Mon Jan 8 02:19:21 UTC 2024 I: starting to build gbrowse/bullseye/amd64 on jenkins on '2024-01-08 02:19' Mon Jan 8 02:19:21 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_3/9850/console.log Mon Jan 8 02:19:21 UTC 2024 I: Downloading source for bullseye/gbrowse=2.56+dfsg-8 --2024-01-08 02:19:23-- http://cdn-fastly.deb.debian.org/debian/pool/main/g/gbrowse/gbrowse_2.56%2bdfsg-8.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2670 (2.6K) [text/prs.lines.tag] Saving to: ‘gbrowse_2.56+dfsg-8.dsc’ 0K .. 100% 290M=0s 2024-01-08 02:19:23 (290 MB/s) - ‘gbrowse_2.56+dfsg-8.dsc’ saved [2670/2670] Mon Jan 8 02:19:23 UTC 2024 I: gbrowse_2.56+dfsg-8.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-8 Maintainer: Debian Med Packaging Team Uploaders: Olivier Sallou , Charles Plessy , Aaron M. Ucko , Andreas Tille Homepage: http://gmod.org/wiki/GBrowse Standards-Version: 4.5.0 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 (= 12), 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 1895ac9ed94d8094f2d721a56b9be38a406647d1 23500 gbrowse_2.56+dfsg-8.debian.tar.xz Checksums-Sha256: f6da1ff315b17ec260810cf439a54ae7ddd66728015be03f7fbb6ba795676f81 4355977 gbrowse_2.56+dfsg.orig.tar.gz 6a42f8fe2df079616cf2b48319e50b87d4d143b902a89594b4a5f401d4b78418 23500 gbrowse_2.56+dfsg-8.debian.tar.xz Files: 9638dd3e43897548172911706277f177 4355977 gbrowse_2.56+dfsg.orig.tar.gz 839747414ba7b8a9e89e08462e72d0b5 23500 gbrowse_2.56+dfsg-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl5JJkARHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFe/A//a2/P+64+7SmcSSed+juGdptlQbn6W1aT vJJzgGAPXqJLnlQx1c1NE97IbVkSBphSKsFLZgFfxyOu7cQgxcqbKnM9I22GgLbG cbY72CO9Ujl1fPtFCdQA0baCfwVWIl7OeDwf35khqRPrud1Hl258CSb53tH6NzDz BWXUxbovRiR9ccTZJDJ1BUl8U68+J4Xirvq+AbQrRwVpHm0G23ZYfWucZgjnazFl nTx4KtxBefFcIeN2Z6DQ58qFAFpX4YtEIgI8woL8JUt2PWjjW9vz02qg//nVTW1W LW6/HYs71/U3yOF6vP0HTyVKSEyAoW63r0j3+i/SXJP9hp5V/PLjaPGg+eS9H/7U JXI9Qdzar0k03OHeIho5Xh7qajxiMa4gyvPfXKHYHfs2Z5PYNh1MpcVWb3d/qDBn MVxUhiuUk6kpbBwkk1nnCRKHRaBLsRRAtcf9IlLGwgQkJmSr8cjeg5HZ75pXUKBe +2UWn34UZOb5hUsPwbVQ4jiI5jZ96+WhIL5FSan7BZP5mwzfQlD0aSf6Nt4i4y9v d4JcEILMoHvnoCOaPu9EQ6u7T5QdTIdIOm4X+AHVeYlCSYPT+qsETgEG5O39IVLo 3eG4kADDoe1cBRDujSkRaq1zorTojwKorv9ulNzflm8S6VzPSBcSoa1wiY5YHRLB lEdSKfM2CI8= =gGZv -----END PGP SIGNATURE----- Mon Jan 8 02:19:23 UTC 2024 I: Checking whether the package is not for us Mon Jan 8 02:19:23 UTC 2024 I: Starting 1st build on remote node ionos1-amd64.debian.net. Mon Jan 8 02:19:23 UTC 2024 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Mon Jan 8 02:30:37 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Jan 7 14:19:30 -12 2024 I: pbuilder-time-stamp: 1704680370 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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-8.dsc] I: copying [./gbrowse_2.56+dfsg.orig.tar.gz] I: copying [./gbrowse_2.56+dfsg-8.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.XQPcAJwf/trustedkeys.kbx': General error gpgv: Signature made Sun Feb 16 11:23:44 2020 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./gbrowse_2.56+dfsg-8.dsc 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-8.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 I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4138624/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,-fixfilepath parallel=15 ' DISTRIBUTION='bullseye' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='54bb502814af430fa2faee7935831ec4' 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='4138624' 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.33exSBP8/pbuilderrc_TRRd --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.33exSBP8/b1 --logfile b1/build.log gbrowse_2.56+dfsg-8.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://78.137.99.97:3128' I: uname -a Linux ionos1-amd64 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 24 2020 date -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd -rwxr-xr-x 1 root root 93936 Sep 24 2020 df -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir -rwxr-xr-x 1 root root 84440 Jan 20 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 7 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 7 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep -rwxr-xr-x 1 root root 39680 Sep 24 2020 false -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 69032 Jan 20 2022 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 Jan 25 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98048 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22600 Nov 7 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls -rwxr-xr-x 1 root root 149736 Jan 20 2022 lsblk -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp -rwxr-xr-x 1 root root 59632 Jan 20 2022 more -rwsr-xr-x 1 root root 55528 Jan 20 2022 mount -rwxr-xr-x 1 root root 18664 Jan 20 2022 mountpoint -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv lrwxrwxrwx 1 root root 8 Nov 7 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jan 7 09:30 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty -rwsr-xr-x 1 root root 71912 Jan 20 2022 su -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch -rwxr-xr-x 1 root root 39680 Sep 24 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jan 20 2022 umount -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir -rwxr-xr-x 1 root root 63744 Jan 20 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 7 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/4138624/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 (= 12), 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 ... 