Tue Apr 30 13:30:27 UTC 2024 I: starting to build gbrowse/trixie/amd64 on jenkins on '2024-04-30 13:30' Tue Apr 30 13:30:27 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_10/4692/console.log Tue Apr 30 13:30:27 UTC 2024 I: Downloading source for trixie/gbrowse=2.56+dfsg-12 --2024-04-30 13:30:27-- http://deb.debian.org/debian/pool/main/g/gbrowse/gbrowse_2.56%2bdfsg-12.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2674 (2.6K) [text/prs.lines.tag] Saving to: ‘gbrowse_2.56+dfsg-12.dsc’ 0K .. 100% 298M=0s 2024-04-30 13:30:27 (298 MB/s) - ‘gbrowse_2.56+dfsg-12.dsc’ saved [2674/2674] Tue Apr 30 13:30:28 UTC 2024 I: gbrowse_2.56+dfsg-12.dsc -----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----- Tue Apr 30 13:30:28 UTC 2024 I: Checking whether the package is not for us Tue Apr 30 13:30:28 UTC 2024 I: Starting 1st build on remote node ionos5-amd64.debian.net. Tue Apr 30 13:30:28 UTC 2024 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Tue Apr 30 13:32:45 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Jun 2 07:53:30 -12 2025 I: pbuilder-time-stamp: 1748894010 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [gbrowse_2.56+dfsg-12.dsc] I: copying [./gbrowse_2.56+dfsg.orig.tar.gz] I: copying [./gbrowse_2.56+dfsg-12.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Dec 7 20:43:33 2023 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 gbrowse-2.56+dfsg 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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1750147/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='3f7f5d9fe62f48299e150504b5d56756' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1750147' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.pJBVuhji/pbuilderrc_ODA5 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.pJBVuhji/b1 --logfile b1/build.log gbrowse_2.56+dfsg-12.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 25 19:07 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1750147/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. 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 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19901 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on bioperl; however: Package bioperl is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-apache2; however: Package dh-apache2 is not installed. pbuilder-satisfydepends-dummy depends on dh-exec; however: Package dh-exec is not installed. pbuilder-satisfydepends-dummy depends on apache2-dev; however: Package apache2-dev is not installed. pbuilder-satisfydepends-dummy depends on libbio-graphics-perl; however: Package libbio-graphics-perl is not installed. pbuilder-satisfydepends-dummy depends on libbio-coordinate-perl; however: Package libbio-coordinate-perl is not installed. pbuilder-satisfydepends-dummy depends on libbio-db-seqfeature-perl; however: Package libbio-db-seqfeature-perl is not installed. pbuilder-satisfydepends-dummy depends on libcapture-tiny-perl; however: Package libcapture-tiny-perl is not installed. pbuilder-satisfydepends-dummy depends on libcgi-session-perl; however: Package libcgi-session-perl is not installed. pbuilder-satisfydepends-dummy depends on libgd-gd2-perl | libgd-gd2-noxpm-perl; however: Package libgd-gd2-perl is not installed. Package libgd-gd2-noxpm-perl is not installed. pbuilder-satisfydepends-dummy depends on libio-string-perl; however: Package libio-string-perl is not installed. pbuilder-satisfydepends-dummy depends on libjson-perl; however: Package libjson-perl is not installed. pbuilder-satisfydepends-dummy depends on libstatistics-descriptive-perl; however: Package libstatistics-descriptive-perl is not installed. pbuilder-satisfydepends-dummy depends on libwww-perl; however: Package libwww-perl is not installed. pbuilder-satisfydepends-dummy depends on libhttp-daemon-perl; however: Package libhttp-daemon-perl is not installed. pbuilder-satisfydepends-dummy depends on sqlite3; however: Package sqlite3 is not installed. pbuilder-satisfydepends-dummy depends on libdbd-sqlite3-perl; however: Package libdbd-sqlite3-perl is not installed. pbuilder-satisfydepends-dummy depends on libterm-readkey-perl; however: Package libterm-readkey-perl is not installed. pbuilder-satisfydepends-dummy depends on libjs-prototype; however: Package libjs-prototype is not installed. pbuilder-satisfydepends-dummy depends on libjs-scriptaculous; however: Package libjs-scriptaculous is not installed. pbuilder-satisfydepends-dummy depends on libvm-ec2-perl; however: Package libvm-ec2-perl is not installed. pbuilder-satisfydepends-dummy depends on libmodule-build-perl; however: Package libmodule-build-perl is not installed. pbuilder-satisfydepends-dummy depends on libcgi-pm-perl; however: Package libcgi-pm-perl is not installed. pbuilder-satisfydepends-dummy depends on rename; however: Package rename is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bioperl{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libabsl20230802{a} libalgorithm-diff-perl{a} libaom3{a} libarchive-zip-perl{a} libavif16{a} libbio-coordinate-perl{a} libbio-perl-perl{a} libbrotli1{a} libbsd0{a} libcapture-tiny-perl{a} libcgi-pm-perl{a} libcgi-session-perl{a} libclass-data-inheritable-perl{a} libclone-perl{a} libdata-stag-perl{a} libdav1d7{a} libdbd-sqlite3-perl{a} libdbi-perl{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libdevel-stacktrace-perl{a} libelf1t64{a} libencode-locale-perl{a} libexception-class-perl{a} libexpat1{a} libexporter-tiny-perl{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libgav1-1{a} libgd-perl{a} libgd3{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhttp-daemon-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libicu72{a} libio-html-perl{a} libio-string-perl{a} libjbig0{a} libjpeg62-turbo{a} libjs-prototype{a} libjs-scriptaculous{a} libjson-perl{a} liblerc4{a} liblist-moreutils-perl{a} liblist-moreutils-xs-perl{a} liblwp-mediatypes-perl{a} libmagic-mgc{a} libmagic1t64{a} libmodule-build-perl{a} libpipeline1{a} libpng16-16t64{a} librav1e0{a} libreadline8t64{a} libsharpyuv0{a} libstatistics-descriptive-perl{a} libsub-override-perl{a} libsub-uplevel-perl{a} libsvtav1enc1d1{a} libterm-readkey-perl{a} libtest-deep-perl{a} libtest-differences-perl{a} libtest-exception-perl{a} libtest-most-perl{a} libtest-warn-perl{a} libtext-diff-perl{a} libtiff6{a} libtimedate-perl{a} libtool{a} libuchardet0{a} liburi-perl{a} libwebp7{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxml2{a} libxpm4{a} libyuv0{a} m4{a} man-db{a} po-debconf{a} readline-common{a} rename{a} sensible-utils{a} sqlite3{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libarchive-cpio-perl libarray-compare-perl libbio-asn1-entrezgene-perl libcache-cache-perl libcgi-fast-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libfreezethaw-perl libgraph-perl libgraphviz-perl libheif-plugin-aomenc libheif-plugin-x265 libhtml-tableextract-perl libio-compress-brotli-perl libjson-xs-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libmodule-signature-perl libpod-readme-perl libpostscript-perl libset-scalar-perl libsoap-lite-perl libsoftware-license-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl libyaml-perl lynx perl-doc perl-tk wget 0 packages upgraded, 112 newly installed, 0 to remove and 0 not upgraded. Need to get 38.9 MB of archives. After unpacking 132 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: dh-apache2 which is a virtual package, provided by: - apache2-dev (2.4.58-1+b1), but it is not installable Depends: apache2-dev but it is not installable Depends: libbio-graphics-perl but it is not installable Depends: libbio-db-seqfeature-perl but it is not installable Depends: libwww-perl but it is not installable Depends: libvm-ec2-perl but it is not installable The following actions will resolve these dependencies: Remove the following packages: 1) libdb5.3 [5.3.28+dfsg2-4+b1 (now)] 2) libssl3 [3.1.5-1 (now)] Install the following packages: 3) apache2-bin [2.4.58-1+b1 (testing)] 4) apache2-dev [2.4.58-1+b1 (testing)] 5) ca-certificates [20240203 (testing)] 6) libanyevent-cachedns-perl [0.08-3 (testing)] 7) libanyevent-http-perl [2.25-2 (testing)] 8) libanyevent-perl [7.170-2+b5 (testing)] 9) libapache-dbi-perl [1.12-3 (testing)] 10) libapache2-mod-perl2 [2.0.13-1+b1 (testing)] 11) libapr1-dev [1.7.2-3.2 (testing)] 12) libapr1t64 [1.7.2-3.2 (testing)] 13) libaprutil1 [1.6.3-1+b1 (testing)] 14) libaprutil1-dbd-mysql [1.6.3-1+b1 (testing)] 15) libaprutil1-dev [1.6.3-1+b1 (testing)] 16) libaprutil1-ldap [1.6.3-1+b1 (testing)] 17) libbio-db-biofetch-perl [1.7.3-4 (testing)] 18) libbio-db-gff-perl [1.7.4-1 (testing)] 19) libbio-db-seqfeature-perl [1.7.4-2 (testing)] 20) libbio-graphics-perl [2.40-6 (testing)] 21) libcommon-sense-perl [3.75-3+b2 (testing)] 22) libcurl4t64 [8.7.1-3 (testing)] 23) libdb5.3t64 [5.3.28+dfsg2-7 (testing)] 24) libdbd-pg-perl [3.18.0-1+b1 (testing)] 25) libdevel-symdump-perl [2.18-5 (testing)] 26) libexpat1-dev [2.6.2-1 (testing)] 27) libfile-listing-perl [6.16-1 (testing)] 28) libhtml-tree-perl [5.07-3 (testing)] 29) libhttp-cookies-perl [6.11-1 (testing)] 30) libhttp-negotiate-perl [6.01-2 (testing)] 31) libio-socket-ssl-perl [2.085-1 (testing)] 32) libldap-2.5-0 [2.5.13+dfsg-5+b3 (testing)] 33) libldap-dev [2.5.13+dfsg-5+b3 (testing)] 34) liblua5.3-0 [5.3.6-2+b2 (testing)] 35) liblwp-protocol-https-perl [6.14-1 (testing)] 36) libmariadb3 [1:10.11.6-2 (testing)] 37) libnet-http-perl [6.23-1 (testing)] 38) libnet-ssleay-perl [1.94-1 (testing)] 39) libnghttp2-14 [1.59.0-1 (testing)] 40) libpcre2-16-0 [10.42-4+b1 (testing)] 41) libpcre2-32-0 [10.42-4+b1 (testing)] 42) libpcre2-dev [10.42-4+b1 (testing)] 43) libpcre2-posix3 [10.42-4+b1 (testing)] 44) libpq5 [16.2-1 (testing)] 45) libpsl5t64 [0.21.2-1.1 (testing)] 46) libpython3-stdlib [3.11.8-1 (testing)] 47) libpython3.11-minimal [3.11.9-1 (testing)] 48) libpython3.11-stdlib [3.11.9-1 (testing)] 49) librtmp1 [2.4+20151223.gitfa8646d.1-2+b4 (testing)] 50) libsasl2-2 [2.1.28+dfsg1-4+b1 (testing)] 51) libsasl2-modules-db [2.1.28+dfsg1-4+b1 (testing)] 52) libsctp-dev [1.0.19+dfsg-2+b1 (testing)] 53) libsctp1 [1.0.19+dfsg-2+b1 (testing)] 54) libssh2-1t64 [1.11.0-4.1+b2 (testing)] 55) libssl3t64 [3.2.1-3 (testing)] 56) libstring-approx-perl [3.28-2+b2 (testing)] 57) libtry-tiny-perl [0.31-2 (testing)] 58) libvm-ec2-perl [1.28-4 (testing)] 59) libwww-perl [6.77-1 (testing)] 60) libwww-robotrules-perl [6.02-1 (testing)] 61) libxml-namespacesupport-perl [1.12-2 (testing)] 62) libxml-parser-perl [2.47-1+b1 (testing)] 63) libxml-sax-base-perl [1.09-3 (testing)] 64) libxml-sax-expat-perl [0.51-2 (testing)] 65) libxml-sax-perl [1.02+dfsg-3 (testing)] 66) libxml-simple-perl [2.25-2 (testing)] 67) mariadb-common [1:10.11.6-2 (testing)] 68) media-types [10.1.0 (testing)] 69) mysql-common [5.8+1.1.0 (testing)] 70) netbase [6.4 (testing)] 71) openssl [3.2.1-3 (testing)] 72) perl-openssl-defaults [7+b2 (testing)] 73) python3 [3.11.8-1 (testing)] 74) python3-minimal [3.11.8-1 (testing)] 75) python3.11 [3.11.9-1 (testing)] 76) python3.11-minimal [3.11.9-1 (testing)] 77) tzdata [2024a-3 (testing)] 78) ucf [3.0043+nmu1 (testing)] 79) uuid-dev [2.39.3-6 (testing)] The following NEW packages will be installed: apache2-bin{a} apache2-dev{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bioperl{a} bsdextrautils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libabsl20230802{a} libalgorithm-diff-perl{a} libanyevent-cachedns-perl{a} libanyevent-http-perl{a} libanyevent-perl{a} libaom3{a} libapache-dbi-perl{a} libapache2-mod-perl2{a} libapr1-dev{a} libapr1t64{a} libaprutil1{a} libaprutil1-dbd-mysql{a} libaprutil1-dev{a} libaprutil1-ldap{a} libarchive-zip-perl{a} libavif16{a} libbio-coordinate-perl{a} libbio-db-biofetch-perl{a} libbio-db-gff-perl{a} libbio-db-seqfeature-perl{a} libbio-graphics-perl{a} libbio-perl-perl{a} libbrotli1{a} libbsd0{a} libcapture-tiny-perl{a} libcgi-pm-perl{a} libcgi-session-perl{a} libclass-data-inheritable-perl{a} libclone-perl{a} libcommon-sense-perl{a} libcurl4t64{a} libdata-stag-perl{a} libdav1d7{a} libdb5.3t64{a} libdbd-pg-perl{a} libdbd-sqlite3-perl{a} libdbi-perl{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libdevel-stacktrace-perl{a} libdevel-symdump-perl{a} libelf1t64{a} libencode-locale-perl{a} libexception-class-perl{a} libexpat1{a} libexpat1-dev{a} libexporter-tiny-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libgav1-1{a} libgd-perl{a} libgd3{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-daemon-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libicu72{a} libio-html-perl{a} libio-socket-ssl-perl{a} libio-string-perl{a} libjbig0{a} libjpeg62-turbo{a} libjs-prototype{a} libjs-scriptaculous{a} libjson-perl{a} libldap-2.5-0{a} libldap-dev{a} liblerc4{a} liblist-moreutils-perl{a} liblist-moreutils-xs-perl{a} liblua5.3-0{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1t64{a} libmariadb3{a} libmodule-build-perl{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnghttp2-14{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpipeline1{a} libpng16-16t64{a} libpq5{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} librav1e0{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsctp-dev{a} libsctp1{a} libsharpyuv0{a} libssh2-1t64{a} libssl3t64{a} libstatistics-descriptive-perl{a} libstring-approx-perl{a} libsub-override-perl{a} libsub-uplevel-perl{a} libsvtav1enc1d1{a} libterm-readkey-perl{a} libtest-deep-perl{a} libtest-differences-perl{a} libtest-exception-perl{a} libtest-most-perl{a} libtest-warn-perl{a} libtext-diff-perl{a} libtiff6{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} liburi-perl{a} libvm-ec2-perl{a} libwebp7{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxml-namespacesupport-perl{a} libxml-parser-perl{a} libxml-sax-base-perl{a} libxml-sax-expat-perl{a} libxml-sax-perl{a} libxml-simple-perl{a} libxml2{a} libxpm4{a} libyuv0{a} m4{a} man-db{a} mariadb-common{a} media-types{a} mysql-common{a} netbase{a} openssl{a} perl-openssl-defaults{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} rename{a} sensible-utils{a} sqlite3{a} tzdata{a} ucf{a} uuid-dev{a} The following packages will be REMOVED: libdb5.3{a} libssl3{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libapache2-reload-perl libarchive-cpio-perl libarray-compare-perl libasync-interrupt-perl libberkeleydb-perl libbio-asn1-entrezgene-perl libbio-scf-perl libbsd-resource-perl libcache-cache-perl libcgi-fast-perl libconvert-binary-c-perl libdata-dump-perl libdbd-mysql-perl libev-perl libevent-perl libfreezethaw-perl libgd-svg-perl libgraph-perl libgraphviz-perl libguard-perl libheif-plugin-aomenc libheif-plugin-x265 libhtml-form-perl libhtml-format-perl libhtml-tableextract-perl libio-compress-brotli-perl libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libmailtools-perl libmldbm-perl libmodule-signature-perl libpod-readme-perl libpostscript-perl libsasl2-modules libset-scalar-perl libsoap-lite-perl libsoftware-license-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-perl libxml-sax-writer-perl libxml-twig-perl libxml-writer-perl libyaml-perl lynx perl-doc perl-tk publicsuffix wget 0 packages upgraded, 189 newly installed, 2 to remove and 0 not upgraded. Need to get 60.3 MB of archives. After unpacking 208 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-7 [697 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libssl3t64 amd64 3.2.1-3 [2244 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-3 [255 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-3+b1 [1180 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.39.3-6 [89.4 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.0-3 [1401 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 libapr1t64 amd64 1.7.2-3.2 [102 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libaprutil1 amd64 1.6.3-1+b1 [88.4 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 mysql-common all 5.8+1.1.0 [6636 B] Get: 32 http://deb.debian.org/debian trixie/main amd64 mariadb-common all 1:10.11.6-2 [25.2 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libmariadb3 amd64 1:10.11.6-2 [174 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libaprutil1-dbd-mysql amd64 1.6.3-1+b1 [15.8 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-4+b1 [19.7 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-4+b1 [57.0 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5+b3 [184 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libaprutil1-ldap amd64 1.6.3-1+b1 [12.1 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.59.0-1 [74.3 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.7.1-3 [441 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 liblua5.3-0 amd64 5.3.6-2+b2 [129 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 apache2-bin amd64 2.4.58-1+b1 [1375 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 61 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 uuid-dev amd64 2.39.3-6 [41.1 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libsctp1 amd64 1.0.19+dfsg-2+b1 [26.1 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libsctp-dev amd64 1.0.19+dfsg-2+b1 [68.6 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libapr1-dev amd64 1.7.2-3.2 [771 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libldap-dev amd64 2.5.13+dfsg-5+b3 [298 