlib (= 3.11.9-1), libquadmath0 (= 14.1.0-1), librav1e0 (= 0.7.1-2), libreadline8t64 (= 8.2-4), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b4), libsasl2-2 (= 2.1.28+dfsg1-6), libsasl2-modules-db (= 2.1.28+dfsg1-6), libsctp-dev (= 1.0.19+dfsg-2+b1), libsctp1 (= 1.0.19+dfsg-2+b1), libseccomp2 (= 2.5.5-1), libselinux1 (= 3.5-2+b2), libsframe1 (= 2.42-4), libsharpyuv0 (= 1.4.0-0.1), libsmartcols1 (= 2.40.1-7), libsqlite3-0 (= 3.46.0-1), libssh2-1t64 (= 1.11.0-5), libssl3t64 (= 3.2.1-3), libstatistics-descriptive-perl (= 3.0801-1), libstdc++-13-dev (= 13.2.0-25), libstdc++6 (= 14.1.0-1), libstring-approx-perl (= 3.28-2+b4), libsub-uplevel-perl (= 0.2800-3), libsvtav1enc1d1 (= 1.7.0+dfsg-2+b1), libsystemd0 (= 256~rc3-7), libtasn1-6 (= 4.19.0-3+b2), libterm-readkey-perl (= 2.38-2+b4), libtest-deep-perl (= 1.204-1), libtest-differences-perl (= 0.71-1), libtest-exception-perl (= 0.43-3), libtest-most-perl (= 0.38-1), libtest-warn-perl (= 0.37-2), libtext-diff-perl (= 1.45-2), libtiff6 (= 4.5.1+git230720-4), libtimedate-perl (= 2.3300-2), libtinfo6 (= 6.5-2), libtool (= 2.4.7-7), libtry-tiny-perl (= 0.31-2), libtsan2 (= 14.1.0-1), libubsan1 (= 14.1.0-1), libuchardet0 (= 0.0.8-1+b1), libudev1 (= 256~rc3-7), libunistring5 (= 1.2-1), liburi-perl (= 5.28-1), libuuid1 (= 2.40.1-7), libvm-ec2-perl (= 1.28-4), libwebp7 (= 1.4.0-0.1), libwww-perl (= 6.77-1), libwww-robotrules-perl (= 6.02-1), libx11-6 (= 2:1.8.7-1+b1), libx11-data (= 2:1.8.7-1), libxau6 (= 1:1.0.9-1+b1), libxcb1 (= 1.17.0-2), libxdmcp6 (= 1:1.1.2-3+b1), libxml-libxml-perl (= 2.0207+dfsg+really+2.0134-3+b1), libxml-namespacesupport-perl (= 1.12-2), libxml-sax-base-perl (= 1.09-3), libxml-sax-perl (= 1.02+dfsg-3), libxml-simple-perl (= 2.25-2), libxml2 (= 2.12.7+dfsg-2), libxpm4 (= 1:3.5.17-1+b1), libyuv0 (= 0.0.1888.20240509-4), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.8.12-1), login (= 1:4.13+dfsg1-5), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.12.1-1), mawk (= 1.3.4.20240123-1), media-types (= 10.1.0), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2), netbase (= 6.4), openssl (= 3.2.1-3), patch (= 2.7.6-7), perl (= 5.40.0~rc1-1), perl-base (= 5.40.0~rc1-1), perl-modules-5.40 (= 5.40.0~rc1-1), perl-openssl-defaults (= 7+b2), po-debconf (= 1.0.21+nmu1), python3 (= 3.11.8-1), python3-minimal (= 3.11.8-1), python3.11 (= 3.11.9-1), python3.11-minimal (= 3.11.9-1), readline-common (= 8.2-4), rename (= 2.02-1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.22), sqlite3 (= 3.46.0-1), sysvinit-utils (= 3.09-1), tar (= 1.35+dfsg-3), tzdata (= 2024a-4), ucf (= 3.0043+nmu1), usr-is-merged (= 39), util-linux (= 2.40.1-7), uuid-dev (= 2.40.1-7), xz-utils (= 5.6.1+really5.4.5-1), zlib1g (= 1:1.3.dfsg+really1.3.1-1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="en_GB.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1701981651" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ gbrowse-calign-dbgsym_2.56+dfsg-12_amd64.deb -------------------------------------------- new Debian package, version 2.0. size 31368 bytes: control archive=556 bytes. 417 bytes, 13 lines control 106 bytes, 1 lines md5sums Package: gbrowse-calign-dbgsym Source: gbrowse Version: 2.56+dfsg-12 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 44 Depends: gbrowse-calign (= 2.56+dfsg-12) Section: debug Priority: optional Multi-Arch: same Description: debug symbols for gbrowse-calign Build-Ids: 89dc5d6a50640f0e0f544779a491b066b2c11325 drwxr-xr-x root/root 0 2023-12-07 20:40 ./ drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/lib/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/lib/debug/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/lib/debug/.build-id/89/ -rw-r--r-- root/root 34264 2023-12-07 20:40 ./usr/lib/debug/.build-id/89/dc5d6a50640f0e0f544779a491b066b2c11325.debug drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/share/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/share/doc/ lrwxrwxrwx root/root 0 2023-12-07 20:40 ./usr/share/doc/gbrowse-calign-dbgsym -> gbrowse-calign gbrowse-calign_2.56+dfsg-12_amd64.deb ------------------------------------- new Debian package, version 2.0. size 34192 bytes: control archive=960 bytes. 