17743 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 (= 12); 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: 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} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libalgorithm-diff-perl{a} libanyevent-cachedns-perl{a} libanyevent-http-perl{a} libanyevent-perl{a} libapache-dbi-perl{a} libapache2-mod-perl2{a} libapr1{a} libapr1-dev{a} libaprutil1{a} libaprutil1-dbd-sqlite3{a} libaprutil1-dev{a} libaprutil1-ldap{a} libarchive-zip-perl{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} libcommon-sense-perl{a} libcurl4{a} libdata-stag-perl{a} libdbd-pg-perl{a} libdbd-sqlite3-perl{a} libdbi-perl{a} libdebhelper-perl{a} libdeflate0{a} libdevel-stacktrace-perl{a} libdevel-symdump-perl{a} libelf1{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} libgd-perl{a} libgd3{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} libicu67{a} libio-html-perl{a} libio-socket-ssl-perl{a} libio-string-perl{a} libjansson4{a} libjbig0{a} libjpeg62-turbo{a} libjs-prototype{a} libjs-scriptaculous{a} libjson-perl{a} libldap-2.4-2{a} libldap2-dev{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} libmagic1{a} libmd0{a} libmodule-build-perl{a} libmpdec3{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnghttp2-14{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix2{a} libpipeline1{a} libpng16-16{a} libpq5{a} libpsl5{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsctp-dev{a} libsctp1{a} libsigsegv2{a} libssh2-1{a} libstatistics-descriptive-perl{a} libstring-approx-perl{a} libsub-override-perl{a} libsub-uplevel-perl{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} libtiff5{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} liburi-perl{a} libvm-ec2-perl{a} libwebp6{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxml-libxml-perl{a} libxml-namespacesupport-perl{a} libxml-sax-base-perl{a} libxml-sax-perl{a} libxml-simple-perl{a} libxml2{a} libxpm4{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} perl-openssl-defaults{a} po-debconf{a} python3{a} python3-minimal{a} python3.9{a} python3.9-minimal{a} readline-common{a} rename{a} sensible-utils{a} sqlite3{a} tzdata{a} ucf{a} uuid-dev{a} The following packages are RECOMMENDED but will NOT be installed: bioperl-run 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-perl-run-perl libbio-scf-perl libbsd-resource-perl libcache-cache-perl libcgi-fast-perl libclone-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 libhtml-form-perl libhtml-format-perl libhtml-tableextract-perl libio-stringy-perl libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libmailtools-perl libmldbm-perl libmodule-signature-perl libpod-parser-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-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-expat-perl libxml-sax-writer-perl libxml-twig-perl libxml-writer-perl libyaml-perl lynx perl-doc perl-tk publicsuffix wget 0 packages upgraded, 171 newly installed, 0 to remove and 0 not upgraded. Need to get 49.4 MB of archives. After unpacking 177 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8+deb11u1 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 tzdata all 2021a-1+deb11u10 [286 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 netbase all 6.3 [19.9 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 openssl amd64 1.1.1w-0+deb11u1 [859 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 ca-certificates all 20210119 [158 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3+deb11u1 [273 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3+deb11u1 [128 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3+deb11u1 [69.2 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 ucf all 3.0043 [74.0 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 libapr1 amd64 1.7.0-6+deb11u2 [106 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 libaprutil1 amd64 1.6.1-5+deb11u1 [92.3 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 libaprutil1-dbd-sqlite3 amd64 1.6.1-5+deb11u1 [19.0 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1+deb11u1 [69.1 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1+deb11u1 [106 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3+deb11u1 [232 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libaprutil1-ldap amd64 1.6.1-5+deb11u1 [17.2 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 libcurl4 amd64 7.74.0-1.3+deb11u9 [347 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libjansson4 amd64 2.13.1-1.1 [39.7 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 liblua5.3-0 amd64 5.3.3-1.1+deb11u1 [123 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 apache2-bin amd64 2.4.56-1~deb11u2 [1431 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 uuid-dev amd64 2.36.1-8+deb11u1 [99.4 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 libsctp1 amd64 1.0.18+dfsg-1 [28.3 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 libsctp-dev amd64 1.0.18+dfsg-1 [81.5 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 libapr1-dev amd64 1.7.0-6+deb11u2 [748 kB] Get: 69 http://deb.debian.org/debian bullseye/main amd64 libldap2-dev amd64 2.4.57+dfsg-3+deb11u1 [341 kB] Get: 70 http://deb.debian.org/debian bullseye/main amd64 libexpat1-dev amd64 2.2.10-2+deb11u5 [141 kB] Get: 71 http://deb.debian.org/debian bullseye/main amd64 libaprutil1-dev amd64 1.6.1-5+deb11u1 [409 kB] Get: 72 http://deb.debian.org/debian bullseye/main amd64 libpcre2-16-0 amd64 10.36-2+deb11u1 [232 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 libpcre2-32-0 amd64 10.36-2+deb11u1 [220 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 libpcre2-posix2 amd64 10.36-2+deb11u1 [49.1 kB] Get: 75 http://deb.debian.org/debian bullseye/main amd64 libpcre2-dev amd64 10.36-2+deb11u1 [733 kB] Get: 76 http://deb.debian.org/debian bullseye/main amd64 apache2-dev amd64 2.4.56-1~deb11u2 [368 kB] Get: 77 http://deb.debian.org/debian bullseye/main amd64 libio-string-perl all 1.08-3.1 [11.8 kB] Get: 78 http://deb.debian.org/debian bullseye/main amd64 libdata-stag-perl all 0.14-2 [448 kB] Get: 79 http://deb.debian.org/debian bullseye/main amd64 libbio-perl-perl all 1.7.7-2 [2607 kB] Get: 80 http://deb.debian.org/debian bullseye/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get: 