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.6.2-1 [155 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libaprutil1-dev amd64 1.6.3-1+b1 [414 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libpcre2-16-0 amd64 10.42-4+b1 [246 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libpcre2-32-0 amd64 10.42-4+b1 [234 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libpcre2-posix3 amd64 10.42-4+b1 [55.8 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libpcre2-dev amd64 10.42-4+b1 [755 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 apache2-dev amd64 2.4.58-1+b1 [310 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get: 83 http://deb.debian.org/debian trixie/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libtest-deep-perl all 1.204-1 [52.9 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libtext-diff-perl all 1.45-2 [27.2 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libtest-differences-perl all 0.71-1 [17.9 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libtest-exception-perl all 0.43-3 [16.9 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libtest-warn-perl all 0.37-2 [14.5 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libtest-most-perl all 0.38-1 [25.1 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 bioperl all 1.7.8-1 [246 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 dh-exec amd64 0.29 [25.4 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libabsl20230802 amd64 20230802.1-4 [464 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libanyevent-perl amd64 7.170-2+b5 [384 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libanyevent-cachedns-perl all 0.08-3 [7708 B] Get: 102 http://deb.debian.org/debian trixie/main amd64 libcommon-sense-perl amd64 3.75-3+b2 [22.9 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libanyevent-http-perl all 2.25-2 [35.2 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libaom3 amd64 3.8.2-2 [1869 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libdevel-symdump-perl all 2.18-5 [15.8 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 liburi-perl all 5.28-1 [98.6 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libhtml-parser-perl amd64 3.81-1+b1 [99.0 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libclone-perl amd64 0.46-1+b1 [13.8 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libhttp-message-perl all 6.45-1 [82.0 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get: 121 http://deb.debian.org/debian trixie/main amd64 libnet-ssleay-perl amd64 1.94-1 [338 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libio-socket-ssl-perl all 2.085-1 [218 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libwww-perl all 6.77-1 [183 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libapache2-mod-perl2 amd64 2.0.13-1+b1 [808 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libdbi-perl amd64 1.643-4+b1 [755 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libapache-dbi-perl all 1.12-3 [48.5 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libdav1d7 amd64 1.4.1-1 [547 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libgav1-1 amd64 0.19.0-2+b1 [351 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 librav1e0 amd64 0.7.1-2 [900 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.3.2-0.4+b1 [108 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libsvtav1enc1d1 amd64 1.7.0+dfsg-2+b1 [2169 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-2+b2 [167 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libyuv0 amd64 0.0~git202401110.af6ac82-1 [169 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libavif16 amd64 1.0.4-2 [106 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libbio-coordinate-perl all 1.7.1-4 [56.7 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libbio-db-biofetch-perl all 1.7.3-4 [17.5 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libcgi-pm-perl all 4.64-1 [217 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libbio-db-gff-perl all 1.7.4-1 [273 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 libpq5 amd64 16.2-1 [216 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libdbd-pg-perl amd64 3.18.0-1+b1 [210 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libdbd-sqlite3-perl amd64 1.74-1+b1 [175 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libbio-db-seqfeature-perl all 1.7.4-2 [169 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 libheif-plugin-dav1d amd64 1.17.6-1+b2 [9856 B] Get: 151 http://deb.debian.org/debian trixie/main amd64 libde265-0 amd64 1.0.15-1+b1 [187 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 libheif-plugin-libde265 amd64 1.17.6-1+b2 [13.1 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libheif1 amd64 1.17.6-1+b2 [284 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.3.2-0.4+b1 [308 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 165 http://deb.debian.org/debian trixie/main amd64 libxpm4 amd64 1:3.5.17-1+b1 [56.1 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 libgd3 amd64 2.3.3-9+b3 [125 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 libgd-perl amd64 2.78-1+b1 [131 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 libbio-graphics-perl all 2.40-6 [610 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 libcgi-session-perl all 4.48-4 [118 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 libexporter-tiny-perl all 1.006002-1 [38.7 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 libhttp-daemon-perl all 6.16-1 [23.5 kB] Get: 172 http://deb.debian.org/debian trixie/main amd64 libjs-prototype all 1.7.3-1 [44.3 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 libjs-scriptaculous all 1.9.0-3 [110 kB] Get: 174 http://deb.debian.org/debian trixie/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 liblist-moreutils-xs-perl amd64 0.430-3+b2 [42.1 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 liblist-moreutils-perl all 0.430-2 [46.9 kB] Get: 177 http://deb.debian.org/debian trixie/main amd64 libmodule-build-perl all 0.423400-2 [252 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 libstatistics-descriptive-perl all 3.0801-1 [62.8 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 libstring-approx-perl amd64 3.28-2+b2 [39.0 kB] Get: 180 http://deb.debian.org/debian trixie/main amd64 libterm-readkey-perl amd64 2.38-2+b2 [24.7 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 libxml-parser-perl amd64 2.47-1+b1 [199 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get: 184 http://deb.debian.org/debian trixie/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 libxml-sax-expat-perl all 0.51-2 [11.1 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 libxml-simple-perl all 2.25-2 [69.8 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 libvm-ec2-perl all 1.28-4 [760 kB] Get: 188 http://deb.debian.org/debian trixie/main amd64 rename all 2.02-1 [21.8 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 sqlite3 amd64 3.45.1-1 [374 kB] Fetched 60.3 MB in 1s (48.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libdb5.3:amd64: dependency problems, but removing anyway as you requested: libperl5.38:amd64 depends on libdb5.3. libpam-modules:amd64 depends on libdb5.3. (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 ... 19901 files and directories currently installed.) Removing libdb5.3:amd64 (5.3.28+dfsg2-4+b1) ... Selecting previously unselected package libdb5.3t64:amd64. (Reading database ... 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(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 ... 19900 files and directories currently installed.) Removing libssl3:amd64 (3.1.5-1) ... Selecting previously unselected package libssl3t64:amd64. (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 ... 19887 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.2.1-3_amd64.deb ... Unpacking libssl3t64:amd64 (3.2.1-3) ... Setting up libssl3t64:amd64 (3.2.1-3) ... Selecting previously unselected package libpython3.11-minimal:amd64. (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 ... 19902 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 ... (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 ... 20218 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. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-3_all.deb ... Unpacking tzdata (2024a-3) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../5-libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (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 ... 21210 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. Preparing to unpack .../006-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../008-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../009-groff-base_1.23.0-3+b1_amd64.deb ... Unpacking groff-base (1.23.0-3+b1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../010-bsdextrautils_2.39.3-6_amd64.