653 bytes, 18 lines control 654 bytes, 7 lines md5sums Package: gbrowse-calign Source: gbrowse Version: 2.56+dfsg-12 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 78 Depends: perl (>= 5.40.0~rc1-1), perlapi-5.40.0, libc6 (>= 2.4), gbrowse Section: science Priority: optional Multi-Arch: same Homepage: http://gmod.org/wiki/GBrowse Description: CAlign helper Generic Genome Browser is a simple but highly configurable web-based genome browser. It is a component of the Generic Model Organism Systems Database project (GMOD). . This package provides the CAlign helper for use with Realign. It speeds up Smith-Waterman alignment. drwxr-xr-x root/root 0 2023-12-07 20:40 ./ drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/lib/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/lib/x86_64-linux-gnu/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/lib/x86_64-linux-gnu/perl5/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/lib/x86_64-linux-gnu/perl5/5.40/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Graphics/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Graphics/Browser2/ -rw-r--r-- root/root 1129 2023-12-07 20:40 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Graphics/Browser2/CAlign.pm drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/lib/x86_64-linux-gnu/perl5/5.40/auto/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/lib/x86_64-linux-gnu/perl5/5.40/auto/Bio/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/lib/x86_64-linux-gnu/perl5/5.40/auto/Bio/Graphics/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/lib/x86_64-linux-gnu/perl5/5.40/auto/Bio/Graphics/Browser2/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/lib/x86_64-linux-gnu/perl5/5.40/auto/Bio/Graphics/Browser2/CAlign/ -rw-r--r-- root/root 0 2023-12-07 20:40 ./usr/lib/x86_64-linux-gnu/perl5/5.40/auto/Bio/Graphics/Browser2/CAlign/CAlign.bs -rw-r--r-- root/root 14176 2023-12-07 20:40 ./usr/lib/x86_64-linux-gnu/perl5/5.40/auto/Bio/Graphics/Browser2/CAlign/CAlign.so drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/share/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/share/doc/gbrowse-calign/ -rw-r--r-- root/root 1054 2023-12-07 20:40 ./usr/share/doc/gbrowse-calign/changelog.Debian.gz -rw-r--r-- root/root 19608 2017-01-15 21:26 ./usr/share/doc/gbrowse-calign/changelog.gz -rw-r--r-- root/root 17948 2023-12-07 20:40 ./usr/share/doc/gbrowse-calign/copyright drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/share/man/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/share/man/man3/ -rw-r--r-- root/root 1213 2023-12-07 20:40 ./usr/share/man/man3/Bio::Graphics::Browser2::CAlign.3pm.gz gbrowse-data_2.56+dfsg-12_all.deb --------------------------------- new Debian package, version 2.0. size 1233348 bytes: control archive=1428 bytes. 575 bytes, 17 lines control 1460 bytes, 17 lines md5sums 407 bytes, 25 lines * postinst #!/bin/bash Package: gbrowse-data Source: gbrowse Version: 2.56+dfsg-12 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 2827 Recommends: gbrowse Section: science Priority: optional Homepage: http://gmod.org/wiki/GBrowse Description: Sample data to use GBrowse Generic Genome Browser is a simple but highly configurable web-based genome browser. It is a component of the Generic Model Organism Systems Database project (GMOD). . This package contains sample data to test the gbrowse tool with the Yeast genome. drwxr-xr-x root/root 0 2023-12-07 20:40 ./ drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/share/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/share/doc/gbrowse-data/ -rw-r--r-- root/root 1056 2023-12-07 20:40 ./usr/share/doc/gbrowse-data/changelog.Debian.gz -rw-r--r-- root/root 19608 2017-01-15 21:26 ./usr/share/doc/gbrowse-data/changelog.gz -rw-r--r-- root/root 17948 2023-12-07 20:40 ./usr/share/doc/gbrowse-data/copyright drwxr-xr-x root/root 0 2023-12-07 20:40 ./var/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./var/lib/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./var/lib/gbrowse/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./var/lib/gbrowse/databases/ drwxr-xr-x root/root 0 2017-01-15 21:26 ./var/lib/gbrowse/databases/admin_uploads/ -rw-r--r-- root/root 144 2017-01-15 21:26 ./var/lib/gbrowse/databases/admin_uploads/README drwxr-xr-x root/root 0 2017-01-15 21:26 ./var/lib/gbrowse/databases/gbrowse_syn/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./var/lib/gbrowse/databases/gbrowse_syn/alignments/ -rw-r--r-- root/root 818177 2023-12-07 20:40 ./var/lib/gbrowse/databases/gbrowse_syn/alignments/rice.aln.gz drwxr-xr-x root/root 0 2017-01-15 21:26 ./var/lib/gbrowse/databases/gbrowse_syn/rice/ -rw-r--r-- root/root 235531 2017-01-15 21:26 ./var/lib/gbrowse/databases/gbrowse_syn/rice/rice.gff3 drwxr-xr-x root/root 0 2017-01-15 21:26 ./var/lib/gbrowse/databases/gbrowse_syn/wild_rice/ -rw-r--r-- root/root 242439 2017-01-15 21:26 ./var/lib/gbrowse/databases/gbrowse_syn/wild_rice/wild_rice.gff3 drwxr-xr-x root/root 0 2017-01-15 21:26 ./var/lib/gbrowse/databases/ideograms/ -rw-r--r-- root/root 81961 2017-01-15 21:26 ./var/lib/gbrowse/databases/ideograms/human_cytobands.gff -rw-r--r-- root/root 38809 2017-01-15 21:26 ./var/lib/gbrowse/databases/ideograms/mouse_cytobands.gff -rw-r--r-- root/root 23546 2017-01-15 21:26 ./var/lib/gbrowse/databases/ideograms/rat_cytobands.gff drwxr-xr-x root/root 0 2017-01-15 21:26 ./var/lib/gbrowse/databases/pop_demo/ -rw-r--r-- root/root 490 2017-01-15 21:26 ./var/lib/gbrowse/databases/pop_demo/pop_demo.gff3 drwxr-xr-x root/root 0 2023-12-07 20:40 ./var/lib/gbrowse/databases/yeast_chr1+2/ -rw-r--r-- root/root 12288 2023-12-07 20:40 ./var/lib/gbrowse/databases/yeast_chr1+2/directory.index -rw-r--r-- root/root 0 2017-01-15 21:26 ./var/lib/gbrowse/databases/yeast_chr1+2/dummy.fa -rw-r--r-- root/root 312303 2017-01-15 21:26 ./var/lib/gbrowse/databases/yeast_chr1+2/yeast_chr1+2.gff3 drwxr-xr-x root/root 0 2017-01-15 21:26 ./var/lib/gbrowse/databases/yeast_scaffolds/ -rw-r--r-- root/root 234051 2017-01-15 21:26 ./var/lib/gbrowse/databases/yeast_scaffolds/chr1.fa -rw-r--r-- root/root 826738 2017-01-15 21:26 ./var/lib/gbrowse/databases/yeast_scaffolds/chr2.fa -rw-r--r-- root/root 192 2017-01-15 21:26 ./var/lib/gbrowse/databases/yeast_scaffolds/chromosomes.gff3 gbrowse_2.56+dfsg-12_all.deb ---------------------------- new Debian package, version 2.0. size 2334240 bytes: control archive=14736 bytes. 2739 bytes, 77 lines conffiles 1664 bytes, 32 lines control 44853 bytes, 516 lines md5sums 1029 bytes, 44 lines * postinst #!/bin/bash 1108 bytes, 45 lines * postrm #!/bin/bash 381 bytes, 15 lines * prerm #!/bin/sh Package: gbrowse Version: 2.56+dfsg-12 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 6978 Depends: perl:any, apache2 | httpd-cgi, bioperl, libbio-graphics-perl, libbio-coordinate-perl, libbio-db-seqfeature-perl, libcgi-session-perl, libgd-gd2-noxpm-perl | libgd-gd2-perl, libio-string-perl, libjson-perl, libstatistics-descriptive-perl, libwww-perl, libhttp-daemon-perl, libterm-readkey-perl, sqlite3, libdbd-sqlite3-perl, libjs-prototype, libjs-scriptaculous, libvm-ec2-perl Recommends: apache2 (>= 2.4.6-4~) | httpd Suggests: gbrowse-data, gbrowse-calign, libfile-nfslock-perl Section: science Priority: optional Multi-Arch: foreign Homepage: http://gmod.org/wiki/GBrowse Description: GMOD Generic Genome Browser Generic Genome Browser is a simple but highly configurable web-based genome browser. It is a component of the Generic Model Organism Systems Database project (GMOD). Some of its features: * Simultaneous bird's