81 http://deb.debian.org/debian bullseye/main amd64 libdevel-stacktrace-perl all 2.0400-1 [28.6 kB] Get: 82 http://deb.debian.org/debian bullseye/main amd64 libexception-class-perl all 1.44-1 [32.3 kB] Get: 83 http://deb.debian.org/debian bullseye/main amd64 libtest-deep-perl all 1.130-1 [49.3 kB] Get: 84 http://deb.debian.org/debian bullseye/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get: 85 http://deb.debian.org/debian bullseye/main amd64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get: 86 http://deb.debian.org/debian bullseye/main amd64 libtext-diff-perl all 1.45-1 [27.7 kB] Get: 87 http://deb.debian.org/debian bullseye/main amd64 libtest-differences-perl all 0.67-1 [18.7 kB] Get: 88 http://deb.debian.org/debian bullseye/main amd64 libsub-uplevel-perl all 0.2800-1.1 [16.5 kB] Get: 89 http://deb.debian.org/debian bullseye/main amd64 libtest-exception-perl all 0.43-1 [18.7 kB] Get: 90 http://deb.debian.org/debian bullseye/main amd64 libtest-warn-perl all 0.36-1 [16.2 kB] Get: 91 http://deb.debian.org/debian bullseye/main amd64 libtest-most-perl all 0.37-1 [24.9 kB] Get: 92 http://deb.debian.org/debian bullseye/main amd64 bioperl all 1.7.7-2 [246 kB] Get: 93 http://deb.debian.org/debian bullseye/main amd64 dh-exec amd64 0.23.2 [26.6 kB] Get: 94 http://deb.debian.org/debian bullseye/main amd64 fonts-dejavu-core all 2.37-2 [1069 kB] Get: 95 http://deb.debian.org/debian bullseye/main amd64 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 96 http://deb.debian.org/debian bullseye/main amd64 libanyevent-perl amd64 7.170-2+b1 [399 kB] Get: 97 http://deb.debian.org/debian bullseye/main amd64 libanyevent-cachedns-perl all 0.08-2.1 [7292 B] Get: 98 http://deb.debian.org/debian bullseye/main amd64 libcommon-sense-perl amd64 3.75-1+b4 [24.6 kB] Get: 99 http://deb.debian.org/debian bullseye/main amd64 libanyevent-http-perl all 2.25-1 [36.5 kB] Get: 100 http://deb.debian.org/debian bullseye/main amd64 libdevel-symdump-perl all 2.18-4 [17.5 kB] Get: 101 http://deb.debian.org/debian bullseye/main amd64 liburi-perl all 5.08-1 [90.6 kB] Get: 102 http://deb.debian.org/debian bullseye/main amd64 libencode-locale-perl all 1.05-1.1 [13.2 kB] Get: 103 http://deb.debian.org/debian bullseye/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 104 http://deb.debian.org/debian bullseye/main amd64 libhttp-date-perl all 6.05-1 [10.4 kB] Get: 105 http://deb.debian.org/debian bullseye/main amd64 libfile-listing-perl all 6.14-1 [12.4 kB] Get: 106 http://deb.debian.org/debian bullseye/main amd64 libhtml-tagset-perl all 3.20-4 [13.0 kB] Get: 107 http://deb.debian.org/debian bullseye/main amd64 libhtml-parser-perl amd64 3.75-1+b1 [105 kB] Get: 108 http://deb.debian.org/debian bullseye/main amd64 libhtml-tree-perl all 5.07-2 [213 kB] Get: 109 http://deb.debian.org/debian bullseye/main amd64 libio-html-perl all 1.004-2 [16.1 kB] Get: 110 http://deb.debian.org/debian bullseye/main amd64 liblwp-mediatypes-perl all 6.04-1 [19.9 kB] Get: 111 http://deb.debian.org/debian bullseye/main amd64 libhttp-message-perl all 6.28-1 [79.6 kB] Get: 112 http://deb.debian.org/debian bullseye/main amd64 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get: 113 http://deb.debian.org/debian bullseye/main amd64 libhttp-negotiate-perl all 6.01-1 [12.8 kB] Get: 114 http://deb.debian.org/debian bullseye/main amd64 perl-openssl-defaults amd64 5 [7360 B] Get: 115 http://deb.debian.org/debian bullseye/main amd64 libnet-ssleay-perl amd64 1.88-3+b1 [321 kB] Get: 116 http://deb.debian.org/debian bullseye/main amd64 libio-socket-ssl-perl all 2.069-1 [215 kB] Get: 117 http://deb.debian.org/debian bullseye/main amd64 libnet-http-perl all 6.20-1 [25.1 kB] Get: 118 http://deb.debian.org/debian bullseye/main amd64 liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get: 119 http://deb.debian.org/debian bullseye/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get: 120 http://deb.debian.org/debian bullseye/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 121 http://deb.debian.org/debian bullseye/main amd64 libwww-perl all 6.52-1 [192 kB] Get: 122 http://deb.debian.org/debian bullseye/main amd64 libapache2-mod-perl2 amd64 2.0.11-4 [887 kB] Get: 123 http://deb.debian.org/debian bullseye/main amd64 libdbi-perl amd64 1.643-3+b1 [780 kB] Get: 124 http://deb.debian.org/debian bullseye/main amd64 libapache-dbi-perl all 1.12-2 [50.7 kB] Get: 125 http://deb.debian.org/debian bullseye/main amd64 libbio-coordinate-perl all 1.7.1-4 [56.7 kB] Get: 126 http://deb.debian.org/debian bullseye/main amd64 libbio-db-biofetch-perl all 1.7.3-4 [17.5 kB] Get: 127 http://deb.debian.org/debian bullseye/main amd64 libcgi-pm-perl all 4.51-1 [224 kB] Get: 128 http://deb.debian.org/debian bullseye/main amd64 libbio-db-gff-perl all 1.7.4-1 [273 kB] Get: 129 http://deb.debian.org/debian bullseye/main amd64 libpq5 amd64 13.11-0+deb11u1 [180 kB] Get: 130 http://deb.debian.org/debian bullseye/main amd64 libdbd-pg-perl amd64 3.14.2-1+b1 [215 kB] Get: 131 http://deb.debian.org/debian bullseye/main amd64 libdbd-sqlite3-perl amd64 1.66-1+b1 [179 kB] Get: 132 http://deb.debian.org/debian bullseye/main amd64 libbio-db-seqfeature-perl all 1.7.4-1 [169 kB] Get: 133 http://deb.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get: 134 http://deb.