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../011-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../012-man-db_2.12.0-3_amd64.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package ucf. Preparing to unpack .../013-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package libapr1t64:amd64. Preparing to unpack .../014-libapr1t64_1.7.2-3.2_amd64.deb ... Unpacking libapr1t64:amd64 (1.7.2-3.2) ... Selecting previously unselected package libaprutil1:amd64. Preparing to unpack .../015-libaprutil1_1.6.3-1+b1_amd64.deb ... Unpacking libaprutil1:amd64 (1.6.3-1+b1) ... Selecting previously unselected package mysql-common. Preparing to unpack .../016-mysql-common_5.8+1.1.0_all.deb ... Unpacking mysql-common (5.8+1.1.0) ... Selecting previously unselected package mariadb-common. Preparing to unpack .../017-mariadb-common_1%3a10.11.6-2_all.deb ... Unpacking mariadb-common (1:10.11.6-2) ... Selecting previously unselected package libmariadb3:amd64. Preparing to unpack .../018-libmariadb3_1%3a10.11.6-2_amd64.deb ... Unpacking libmariadb3:amd64 (1:10.11.6-2) ... Selecting previously unselected package libaprutil1-dbd-mysql:amd64. Preparing to unpack .../019-libaprutil1-dbd-mysql_1.6.3-1+b1_amd64.deb ... Unpacking libaprutil1-dbd-mysql:amd64 (1.6.3-1+b1) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../020-libsasl2-modules-db_2.1.28+dfsg1-4+b1_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-4+b1) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../021-libsasl2-2_2.1.28+dfsg1-4+b1_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-4+b1) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../022-libldap-2.5-0_2.5.13+dfsg-5+b3_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.13+dfsg-5+b3) ... Selecting previously unselected package libaprutil1-ldap:amd64. Preparing to unpack .../023-libaprutil1-ldap_1.6.3-1+b1_amd64.deb ... Unpacking libaprutil1-ldap:amd64 (1.6.3-1+b1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../024-libbrotli1_1.1.0-2+b3_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b3) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../025-libnghttp2-14_1.59.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.59.0-1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../026-libpsl5t64_0.21.2-1.1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../027-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../028-libssh2-1t64_1.11.0-4.1+b2_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Selecting previously unselected package libcurl4t64:amd64. Preparing to unpack .../029-libcurl4t64_8.7.1-3_amd64.deb ... Unpacking libcurl4t64:amd64 (8.7.1-3) ... Selecting previously unselected package liblua5.3-0:amd64. 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Setting up bsdextrautils (2.39.3-6) ... Setting up libtest-deep-perl (1.204-1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libclone-perl:amd64 (0.46-1+b1) ... 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 (1.59.0-1) ... Setting up libdeflate0:amd64 (1.20-1) ... Setting up perl-openssl-defaults:amd64 (7+b2) ... Setting up libcommon-sense-perl:amd64 (3.75-3+b2) ... 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 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 libelf1t64:amd64 (0.191-1+b1) ... Setting up libmodule-build-perl (0.423400-2) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-4+b1) ... Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Jun 2 19:54:32 UTC 2025. Universal Time is now: Mon Jun 2 19:54:32 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up mariadb-common (1:10.11.6-2) ... update-alternatives: using /etc/mysql/mariadb.cnf to provide /etc/mysql/my.cnf (my.cnf) 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 (1:2.1.5-2+b2) ... 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 uuid-dev:amd64 (2.39.3-6) ... 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 libmariadb3:amd64 (1:10.11.6-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up liblist-moreutils-xs-perl (0.430-3+b2) ... Setting up libjs-prototype (1.7.3-1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-4+b1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:amd64 (1.3.2-0.4+b1) ... 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 (1.4.1-1) ... 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 libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up libabsl20230802:amd64 (20230802.1-4) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libdevel-symdump-perl (2.18-5) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Setting up libexporter-tiny-perl (1.006002-1) ... Setting up libterm-readkey-perl (2.38-2+b2) ... 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~git202401110.af6ac82-1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up liburi-perl (5.28-1) ... Setting up libdbi-perl:amd64 (1.643-4+b1) ... Setting up libaprutil1:amd64 (1.6.3-1+b1) ... Setting up libnet-ssleay-perl:amd64 (1.94-1) ... 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 (1.13.1-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up libxcb1:amd64 (1.15-1) ... 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 libtest-differences-perl (0.71-1) ... Setting up libnet-http-perl (6.23-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5+b3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libtest-exception-perl (0.43-3) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Setting up libldap-dev:amd64 (2.5.13+dfsg-5+b3) ... 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 libreadline8t64:amd64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libaprutil1-dbd-mysql:amd64 (1.6.3-1+b1) ... Setting up groff-base (1.23.0-3+b1) ... Setting up libhtml-parser-perl:amd64 (3.81-1+b1) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libdbd-sqlite3-perl:amd64 (1.74-1+b1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up sqlite3 (3.45.1-1) ... Setting up libio-socket-ssl-perl (2.085-1) ... Setting up libhttp-message-perl (6.45-1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up libavif16:amd64 (1.0.4-2) ... Setting up libstatistics-descriptive-perl (3.0801-1) ... Setting up libxpm4:amd64 (1:3.5.17-1+b1) ... Setting up libcurl4t64:amd64 (8.7.1-3) ... 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 libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up libcgi-pm-perl (4.64-1) ... Setting up libpq5:amd64 (16.2-1) ... Setting up libdbd-pg-perl (3.18.0-1+b1) ... Setting up libaprutil1-ldap:amd64 (1.6.3-1+b1) ... Setting up apache2-bin (2.4.58-1+b1) ... Setting up man-db (2.12.0-3) ... 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 libhttp-daemon-perl (6.16-1) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up bioperl (1.7.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up dh-exec (0.29) ... Setting up libbio-coordinate-perl (1.7.1-4) ... Setting up libapr1-dev (1.7.2-3.2) ... Setting up libaprutil1-dev (1.6.3-1+b1) ... Setting up apache2-dev (2.4.58-1+b1) ... Setting up libwww-perl (6.77-1) ... Setting up libapache2-mod-perl2 (2.0.13-1+b1) ... 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 libxml-parser-perl (2.47-1+b1) ... 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 libxml-sax-expat-perl (0.51-2) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::Expat 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 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+b1) ... Setting up libxml-simple-perl (2.25-2) ... Setting up libbio-graphics-perl (2.40-6) ... Setting up libvm-ec2-perl (1.28-4) ... Processing triggers for libc-bin (2.37-18) ... 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. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/gbrowse-2.56+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../gbrowse_2.56+dfsg-12_source.changes 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 --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with apache2 dh_clean debian/rules binary dh binary --with apache2 dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/gbrowse-2.56+dfsg' 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=/build/reproducible-path/gbrowse-2.56+dfsg=. -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=/build/reproducible-path/gbrowse-2.56+dfsg=. -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 '/build/reproducible-path/gbrowse-2.56+dfsg' dh_auto_build /usr/bin/perl Build NOTE: Run ./Build reconfig to change existing configuration. Building GBrowse x86_64-linux-gnu-gcc -I/build/reproducible-path/gbrowse-2.56+dfsg/libalign -I/usr/lib/x86_64-linux-gnu/perl/5.38/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=/build/reproducible-path/gbrowse-2.56+dfsg=.' -fstack-protector-strong -fstack-clash-protection -Wformat '-Werror=format-security' -fcf-protection -g -O2 '-Werror=implicit-function-declaration' '-ffile-prefix-map=/build/reproducible-path/gbrowse-2.56+dfsg=.' -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=/build/reproducible-path/gbrowse-2.56+dfsg=.' -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 /build/reproducible-path/gbrowse-2.56+dfsg/install_util/GBrowseInstall.pm line 778. debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/gbrowse-2.56+dfsg' 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 /build/reproducible-path/gbrowse-2.56+dfsg/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 /build/reproducible-path/gbrowse-2.56+dfsg/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 /build/reproducible-path/gbrowse-2.56+dfsg/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\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 /build/reproducible-path/gbrowse-2.56+dfsg/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\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 /build/reproducible-path/gbrowse-2.56+dfsg/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 5.038002 for linux # Current time local: Mon Jun 2 07:55:24 2025 # Current time GMT: Mon Jun 2 19:55:24 2025 # 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, 30 wallclock secs ( 0.09 usr 0.03 sys + 15.01 cusr 4.38 csys = 19.51 CPU) Result: PASS make[1]: Leaving directory '/build/reproducible-path/gbrowse-2.56+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_installdirs make[1]: Entering directory '/build/reproducible-path/gbrowse-2.56+dfsg' # svn(-buildpackage) seems to ignore the x bit chmod +x debian/gbrowse-calign.dirs dh_installdirs make[1]: Leaving directory '/build/reproducible-path/gbrowse-2.56+dfsg' debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/gbrowse-2.56+dfsg' ./Build --install_base=debian/gbrowse debianinstall NOTE: Run ./Build reconfig to change existing configuration. Use of uninitialized value in pattern match (m//) at /build/reproducible-path/gbrowse-2.56+dfsg/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/bed2gff3.pl.1p Installing debian/gbrowse/man/man1/make_das_conf.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/wiggle2gff3.pl.1p Installing debian/gbrowse/man/man1/gbrowse_clean.pl.1p Installing debian/gbrowse/man/man1/gbrowse_sync_aws_slave.pl.1p Installing debian/gbrowse/man/man1/ucsc_genes2gff.pl.1p Installing debian/gbrowse/man/man1/load_genbank.pl.1p Installing debian/gbrowse/man/man1/gbrowse_grow_cloud_vol.pl.1p Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_img 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_key_img Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_details Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbgff Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_gmap Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_login Installing debian/gbrowse/etc/gbrowse/enzymes.txt Installing debian/gbrowse/etc/gbrowse/volvox.conf Installing debian/gbrowse/etc/gbrowse/detail_select_menu.conf Installing debian/gbrowse/etc/gbrowse/aws_balancer.conf Installing debian/gbrowse/etc/gbrowse/renderfarm.conf Installing debian/gbrowse/etc/gbrowse/yeast_chr1+2.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/yeast_renderfarm.conf Installing debian/gbrowse/etc/gbrowse/yeast_simple.conf Installing debian/gbrowse/etc/gbrowse/log4perl.conf Installing debian/gbrowse/etc/gbrowse/pop_demo.conf Installing debian/gbrowse/etc/gbrowse/languages/en.pm Installing debian/gbrowse/etc/gbrowse/languages/POSIX.pm Installing debian/gbrowse/etc/gbrowse/languages/is.pm Installing debian/gbrowse/etc/gbrowse/languages/de.pm Installing debian/gbrowse/etc/gbrowse/languages/ru.pm Installing debian/gbrowse/etc/gbrowse/languages/it.pm Installing debian/gbrowse/etc/gbrowse/languages/ko.pm Installing debian/gbrowse/etc/gbrowse/languages/nl.pm Installing debian/gbrowse/etc/gbrowse/languages/pl.pm Installing debian/gbrowse/etc/gbrowse/languages/zh.pm Installing debian/gbrowse/etc/gbrowse/languages/zh_cn.pm Installing debian/gbrowse/etc/gbrowse/languages/es.pm Installing debian/gbrowse/etc/gbrowse/languages/ja.pm Installing debian/gbrowse/etc/gbrowse/languages/fr.pm Installing debian/gbrowse/etc/gbrowse/themes/warm_colors Installing debian/gbrowse/etc/gbrowse/themes/solid_gray_colors Installing debian/gbrowse/etc/gbrowse/themes/transparent_colors Installing debian/gbrowse/etc/gbrowse/MobyServices/text_plain_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/b64_encoded_gif_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/MobyServices/moby.conf Installing debian/gbrowse/etc/gbrowse/MobyServices/text_html_renderer.pm Installing debian/gbrowse/etc/gbrowse/plugins/Blat.pm Installing debian/gbrowse/etc/gbrowse/plugins/GeneFinder.pm Installing debian/gbrowse/etc/gbrowse/plugins/AttributeHiliter.pm Installing debian/gbrowse/etc/gbrowse/plugins/RestrictionAnnotator.pm Installing debian/gbrowse/etc/gbrowse/plugins/TestFinder.pm Installing debian/gbrowse/etc/gbrowse/plugins/TrackFinder.pm Installing debian/gbrowse/etc/gbrowse/plugins/FilterTest.pm Installing debian/gbrowse/etc/gbrowse/plugins/AlignTwoSequences.pm Installing debian/gbrowse/etc/gbrowse/plugins/Aligner.pm Installing debian/gbrowse/etc/gbrowse/plugins/LDAPAuthenticate.pm Installing debian/gbrowse/etc/gbrowse/plugins/ProteinDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/test.pm Installing debian/gbrowse/etc/gbrowse/plugins/SourceTrackFinder.pm Installing debian/gbrowse/etc/gbrowse/plugins/BatchDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/CreateBlastDB.pm Installing debian/gbrowse/etc/gbrowse/plugins/TrackDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/OligoFinder.pm Installing debian/gbrowse/etc/gbrowse/plugins/Submitter.pm Installing debian/gbrowse/etc/gbrowse/plugins/SimpleTrackFinder.pm Installing debian/gbrowse/etc/gbrowse/plugins/FBTableDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/PamAuthenticate.pm Installing debian/gbrowse/etc/gbrowse/plugins/RandomGene.pm Installing debian/gbrowse/etc/gbrowse/plugins/SequenceDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/FastaDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/TestAuthenticator.pm Installing debian/gbrowse/etc/gbrowse/plugins/Spectrogram.pm Installing debian/gbrowse/etc/gbrowse/plugins/CMapDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/SinWave.pm Installing debian/gbrowse/etc/gbrowse/plugins/PrimerDesigner.pm Installing debian/gbrowse/etc/gbrowse/synteny/rice_synteny.conf Installing debian/gbrowse/etc/gbrowse/synteny/wild_rice_synteny.conf Installing debian/gbrowse/etc/gbrowse/synteny/oryza.synconf.disabled.conf Installing debian/gbrowse/var/lib/gbrowse/databases/gbrowse_syn/alignments/rice.aln.gz Installing debian/gbrowse/var/lib/gbrowse/databases/gbrowse_syn/rice/rice.gff3 Installing debian/gbrowse/var/lib/gbrowse/databases/gbrowse_syn/wild_rice/wild_rice.gff3 Installing debian/gbrowse/var/lib/gbrowse/databases/ideograms/mouse_cytobands.gff Installing debian/gbrowse/var/lib/gbrowse/databases/ideograms/human_cytobands.gff Installing debian/gbrowse/var/lib/gbrowse/databases/ideograms/rat_cytobands.gff Installing debian/gbrowse/var/lib/gbrowse/databases/yeast_chr1+2/dummy.fa Installing debian/gbrowse/var/lib/gbrowse/databases/yeast_chr1+2/yeast_chr1+2.gff3 Installing debian/gbrowse/var/lib/gbrowse/databases/yeast_scaffolds/chromosomes.gff3 Installing debian/gbrowse/var/lib/gbrowse/databases/yeast_scaffolds/chr2.fa Installing debian/gbrowse/var/lib/gbrowse/databases/yeast_scaffolds/chr1.fa 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/usr/share/gbrowse/htdocs/gbrowse_karyotype_help.html Installing debian/gbrowse/usr/share/gbrowse/htdocs/gbrowse_syn_help.html Installing debian/gbrowse/usr/share/gbrowse/htdocs/gmod_cog.jpeg Installing debian/gbrowse/usr/share/gbrowse/htdocs/general_help.html Installing debian/gbrowse/usr/share/gbrowse/htdocs/vbox_index.html Installing debian/gbrowse/usr/share/gbrowse/htdocs/cloud_index.html Installing debian/gbrowse/usr/share/gbrowse/htdocs/general_help.html.zh Installing debian/gbrowse/usr/share/gbrowse/htdocs/index.html Installing debian/gbrowse/usr/share/gbrowse/htdocs/annotation_help.html Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/tutorial.css Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/tutorial.html Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/tutorial.phyTreeEdit.html Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_phyloalign.fa Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/elegans.fa Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_array.gff3 Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/elegans_expression.gff3 Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/elegans_core.gff3 Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/elegans_acceptor.gff3 Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/elegans_extra.gff3 Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_remarks.gff3 Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/volvox.gff3 Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_trace.gff3 Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/dog1_1700.wig Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_microarray.gff3 Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_trace.scf Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/volvox.fa Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_genes_simple.gff3 Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_genes.gff3 Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_est.gff3 Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/elegans_deletion.gff3 Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_matches.gff3 Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/elegans_repeats.gff3 Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/species.tre Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_bacs.gff3 Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_domains.gff3 Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/HEADER.html Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_all.gff3 Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_all.fa Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/elegans_sts.gff3 Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_phyloalign_wigentries.gff3 Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_geneproducts.gff3 Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/ests.fa Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_phyloalign.gff3 Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_est_targets.gff3 Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_microarray.wig Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/bin/reformat.pl Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/bin/expression_levels.pl Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/bin/random_segments.pl Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/bin/make_exon.pl Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/bin/random_dna.pl Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/bin/random_feature.pl Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/conf_files/elegans_extra.conf Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/conf_files/volvox_final_withPhylo.conf Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/conf_files/volvox.conf Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/conf_files/volvox_refactored.conf Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/conf_files/volvox_quarter.conf Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/conf_files/volvox_final.conf Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/conf_files/elegans_core.conf Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/conf_files/HEADER.html Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/conf_files/volvox_Phylo.conf Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/conf_files/volvox_halfway.conf Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/figures/phylo_align3.gif Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/figures/figure20.gif Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/figures/multiple_alignments1.gif Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/figures/figure14.gif Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/figures/trace1.png Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/figures/enhancements3.gif Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/figures/third_party2.gif Installing 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debian/gbrowse/usr/share/gbrowse/htdocs/js/track_configure.js Installing debian/gbrowse/usr/share/gbrowse/htdocs/example_scripts/gbrowse_new_sessionid.pl Installing debian/gbrowse/usr/share/gbrowse/htdocs/example_scripts/test_file.bed Installing debian/gbrowse/usr/share/gbrowse/htdocs/example_scripts/gbrowse_upload_file.pl Installing debian/gbrowse/usr/share/gbrowse/htdocs/example_scripts/gbrowse_get_sessionid.pl Installing debian/gbrowse/usr/share/gbrowse/htdocs/example_scripts/index.html Installing debian/gbrowse/usr/share/gbrowse/htdocs/example_scripts/README Installing debian/gbrowse/usr/share/gbrowse/htdocs/example_scripts/gbrowse_upload_data.pl Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/GBrowse/ConfigData.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/CGI/Toggle.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Legacy/Graphics/Browser.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Legacy/Graphics/Browser/PageSettings.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Legacy/Graphics/Browser/Util.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Legacy/Graphics/Browser/Synteny.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Legacy/Graphics/Browser/I18n.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Legacy/DB/SyntenyIO.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Legacy/DB/SyntenyBlock.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Karyotype.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/GBrowseFeature.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/UserTracks.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/ExternalData.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Region.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/OptionPick.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/DataLoader.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Util.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Action.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Render.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/DataBase.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Session.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/GFFhelper.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/CAlign.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/RemoteSet.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Realign.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Shellwords.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/TrackDumper.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/PadAlignment.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/DataSource.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/I18n.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Plugin.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Markup.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/PluginSet.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/SendMail.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/CachedTrack.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/UserDB.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/UserTracks/Filesystem.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/UserTracks/Database.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Render/Slave.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Render/TrackConfig.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Render/SnapshotManager.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Render/Login.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Render/HTML/TrackListing.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Render/HTML/TrackListing/Categories.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Render/Slave/AWS_Balancer.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Render/Slave/Status.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Plugin/AuthPlugin.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/DataLoader/bed.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/DataLoader/generic.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/DataLoader/gff.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/DataLoader/gff3.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/DataLoader/bigbed.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/DataLoader/useq.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/DataLoader/sam.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/DataLoader/featurefile.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/DataLoader/bam.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/DataLoader/bigwig.