eye and detailed views of the genome; * Scroll, zoom, center; * Attach arbitrary URLs to any annotation; * Order and appearance of tracks are customizable by administrator and end-user; * Search by annotation ID, name, or comment; * Supports third party annotation using GFF formats; * Settings persist across sessions; * DNA and GFF dumps; * Connectivity to different databases, including BioSQL and Chado; * Multi-language support; * Third-party feature loading; * Customizable plug-in architecture (e.g. run BLAST, dump & import many formats, find oligonucleotides, design primers, create restriction maps, edit features). drwxr-xr-x root/root 0 2023-12-07 20:40 ./ drwxr-xr-x root/root 0 2023-12-07 20:40 ./etc/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./etc/apache2/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./etc/apache2/conf-available/ -rw-r--r-- root/root 1651 2023-12-07 20:40 ./etc/apache2/conf-available/gbrowse.conf drwxr-xr-x root/root 0 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./usr/share/perl5/Bio/Graphics/Browser2/UserTracks.pm drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/share/perl5/Bio/Graphics/Browser2/UserTracks/ -rw-r--r-- root/root 27207 2023-12-07 20:40 ./usr/share/perl5/Bio/Graphics/Browser2/UserTracks/Database.pm -rw-r--r-- root/root 6449 2023-12-07 20:40 ./usr/share/perl5/Bio/Graphics/Browser2/UserTracks/Filesystem.pm -rw-r--r-- root/root 4376 2023-12-07 20:40 ./usr/share/perl5/Bio/Graphics/Browser2/Util.pm -rw-r--r-- root/root 304 2023-12-07 20:40 ./usr/share/perl5/Bio/Graphics/GBrowseFeature.pm -rw-r--r-- root/root 11495 2023-12-07 20:40 ./usr/share/perl5/Bio/Graphics/Karyotype.pm drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/share/perl5/CGI/ -rw-r--r-- root/root 5290 2023-12-07 20:40 ./usr/share/perl5/CGI/Toggle.pm drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/share/perl5/GBrowse/ lrwxrwxrwx root/root 0 2023-12-07 20:40 ./usr/share/perl5/GBrowse/ConfigData.pm -> /etc/gbrowse/ConfigData.pm drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/share/perl5/Legacy/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/share/perl5/Legacy/DB/ -rw-r--r-- root/root 2622 2023-12-07 20:40 ./usr/share/perl5/Legacy/DB/SyntenyBlock.pm -rw-r--r-- root/root 5390 2023-12-07 20:40 ./usr/share/perl5/Legacy/DB/SyntenyIO.pm drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/share/perl5/Legacy/Graphics/ -rw-r--r-- root/root 106254 2023-12-07 20:40 ./usr/share/perl5/Legacy/Graphics/Browser.pm drwxr-xr-x root/root 0 2023-12-07 20:40 ./usr/share/perl5/Legacy/Graphics/Browser/ -rw-r--r-- root/root 1509 2023-12-07 20:40 ./usr/share/perl5/Legacy/Graphics/Browser/I18n.pm -rw-r--r-- root/root 1628 2023-12-07 20:40 ./usr/share/perl5/Legacy/Graphics/Browser/PageSettings.pm -rw-r--r-- root/root 26506 2023-12-07 20:40 ./usr/share/perl5/Legacy/Graphics/Browser/Synteny.pm -rw-r--r-- root/root 16766 2023-12-07 20:40 ./usr/share/perl5/Legacy/Graphics/Browser/Util.pm drwxr-xr-x root/root 0 2023-12-07 20:40 ./var/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./var/cache/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./var/cache/gbrowse/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./var/cache/gbrowse/sessions/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./var/lib/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./var/lib/gbrowse/ drwxr-xr-x root/root 0 2023-12-07 20:40 ./var/lib/gbrowse/databases/ +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 40544 Build-Time: 27 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 14 Job: /srv/debomatic/incoming/gbrowse_2.56+dfsg-12.dsc Machine Architecture: amd64 Package: gbrowse Package-Time: 52 Source-Version: 2.56+dfsg-12 Space: 40544 Status: successful Version: 2.56+dfsg-12 -------------------------------------------------------------------------------- Finished at 2024-06-03T06:29:46Z Build needed 00:00:52, 40544k disk space