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.4+dfsg-1+deb11u1 [418 kB] Get: 135 http://deb.debian.org/debian bullseye/main amd64 libfontconfig1 amd64 2.13.1-4.2 [347 kB] Get: 136 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get: 137 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get: 138 http://deb.debian.org/debian bullseye/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get: 139 http://deb.debian.org/debian bullseye/main amd64 libwebp6 amd64 0.6.1-2.1+deb11u2 [259 kB] Get: 140 http://deb.debian.org/debian bullseye/main amd64 libtiff5 amd64 4.2.0-1+deb11u4 [290 kB] Get: 141 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 142 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get: 143 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1+deb11u1 [108 kB] Get: 144 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 145 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get: 146 http://deb.debian.org/debian bullseye/main amd64 libx11-data all 2:1.7.2-1+deb11u1 [311 kB] Get: 147 http://deb.debian.org/debian bullseye/main amd64 libx11-6 amd64 2:1.7.2-1+deb11u1 [772 kB] Get: 148 http://deb.debian.org/debian bullseye/main amd64 libxpm4 amd64 1:3.5.12-1.1~deb11u1 [49.6 kB] Get: 149 http://deb.debian.org/debian bullseye/main amd64 libgd3 amd64 2.3.0-2 [137 kB] Get: 150 http://deb.debian.org/debian bullseye/main amd64 libgd-perl amd64 2.73-1+b1 [141 kB] Get: 151 http://deb.debian.org/debian bullseye/main amd64 libbio-graphics-perl all 2.40-6 [610 kB] Get: 152 http://deb.debian.org/debian bullseye/main amd64 libcgi-session-perl all 4.48-3 [119 kB] Get: 153 http://deb.debian.org/debian bullseye/main amd64 libexporter-tiny-perl all 1.002002-1 [37.8 kB] Get: 154 http://deb.debian.org/debian bullseye/main amd64 libhttp-daemon-perl all 6.12-1+deb11u1 [23.4 kB] Get: 155 http://deb.debian.org/debian bullseye/main amd64 libjs-prototype all 1.7.1-3.1 [39.2 kB] Get: 156 http://deb.debian.org/debian bullseye/main amd64 libjs-scriptaculous all 1.9.0-2.1 [110 kB] Get: 157 http://deb.debian.org/debian bullseye/main amd64 libjson-perl all 4.03000-1 [88.6 kB] Get: 158 http://deb.debian.org/debian bullseye/main amd64 liblist-moreutils-xs-perl amd64 0.430-2 [40.9 kB] Get: 159 http://deb.debian.org/debian bullseye/main amd64 liblist-moreutils-perl all 0.430-2 [46.9 kB] Get: 160 http://deb.debian.org/debian bullseye/main amd64 libmodule-build-perl all 0.423100-1 [258 kB] Get: 161 http://deb.debian.org/debian bullseye/main amd64 libstatistics-descriptive-perl all 3.0800-1 [65.6 kB] Get: 162 http://deb.debian.org/debian bullseye/main amd64 libstring-approx-perl amd64 3.28-1+b3 [40.3 kB] Get: 163 http://deb.debian.org/debian bullseye/main amd64 libterm-readkey-perl amd64 2.38-1+b2 [27.8 kB] Get: 164 http://deb.debian.org/debian bullseye/main amd64 libxml-namespacesupport-perl all 1.12-1.1 [14.9 kB] Get: 165 http://deb.debian.org/debian bullseye/main amd64 libxml-sax-base-perl all 1.09-1.1 [20.7 kB] Get: 166 http://deb.debian.org/debian bullseye/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get: 167 http://deb.debian.org/debian bullseye/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-2+b1 [337 kB] Get: 168 http://deb.debian.org/debian bullseye/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get: 169 http://deb.debian.org/debian bullseye/main amd64 libvm-ec2-perl all 1.28-2 [768 kB] Get: 170 http://deb.debian.org/debian bullseye/main amd64 rename all 1.13-1 [18.0 kB] Get: 171 http://deb.debian.org/debian bullseye/main amd64 sqlite3 amd64 3.34.1-3 [1201 kB] Fetched 49.4 MB in 4s (14.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 17743 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8+deb11u1_amd64.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../1-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. 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Setting up libexpat1:amd64 (2.2.10-2+deb11u5) ... Setting up python3.9-minimal (3.9.2-1) ... 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 ... 18610 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_amd64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... 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Preparing to unpack .../053-libaprutil1-dev_1.6.1-5+deb11u1_amd64.deb ... Unpacking libaprutil1-dev (1.6.1-5+deb11u1) ... Selecting previously unselected package libpcre2-16-0:amd64. Preparing to unpack .../054-libpcre2-16-0_10.36-2+deb11u1_amd64.deb ... Unpacking libpcre2-16-0:amd64 (10.36-2+deb11u1) ... Selecting previously unselected package libpcre2-32-0:amd64. Preparing to unpack .../055-libpcre2-32-0_10.36-2+deb11u1_amd64.deb ... Unpacking libpcre2-32-0:amd64 (10.36-2+deb11u1) ... Selecting previously unselected package libpcre2-posix2:amd64. Preparing to unpack .../056-libpcre2-posix2_10.36-2+deb11u1_amd64.deb ... Unpacking libpcre2-posix2:amd64 (10.36-2+deb11u1) ... Selecting previously unselected package libpcre2-dev:amd64. Preparing to unpack .../057-libpcre2-dev_10.36-2+deb11u1_amd64.deb ... Unpacking libpcre2-dev:amd64 (10.36-2+deb11u1) ... Selecting previously unselected package apache2-dev. Preparing to unpack .../058-apache2-dev_2.4.56-1~deb11u2_amd64.deb ... 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Adding 'diversion of /usr/bin/config_data to /usr/bin/config_data.diverted by libmodule-build-perl' Adding 'diversion of /usr/share/man/man1/config_data.1.gz to /usr/share/man/man1/config_data.diverted.1.gz by libmodule-build-perl' Unpacking libmodule-build-perl (0.423100-1) ... Selecting previously unselected package libstatistics-descriptive-perl. Preparing to unpack .../143-libstatistics-descriptive-perl_3.0800-1_all.deb ... Unpacking libstatistics-descriptive-perl (3.0800-1) ... Selecting previously unselected package libstring-approx-perl. Preparing to unpack .../144-libstring-approx-perl_3.28-1+b3_amd64.deb ... Unpacking libstring-approx-perl (3.28-1+b3) ... Selecting previously unselected package libterm-readkey-perl. Preparing to unpack .../145-libterm-readkey-perl_2.38-1+b2_amd64.deb ... Unpacking libterm-readkey-perl (2.38-1+b2) ... Selecting previously unselected package libxml-namespacesupport-perl. 