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/DataLoader/archive.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/DataLoader/wig2bigwig.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/DataLoader/wiggle.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/TrackDumper/RichSeqMaker.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/DB/Tagger.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/DB/GFF/Aggregator/waba_alignment.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/DB/GFF/Aggregator/wormbase_gene.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/DB/GFF/Aggregator/match_gap.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/DB/GFF/Aggregator/reftranscript.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/DB/SeqFeature/Store/Alias.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/DB/SeqFeature/Store/BedLoader.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/DB/Tagger/mysql.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/DB/Tagger/Tag.pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataLoader::archive.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::OptionPick.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Plugin.3pm Installing debian/gbrowse/man/man3/Bio::DB::SeqFeature::Store::Alias.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataLoader::useq.3pm Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::CAlign.3pm Installing debian/gbrowse/man/man3/Bio::DB::Tagger.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RemoteSet.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render::Slave::AWS_Balancer.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::GFFhelper.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Plugin::AuthPlugin.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataSource.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RenderPanels.3pm Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm Installing debian/gbrowse/man/man3/GBrowse::ConfigData.3pm Installing debian/gbrowse/man/man3/CGI::Toggle.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Markup.3pm Installing debian/gbrowse/man/man3/Legacy::Graphics::Browser.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Realign.3pm Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::match_gap.3pm Installing debian/gbrowse/man/man3/Bio::DB::Tagger::Tag.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RegionSearch.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Region.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render::Slave::Status.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::AuthorizedFeatureFile.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::PadAlignment.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataBase.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::PluginSet.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Util.3pm Installing debian/gbrowse/bin/ucsc_genes2gff.pl Installing debian/gbrowse/bin/scan_gbrowse.pl Installing debian/gbrowse/bin/gbrowse_change_passwd.pl Installing debian/gbrowse/bin/gbrowse_clean.pl Installing debian/gbrowse/bin/gbrowse_syn_load_alignments_msa.pl Installing debian/gbrowse/bin/gbrowse_sync_aws_slave.pl Installing debian/gbrowse/bin/gbrowse_syn_load_alignment_database.pl Installing debian/gbrowse/bin/gtf2gff3.pl Installing debian/gbrowse/bin/gbrowse_configure_slaves.pl Installing debian/gbrowse/bin/gbrowse_create_account.pl Installing debian/gbrowse/bin/bed2gff3.pl Installing debian/gbrowse/bin/make_das_conf.pl Installing debian/gbrowse/bin/gbrowse_set_admin_passwd.pl Installing debian/gbrowse/bin/gbrowse_aws_balancer.pl Installing debian/gbrowse/bin/gbrowse_grow_cloud_vol.pl Installing debian/gbrowse/bin/load_genbank.pl Installing debian/gbrowse/bin/gbrowse_import_ucsc_db.pl Installing debian/gbrowse/bin/gbrowse_slave Installing debian/gbrowse/bin/gbrowse_metadb_config.pl Installing debian/gbrowse/bin/wiggle2gff3.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 /build/reproducible-path/gbrowse-2.56+dfsg/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 /build/reproducible-path/gbrowse-2.56+dfsg/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-aws-balancer Installing debian/gbrowse/etc/init.d/gbrowse-slave Installing debian/gbrowse/etc/default/gbrowse-aws-balancer Installing debian/gbrowse/etc/default/gbrowse-slave 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/perl5/5.38/auto/Bio/Graphics/Browser2/CAlign/ mkdir -p debian/gbrowse-calign/usr/lib/x86_64-linux-gnu/perl5/5.38/Bio/Graphics/Browser2/ mv debian/gbrowse/usr/share/perl5/auto/Bio/Graphics/Browser2/CAlign/* debian/gbrowse-calign/usr/lib/x86_64-linux-gnu/perl5/5.38/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/perl5/5.38/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 /build/reproducible-path/gbrowse-2.56+dfsg/debian/gbrowse/etc -name '*.new' | xargs file-rename 's/.new//' rm -rf /build/reproducible-path/gbrowse-2.56+dfsg/debian/gbrowse/usr/share/perl5/auto # Update conf files sed -i 's/gbrowse2/gbrowse/g' /build/reproducible-path/gbrowse-2.56+dfsg/debian/gbrowse/etc/gbrowse/yeast*.conf sed -i 's/gbrowse2/gbrowse/g' /build/reproducible-path/gbrowse-2.56+dfsg/debian/gbrowse/etc/gbrowse/slave*.conf # move OpenID constumer secret to /etc/gbrowse to make it system admin configurable mv /build/reproducible-path/gbrowse-2.56+dfsg/debian/gbrowse/usr/share/perl5/GBrowse/ConfigData.pm /build/reproducible-path/gbrowse-2.56+dfsg/debian/gbrowse/etc/gbrowse/ConfigData.pm make[1]: Leaving directory '/build/reproducible-path/gbrowse-2.56+dfsg' dh_install dh_apache2 dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/gbrowse-2.56+dfsg' #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 '/build/reproducible-path/gbrowse-2.56+dfsg' dh_lintian dh_perl debian/rules override_dh_link make[1]: Entering directory '/build/reproducible-path/gbrowse-2.56+dfsg' 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 '/build/reproducible-path/gbrowse-2.56+dfsg' dh_strip_nondeterminism dh_strip_nondeterminism: warning: Ignoring unwritable file: trace1.png dh_strip_nondeterminism: warning: Ignoring unwritable file: config_editing.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: setting_popup.png dh_strip_nondeterminism: warning: Ignoring unwritable file: trace2.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: sugarcane_sorghum_synteny.png dh_strip_nondeterminism: warning: Ignoring unwritable file: multiple_hits.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: upload.png dh_strip_nondeterminism: warning: Ignoring unwritable file: worm_exons_spec.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: upload_list.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: worm_telomeric_spec.png dh_strip_nondeterminism: warning: Ignoring unwritable file: detail_scale.png dh_strip_nondeterminism: warning: Ignoring unwritable file: remote.png dh_strip_nondeterminism: warning: Ignoring unwritable file: grey_0.4_pixel.png dh_strip_nondeterminism: warning: Ignoring unwritable file: snap_mail.png dh_strip_nondeterminism: warning: Ignoring unwritable file: empty.png dh_strip_nondeterminism: warning: Ignoring unwritable file: panleft2.png dh_strip_nondeterminism: warning: Ignoring unwritable file: mminus.png dh_strip_nondeterminism: warning: Ignoring unwritable file: red_peaks.png dh_strip_nondeterminism: warning: Ignoring unwritable file: snap_share.png dh_strip_nondeterminism: warning: Ignoring unwritable file: ex.png dh_strip_nondeterminism: warning: Ignoring unwritable file: pop_in.png dh_strip_nondeterminism: warning: Ignoring unwritable file: menu.png dh_strip_nondeterminism: warning: Ignoring unwritable file: snap_down.png dh_strip_nondeterminism: warning: Ignoring unwritable file: panright.png dh_strip_nondeterminism: warning: Ignoring unwritable file: mplus.png dh_strip_nondeterminism: warning: Ignoring unwritable file: ruler-icon.png dh_strip_nondeterminism: warning: Ignoring unwritable file: panleft.png dh_strip_nondeterminism: warning: Ignoring unwritable file: pop_out.png dh_strip_nondeterminism: warning: Ignoring unwritable file: panright2.png dh_strip_nondeterminism: warning: Ignoring unwritable file: ruler.png dh_strip_nondeterminism: warning: Ignoring unwritable file: dark_0.4_pixel.png dh_strip_nondeterminism: warning: Ignoring unwritable file: minus12.png dh_strip_nondeterminism: warning: Ignoring unwritable file: tools.png dh_strip_nondeterminism: warning: Ignoring unwritable file: snap_check.png dh_strip_nondeterminism: warning: Ignoring unwritable file: blue_peaks.png dh_strip_nondeterminism: warning: Ignoring unwritable file: ficon_2.png dh_strip_nondeterminism: warning: Ignoring unwritable file: square.png dh_strip_nondeterminism: warning: Ignoring unwritable file: trash.png dh_strip_nondeterminism: warning: Ignoring unwritable file: download.png dh_strip_nondeterminism: warning: Ignoring unwritable file: snap_ex.png dh_strip_nondeterminism: warning: Ignoring unwritable file: opacity_thumb.png dh_strip_nondeterminism: warning: Ignoring unwritable file: plus.png dh_strip_nondeterminism: warning: Ignoring unwritable file: query.png dh_strip_nondeterminism: warning: Ignoring unwritable file: fmini_2.png dh_strip_nondeterminism: warning: Ignoring unwritable file: open_open.png dh_strip_nondeterminism: warning: Ignoring unwritable file: minus.png dh_strip_nondeterminism: warning: Ignoring unwritable file: check.png dh_strip_nondeterminism: warning: Ignoring unwritable file: ficon.png dh_strip_nondeterminism: warning: Ignoring unwritable file: share.png dh_strip_nondeterminism: warning: Ignoring unwritable file: grey.