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Setting up libbrotli1:amd64 (1.0.9-2+b2) ... Setting up liblwp-mediatypes-perl (6.04-1) ... Setting up libtry-tiny-perl (0.30-1) ... Setting up libnghttp2-14:amd64 (1.43.0-1) ... Setting up libmagic1:amd64 (1:5.39-3+deb11u1) ... Setting up libdeflate0:amd64 (1.7-1) ... Setting up libapr1:amd64 (1.7.0-6+deb11u2) ... Setting up perl-openssl-defaults:amd64 (5) ... Setting up libcommon-sense-perl (3.75-1+b4) ... Setting up libxml-namespacesupport-perl (1.12-1.1) ... Setting up gettext-base (0.21-4) ... Setting up libanyevent-http-perl (2.25-1) ... Setting up libencode-locale-perl (1.05-1.1) ... Setting up rename (1.13-1) ... update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode Setting up file (1:5.39-3+deb11u1) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up libpcre2-16-0:amd64 (10.36-2+deb11u1) ... Setting up libjansson4:amd64 (2.13.1-1.1) ... Setting up libmodule-build-perl (0.423100-1) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up tzdata (2021a-1+deb11u10) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Jan 8 02:22:39 UTC 2024. Universal Time is now: Mon Jan 8 02:22:39 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxml-sax-base-perl (1.09-1.1) ... Setting up libio-string-perl (1.08-3.1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libpcre2-32-0:amd64 (10.36-2+deb11u1) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libexpat1-dev:amd64 (2.2.10-2+deb11u5) ... Setting up libjpeg62-turbo:amd64 (1:2.0.6-4) ... Setting up libx11-data (2:1.7.2-1+deb11u1) ... Setting up libtext-diff-perl (1.45-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up uuid-dev:amd64 (2.36.1-8+deb11u1) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up libanyevent-cachedns-perl (0.08-2.1) ... Setting up libpng16-16:amd64 (1.6.37-3) ... Setting up libio-html-perl (1.004-2) ... Setting up autopoint (0.21-4) ... Setting up libwebp6:amd64 (0.6.1-2.1+deb11u2) ... Setting up fonts-dejavu-core (2.37-2) ... Setting up liblist-moreutils-xs-perl (0.430-2) ... Setting up libpcre2-posix2:amd64 (10.36-2+deb11u1) ... Setting up libjs-prototype (1.7.1-3.1) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libmd0:amd64 (1.0.3-3) ... Setting up libsctp1:amd64 (1.0.18+dfsg-1) ... Setting up libdata-stag-perl (0.14-2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up liblua5.3-0:amd64 (5.3.3-1.1+deb11u1) ... Setting up libjson-perl (4.03000-1) ... Setting up libmpdec3:amd64 (2.5.1-1) ... Setting up libsub-uplevel-perl (0.2800-1.1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:amd64 (1.9.0-2) ... Setting up netbase (6.3) ... Setting up libdevel-stacktrace-perl (2.0400-1) ... Setting up libtiff5:amd64 (4.2.0-1+deb11u4) ... Setting up libdevel-symdump-perl (2.18-4) ... Setting up libbio-perl-perl (1.7.7-2) ... Setting up libexporter-tiny-perl (1.002002-1) ... Setting up libterm-readkey-perl (2.38-1+b2) ... Setting up openssl (1.1.1w-0+deb11u1) ... Setting up libbsd0:amd64 (0.11.3-1+deb11u1) ... Setting up libelf1:amd64 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Setting up liburi-perl (5.08-1) ... Setting up libdbi-perl:amd64 (1.643-3+b1) ... Setting up libaprutil1:amd64 (1.6.1-5+deb11u1) ... Setting up libnet-ssleay-perl (1.88-3+b1) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libhttp-date-perl (6.05-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libxcb1:amd64 (1.14-3) ... Setting up gettext (0.21-4) ... Setting up libfile-listing-perl (6.14-1) ... Setting up libpcre2-dev:amd64 (10.36-2+deb11u1) ... Setting up libtool (2.4.6-15) ... Setting up libjs-scriptaculous (1.9.0-2.1) ... Setting up liblist-moreutils-perl (0.430-2) ... Setting up libtest-warn-perl (0.36-1) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up libtest-differences-perl (0.67-1) ... Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Setting up libnet-http-perl (6.20-1) ... Setting up m4 (1.4.18-5) ... Setting up libexception-class-perl (1.44-1) ... Setting up libaprutil1-ldap:amd64 (1.6.1-5+deb11u1) ... Setting up libaprutil1-dbd-sqlite3:amd64 (1.6.1-5+deb11u1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libldap2-dev:amd64 (2.4.57+dfsg-3+deb11u1) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libtest-exception-perl (0.43-1) ... Setting up libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Setting up libsctp-dev:amd64 (1.0.18+dfsg-1) ... Setting up ucf (3.0043) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up libhtml-parser-perl (3.75-1+b1) ... Setting up libcurl4:amd64 (7.74.0-1.3+deb11u9) ... Setting up libx11-6:amd64 (2:1.7.2-1+deb11u1) ... Setting up libdbd-sqlite3-perl:amd64 (1.66-1+b1) ... Setting up sqlite3 (3.34.1-3) ... Setting up libio-socket-ssl-perl (2.069-1) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up libhttp-message-perl (6.28-1) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libhttp-negotiate-perl (6.01-1) ... Setting up libstatistics-descriptive-perl (3.0800-1) ... Setting up libxpm4:amd64 (1:3.5.12-1.1~deb11u1) ... Setting up libhttp-cookies-perl (6.10-1) ... Setting up libtest-most-perl (0.37-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-2) ... Setting up libcgi-pm-perl (4.51-1) ... Setting up libpq5:amd64 (13.11-0+deb11u1) ... Setting up libdbd-pg-perl (3.14.2-1+b1) ... Setting up apache2-bin (2.4.56-1~deb11u2) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-1) ... 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 dh-autoreconf (20) ... Setting up libcgi-session-perl (4.48-3) ... Setting up libxml-libxml-perl (2.0134+dfsg-2+b1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libhttp-daemon-perl (6.12-1+deb11u1) ... Setting up libfontconfig1:amd64 (2.13.1-4.2) ... Setting up python3.9 (3.9.2-1) ... Setting up bioperl (1.7.7-2) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up dh-exec (0.23.2) ... Setting up libbio-coordinate-perl (1.7.1-4) ... Setting up libapr1-dev (1.7.0-6+deb11u2) ... Setting up libgd3:amd64 (2.3.0-2) ... Setting up libxml-simple-perl (2.25-1) ... Setting up libaprutil1-dev (1.6.1-5+deb11u1) ... Setting up apache2-dev (2.4.56-1~deb11u2) ... Setting up libgd-perl (2.73-1+b1) ... Setting up liblwp-protocol-https-perl (6.10-1) ... Setting up libwww-perl (6.52-1) ... Setting up libapache2-mod-perl2 (2.0.11-4) ... Setting up libbio-db-biofetch-perl (1.7.3-4) ... Setting up libvm-ec2-perl (1.28-2) ... Setting up libapache-dbi-perl (1.12-2) ... Setting up libbio-db-gff-perl (1.7.4-1) ... Setting up libbio-db-seqfeature-perl (1.7.4-1) ... Setting up libbio-graphics-perl (2.40-6) ... Processing triggers for libc-bin (2.31-13+deb11u6) ... Processing triggers for ca-certificates (20210119) ... 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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.25.3-1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 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-8_source.changes dpkg-buildpackage: info: source package gbrowse dpkg-buildpackage: info: source version 2.56+dfsg-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with apache2 dh_clean debian/rules build dh build --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 perl Build.PL --installdirs vendor --config "optimize=-g -O2 -fdebug-prefix-map=/build/reproducible-path/gbrowse-2.56+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" --config "ld=x86_64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/gbrowse-2.56+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 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/5.32/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 -fdebug-prefix-map=/build/reproducible-path/gbrowse-2.56+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/gbrowse-2.56+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/reproducible-path/gbrowse-2.56+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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" 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. 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. cannot remove directory for /tmp/gbrowse_testing/f9e529acVB: No such file or directory at t/05.deferredrendering.t line 178. 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 5.032001 for linux # Current time local: Sun Jan 7 14:28:08 2024 # Current time GMT: Mon Jan 8 02:28:08 2024 # Using Test.pm version 1.31 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok All tests successful. Files=10, Tests=448, 174 wallclock secs ( 0.59 usr 0.17 sys + 132.97 cusr 30.77 csys = 164.50 CPU) Result: PASS make[1]: Leaving directory '/build/reproducible-path/gbrowse-2.56+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with apache2 dh_testroot 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/wiggle2gff3.pl.1p Installing debian/gbrowse/man/man1/ucsc_genes2gff.pl.1p Installing debian/gbrowse/man/man1/make_das_conf.pl.1p Installing debian/gbrowse/man/man1/load_genbank.pl.1p Installing debian/gbrowse/man/man1/gtf2gff3.pl.1p Installing debian/gbrowse/man/man1/gbrowse_sync_aws_slave.pl.1p Installing debian/gbrowse/man/man1/gbrowse_grow_cloud_vol.pl.1p Installing debian/gbrowse/man/man1/gbrowse_clean.pl.1p Installing debian/gbrowse/man/man1/gbrowse_aws_balancer.pl.1p Installing debian/gbrowse/man/man1/bed2gff3.pl.1p Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_syn Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_login Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_key_img Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_img Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_gmap Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_details Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbgff Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/das Installing debian/gbrowse/etc/gbrowse/yeast_simple.conf Installing debian/gbrowse/etc/gbrowse/yeast_renderfarm.conf Installing debian/gbrowse/etc/gbrowse/yeast_chr1+2.conf Installing debian/gbrowse/etc/gbrowse/volvox.conf Installing debian/gbrowse/etc/gbrowse/submitter_plugin.conf Installing debian/gbrowse/etc/gbrowse/slave_preload.conf Installing debian/gbrowse/etc/gbrowse/renderfarm.conf Installing debian/gbrowse/etc/gbrowse/pop_demo.conf Installing debian/gbrowse/etc/gbrowse/log4perl.conf Installing debian/gbrowse/etc/gbrowse/GBrowse.conf Installing debian/gbrowse/etc/gbrowse/enzymes.txt Installing debian/gbrowse/etc/gbrowse/detail_select_menu.conf Installing debian/gbrowse/etc/gbrowse/aws_balancer.conf Installing debian/gbrowse/etc/gbrowse/themes/warm_colors Installing debian/gbrowse/etc/gbrowse/themes/transparent_colors Installing debian/gbrowse/etc/gbrowse/themes/solid_gray_colors Installing debian/gbrowse/etc/gbrowse/synteny/wild_rice_synteny.conf Installing debian/gbrowse/etc/gbrowse/synteny/rice_synteny.conf Installing debian/gbrowse/etc/gbrowse/synteny/oryza.synconf.disabled.conf Installing debian/gbrowse/etc/gbrowse/plugins/TrackFinder.pm Installing debian/gbrowse/etc/gbrowse/plugins/TrackDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/TestFinder.pm Installing debian/gbrowse/etc/gbrowse/plugins/TestAuthenticator.pm Installing debian/gbrowse/etc/gbrowse/plugins/test.pm Installing debian/gbrowse/etc/gbrowse/plugins/Submitter.pm Installing debian/gbrowse/etc/gbrowse/plugins/Spectrogram.pm Installing debian/gbrowse/etc/gbrowse/plugins/SourceTrackFinder.pm Installing debian/gbrowse/etc/gbrowse/plugins/SinWave.pm Installing debian/gbrowse/etc/gbrowse/plugins/SimpleTrackFinder.pm Installing debian/gbrowse/etc/gbrowse/plugins/SequenceDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/RestrictionAnnotator.pm Installing debian/gbrowse/etc/gbrowse/plugins/RandomGene.pm Installing debian/gbrowse/etc/gbrowse/plugins/ProteinDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/PrimerDesigner.pm Installing debian/gbrowse/etc/gbrowse/plugins/PamAuthenticate.pm Installing debian/gbrowse/etc/gbrowse/plugins/OligoFinder.pm Installing debian/gbrowse/etc/gbrowse/plugins/LDAPAuthenticate.pm Installing debian/gbrowse/etc/gbrowse/plugins/GeneFinder.pm Installing debian/gbrowse/etc/gbrowse/plugins/FilterTest.pm Installing debian/gbrowse/etc/gbrowse/plugins/FBTableDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/FastaDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/CreateBlastDB.pm Installing