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: blogspot-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: balloon.png dh_strip_nondeterminism: warning: Ignoring unwritable file: down_left.png dh_strip_nondeterminism: warning: Ignoring unwritable file: up_left.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: close.png dh_strip_nondeterminism: warning: Ignoring unwritable file: balloon.png dh_strip_nondeterminism: warning: Ignoring unwritable file: down_left.png dh_strip_nondeterminism: warning: Ignoring unwritable file: balloon_ie.png dh_strip_nondeterminism: warning: Ignoring unwritable file: up_left.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: close.png dh_strip_nondeterminism: warning: Ignoring unwritable file: menulink.png dh_strip_nondeterminism: warning: Ignoring unwritable file: menulink_active.png dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-right.png dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-left-open.png dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-left-on.png dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-up-open.png dh_strip_nondeterminism: warning: Ignoring unwritable file: pattern3.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: icon.png dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-up-on.png dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-down-on.png dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-right-open.png dh_strip_nondeterminism: warning: Ignoring unwritable file: pattern1.png dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-up.png dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-down.png dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-right-on.png dh_strip_nondeterminism: warning: Ignoring unwritable file: pattern2.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-data' in '../gbrowse-data_2.56+dfsg-12_all.deb'. dpkg-deb: building package 'gbrowse-calign' in '../gbrowse-calign_2.56+dfsg-12_amd64.deb'. dpkg-deb: building package 'gbrowse-calign-dbgsym' in '../gbrowse-calign-dbgsym_2.56+dfsg-12_amd64.deb'. dpkg-deb: building package 'gbrowse' in '../gbrowse_2.56+dfsg-12_all.deb'. dpkg-genbuildinfo --build=binary -O../gbrowse_2.56+dfsg-12_amd64.buildinfo dpkg-genchanges --build=binary -O../gbrowse_2.56+dfsg-12_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1750147 and its subdirectories I: Current time: Mon Jun 2 07:55:44 -12 2025 I: pbuilder-time-stamp: 1748894144 Tue Apr 30 13:32:46 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Tue Apr 30 13:32:46 UTC 2024 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Tue Apr 30 13:44:28 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Tue Apr 30 13:44:29 UTC 2024 I: 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: amd64 all Version: 2.56+dfsg-12 Distribution: unstable 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: 45c22824a6f4cda4a11b2d1b7817134f3d13c362 31412 gbrowse-calign-dbgsym_2.56+dfsg-12_amd64.deb c855d9bc7e54fbc37d7ddf4d4d3dc98a3403b15c 34192 gbrowse-calign_2.56+dfsg-12_amd64.deb f64eafe90ccc5ee966264c7555d8e3fdc7e79fb7 1233800 gbrowse-data_2.56+dfsg-12_all.deb 39923cb4c406227c967858c51e693055bbe90f5d 2334128 gbrowse_2.56+dfsg-12_all.deb 92a75f551d85226e38a4bc2d223acc6a04a6a93c 11208 gbrowse_2.56+dfsg-12_amd64.buildinfo Checksums-Sha256: bea69e4d5ff35e48ab22a06f22463272383a5e8cd6c019ad19a5933b074c210f 31412 gbrowse-calign-dbgsym_2.56+dfsg-12_amd64.deb a9598ff6945434c63384ddc4cfb579744a26db9f646b75338907518b9729ce48 34192 gbrowse-calign_2.56+dfsg-12_amd64.deb 0851635d6fbcfc33f83e78687df91d23e0e86a8c980d257d75868ea93eddfe0d 1233800 gbrowse-data_2.56+dfsg-12_all.deb d0284a1a1b857ece067ba7afe097e47a6aecf1e29d8ab3c69da32ca63ed67acb 2334128 gbrowse_2.56+dfsg-12_all.deb 51f270e042269ca4563bd29df452c335fd216e2b73fe41df91073dae9578d1c4 11208 gbrowse_2.56+dfsg-12_amd64.buildinfo Files: 204e7a74803a4892b0e1baabaaa77f07 31412 debug optional gbrowse-calign-dbgsym_2.56+dfsg-12_amd64.deb 47a2ea4f008c27b68aaca848f75f8ba4 34192 science optional gbrowse-calign_2.56+dfsg-12_amd64.deb 875255332318ea9349dcecb73533f53f 1233800 science optional gbrowse-data_2.56+dfsg-12_all.deb f922bf5648b8f99fac6b7f15dd5a7cd7 2334128 science optional gbrowse_2.56+dfsg-12_all.deb f9bffd0cb49250addb203d525c9c19cf 11208 science optional gbrowse_2.56+dfsg-12_amd64.buildinfo Tue Apr 30 13:44:30 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_10-4692.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.pJBVuhji/gbrowse_2.56+dfsg-12.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.pJBVuhji/gbrowse_2.56+dfsg-12.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.pJBVuhji/gbrowse_2.56+dfsg-12.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.pJBVuhji/b1/gbrowse_2.56+dfsg-12_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.pJBVuhji/b2/gbrowse_2.56+dfsg-12_amd64.changes ## close_archive (total time: 0.000s) 0.000s 4 calls diffoscope.comparators.xz.XzContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer ## command (total time: 0.386s) 0.252s 6 calls xz 0.066s 7 calls diff 0.045s 10 calls xxd 0.010s 2 calls cmp 0.010s 2 calls cmp (external) 0.002s 10 calls db_dump 0.001s 13 calls cmp (internal) ## compare_files (cumulative) (total time: 1.637s) 0.504s 1 call abc.DotChangesFile 0.468s 1 call abc.DebFile 0.434s 2 calls abc.XzFile 0.140s 1 call abc.DebDataTarFile 0.056s 1 call abc.BerkeleyDBFile 0.030s 1 call abc.TarFile 0.005s 1 call abc.Md5sumsFile ## container_extract (total time: 0.287s) 0.252s 6 calls diffoscope.comparators.xz.XzContainer 0.022s 34 calls diffoscope.comparators.deb.DebTarContainer 0.008s 8 calls diffoscope.comparators.deb.DebContainer 0.004s 8 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 0.010s) 0.010s 4 calls linediff ## has_same_content_as (total time: 0.012s) 0.006s 4 calls abc.DebFile 0.005s 1 call abc.DebDataTarFile 0.000s 3 calls abc.TextFile 0.000s 2 calls abc.Md5sumsFile 0.000s 2 calls abc.XzFile 0.000s 1 call abc.DotChangesFile 0.000s 1 call abc.TarFile 0.000s 1 call abc.BerkeleyDBFile ## main (total time: 0.936s) 0.929s 2 calls outputs 0.008s 1 call cleanup ## open_archive (total time: 0.000s) 0.000s 6 calls diffoscope.comparators.xz.XzContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer 0.000s 2 calls diffoscope.comparators.deb.DebContainer 0.000s 2 calls diffoscope.comparators.deb.DebTarContainer ## output (total time: 0.036s) 0.035s 1 call html 0.001s 1 call text 0.000s 1 call json ## recognizes (total time: 0.126s) 0.056s 12 calls diffoscope.comparators.binary.FilesystemFile 0.036s 722 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.018s 216 calls diffoscope.comparators.debian.DebControlMember 0.016s 260 calls diffoscope.comparators.utils.archive.ArchiveMember ## specialize (total time: 0.065s) 0.065s 15 calls specialize Finished with result: success Main processes terminated with: code=exited/status=1 Service runtime: 1.255s CPU time consumed: 1.290s Tue Apr 30 13:44:32 UTC 2024 W: Diffoscope claims the build is reproducible, but there is a diffoscope file. Please investigate. Tue Apr 30 13:44:32 UTC 2024 E: gbrowse failed to build reproducibly in trixie on amd64. Tue Apr 30 13:44:34 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Apr 30 13:44:34 UTC 2024 I: Submitting 12K b1/gbrowse_2.56+dfsg-12_amd64.buildinfo.asc Tue Apr 30 13:44:35 UTC 2024 I: Submitting 12K b2/gbrowse_2.56+dfsg-12_amd64.buildinfo.asc Tue Apr 30 13:44:36 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Apr 30 13:44:36 UTC 2024 I: Done submitting .buildinfo files. Tue Apr 30 13:44:36 UTC 2024 I: Removing signed gbrowse_2.56+dfsg-12_amd64.buildinfo.asc files: removed './b1/gbrowse_2.56+dfsg-12_amd64.buildinfo.asc' removed './b2/gbrowse_2.56+dfsg-12_amd64.buildinfo.asc'