debian/gbrowse/etc/gbrowse/plugins/CMapDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/Blat.pm Installing debian/gbrowse/etc/gbrowse/plugins/BatchDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/AttributeHiliter.pm Installing debian/gbrowse/etc/gbrowse/plugins/AlignTwoSequences.pm Installing debian/gbrowse/etc/gbrowse/plugins/Aligner.pm Installing debian/gbrowse/etc/gbrowse/MobyServices/text_xml_renderer.pm Installing debian/gbrowse/etc/gbrowse/MobyServices/text_plain_renderer.pm Installing debian/gbrowse/etc/gbrowse/MobyServices/text_html_renderer.pm Installing debian/gbrowse/etc/gbrowse/MobyServices/text_formatted_renderer.pm Installing debian/gbrowse/etc/gbrowse/MobyServices/moby.conf Installing debian/gbrowse/etc/gbrowse/MobyServices/GbrowseServices.PMS Installing debian/gbrowse/etc/gbrowse/MobyServices/GbrowseServices.pm Installing debian/gbrowse/etc/gbrowse/MobyServices/b64_encoded_jpeg_renderer.pm Installing debian/gbrowse/etc/gbrowse/MobyServices/b64_encoded_gif_renderer.pm Installing debian/gbrowse/etc/gbrowse/languages/zh_cn.pm Installing debian/gbrowse/etc/gbrowse/languages/zh.pm Installing debian/gbrowse/etc/gbrowse/languages/ru.pm Installing debian/gbrowse/etc/gbrowse/languages/POSIX.pm Installing debian/gbrowse/etc/gbrowse/languages/pl.pm Installing debian/gbrowse/etc/gbrowse/languages/nl.pm Installing debian/gbrowse/etc/gbrowse/languages/ko.pm Installing debian/gbrowse/etc/gbrowse/languages/ja.pm Installing debian/gbrowse/etc/gbrowse/languages/it.pm Installing debian/gbrowse/etc/gbrowse/languages/is.pm Installing debian/gbrowse/etc/gbrowse/languages/fr.pm Installing debian/gbrowse/etc/gbrowse/languages/es.pm Installing debian/gbrowse/etc/gbrowse/languages/en.pm Installing debian/gbrowse/etc/gbrowse/languages/de.pm 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/yeast_chr1+2/yeast_chr1+2.gff3 Installing debian/gbrowse/var/lib/gbrowse/databases/yeast_chr1+2/dummy.fa Installing debian/gbrowse/var/lib/gbrowse/databases/pop_demo/pop_demo.gff3 Installing debian/gbrowse/var/lib/gbrowse/databases/ideograms/rat_cytobands.gff 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/gbrowse_syn/wild_rice/wild_rice.gff3 Installing debian/gbrowse/var/lib/gbrowse/databases/gbrowse_syn/rice/rice.gff3 Installing debian/gbrowse/var/lib/gbrowse/databases/gbrowse_syn/alignments/rice.aln.gz Installing debian/gbrowse/var/lib/gbrowse/databases/admin_uploads/README Installing debian/gbrowse/usr/share/gbrowse/htdocs/vbox_index.html Installing debian/gbrowse/usr/share/gbrowse/htdocs/index.html Installing debian/gbrowse/usr/share/gbrowse/htdocs/gmod_cog.jpeg Installing debian/gbrowse/usr/share/gbrowse/htdocs/general_help.html.zh Installing debian/gbrowse/usr/share/gbrowse/htdocs/general_help.html Installing debian/gbrowse/usr/share/gbrowse/htdocs/gbrowse_syn_help.html Installing debian/gbrowse/usr/share/gbrowse/htdocs/gbrowse_karyotype_help.html Installing debian/gbrowse/usr/share/gbrowse/htdocs/cloud_index.html Installing debian/gbrowse/usr/share/gbrowse/htdocs/annotation_help.html Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/tutorial.phyTreeEdit.html Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/tutorial.html Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/tutorial.css Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/figures/wiggle_density.png Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/figures/wiggle_density.gif Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/figures/trace2.png Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/figures/trace1.png Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/figures/third_party5.gif Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/figures/third_party4.gif Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/figures/third_party3.gif Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/figures/third_party2.gif Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/figures/third_party1.gif Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/figures/setting_popup.png Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/figures/semantic_zooming1.gif Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/figures/segmented_features2.gif Installing 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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/Region.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/PluginSet.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/PadAlignment.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/Markup.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/GFFhelper.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/DataSource.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/DataBase.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/CAlign.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/Action.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/TrackDumper/RichSeqMaker.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/Slave.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.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/Render/Slave/AWS_Balancer.pm Installing 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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/featurefile.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/bigbed.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/bam.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/DB/Tagger.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/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/SeqFeature/Store/Alias.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/waba_alignment.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/GFF/Aggregator/match_gap.pm Installing debian/gbrowse/man/man3/Legacy::Graphics::Browser.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::Util.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RenderPanels.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render::Slave::Status.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render::Slave::AWS_Balancer.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RemoteSet.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::Realign.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::PluginSet.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Plugin::AuthPlugin.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Plugin.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::PadAlignment.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::OptionPick.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Markup.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::GFFhelper.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataSource.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataLoader::useq.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataLoader::archive.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataBase.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::CAlign.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::AuthorizedFeatureFile.3pm Installing debian/gbrowse/man/man3/Bio::DB::Tagger::Tag.3pm Installing debian/gbrowse/man/man3/Bio::DB::Tagger.3pm Installing debian/gbrowse/man/man3/Bio::DB::SeqFeature::Store::Alias.3pm Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.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::DB::GFF::Aggregator::match_gap.3pm Installing debian/gbrowse/bin/wiggle2gff3.pl Installing debian/gbrowse/bin/ucsc_genes2gff.pl Installing debian/gbrowse/bin/scan_gbrowse.pl Installing debian/gbrowse/bin/make_das_conf.pl Installing debian/gbrowse/bin/load_genbank.pl Installing debian/gbrowse/bin/gtf2gff3.pl Installing debian/gbrowse/bin/gbrowse_sync_aws_slave.pl Installing debian/gbrowse/bin/gbrowse_syn_load_alignments_msa.pl Installing debian/gbrowse/bin/gbrowse_syn_load_alignment_database.pl Installing debian/gbrowse/bin/gbrowse_slave Installing debian/gbrowse/bin/gbrowse_set_admin_passwd.pl Installing debian/gbrowse/bin/gbrowse_metadb_config.pl Installing debian/gbrowse/bin/gbrowse_import_ucsc_db.pl Installing debian/gbrowse/bin/gbrowse_grow_cloud_vol.pl Installing debian/gbrowse/bin/gbrowse_create_account.pl Installing debian/gbrowse/bin/gbrowse_configure_slaves.pl Installing debian/gbrowse/bin/gbrowse_clean.pl Installing debian/gbrowse/bin/gbrowse_change_passwd.pl Installing debian/gbrowse/bin/gbrowse_aws_balancer.pl Installing debian/gbrowse/bin/bed2gff3.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-slave Installing debian/gbrowse/etc/init.d/gbrowse-aws-balancer Installing debian/gbrowse/etc/default/gbrowse-slave Installing debian/gbrowse/etc/default/gbrowse-aws-balancer Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/GBrowse/ConfigData.pm mv debian/gbrowse/lib/perl5/* debian/gbrowse/usr/share/perl5 # Remove arch dependant data mkdir -p debian/gbrowse-calign/usr/lib/x86_64-linux-gnu/perl5/5.32/auto/Bio/Graphics/Browser2/CAlign/ mkdir -p debian/gbrowse-calign/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Graphics/Browser2/ mv debian/gbrowse/usr/share/perl5/auto/Bio/Graphics/Browser2/CAlign/* debian/gbrowse-calign/usr/lib/x86_64-linux-gnu/perl5/5.32/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/perl5/5.32/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_compress dh_fixperms dh_missing dh_dwz dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'gbrowse-calign' in '../gbrowse-calign_2.56+dfsg-8_amd64.deb'. dpkg-deb: building package 'gbrowse-calign-dbgsym' in '../gbrowse-calign-dbgsym_2.56+dfsg-8_amd64.deb'. dpkg-deb: building package 'gbrowse-data' in '../gbrowse-data_2.56+dfsg-8_all.deb'. dpkg-deb: building package 'gbrowse' in '../gbrowse_2.56+dfsg-8_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../gbrowse_2.56+dfsg-8_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/4138624 and its subdirectories I: Current time: Sun Jan 7 14:30:35 -12 2024 I: pbuilder-time-stamp: 1704681035 Mon Jan 8 02:30:38 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Mon Jan 8 02:30:38 UTC 2024 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Mon Jan 8 02:32:12 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Mon Jan 8 02:32:12 UTC 2024 I: gbrowse_2.56+dfsg-8_amd64.changes: Format: 1.8 Date: Sun, 16 Feb 2020 12:19:11 +0100 Source: gbrowse Binary: gbrowse gbrowse-calign gbrowse-calign-dbgsym gbrowse-data Architecture: amd64 all Version: 2.56+dfsg-8 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: 785314 950746 Changes: gbrowse (2.56+dfsg-8) unstable; urgency=medium . * Multi-Arch: foreign Closes: #785314 * Fix homepage Closes: #950746 * Standards-Version: 4.5.0 (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. Checksums-Sha1: a01a20f99596b7b17f762441ba2242691b4e54a2 27516 gbrowse-calign-dbgsym_2.56+dfsg-8_amd64.deb 58e1be0e73b0e5fdcc2534bb4e1a1e7cc35b87b7 36564 gbrowse-calign_2.56+dfsg-8_amd64.deb 9d03e837394e760442f472611eb58a8e343db5d7 1235028 gbrowse-data_2.56+dfsg-8_all.deb 6026abf6f8f9275aee9111c64bd886511c14b894 2374176 gbrowse_2.56+dfsg-8_all.deb f811c2a4d570ce149de97ed428e44ae8bba8a51c 10738 gbrowse_2.56+dfsg-8_amd64.buildinfo Checksums-Sha256: 4a32af2bc9880569432f40479dabde0487a51be6020d04b5e27ce7859ed41ba7 27516 gbrowse-calign-dbgsym_2.56+dfsg-8_amd64.deb 8dfbc046d6c0b7cd5b2b10547ba321e5a0828d87348c26eb33adbf290db140d7 36564 gbrowse-calign_2.56+dfsg-8_amd64.deb 8ed7db89350388410eb7f05e337ec0d32ab32ca1969ceb9819046052db0c75bf 1235028 gbrowse-data_2.56+dfsg-8_all.deb 71eb171519f883684b584649c0d23def3cafe407058f0bf0940d07b252e90d88 2374176 gbrowse_2.56+dfsg-8_all.deb f1eedfad918124f2cc4bb058eff85fe4d6752239a4658069b1f1270bc97b4bc3 10738 gbrowse_2.56+dfsg-8_amd64.buildinfo Files: b7cd6c36e1f3798d5db60c02eb6f996f 27516 debug optional gbrowse-calign-dbgsym_2.56+dfsg-8_amd64.deb e11e14de447d0afa8362a23c336a01d3 36564 science optional gbrowse-calign_2.56+dfsg-8_amd64.deb c449edc8f492e5ea6680f6d4cb7e4312 1235028 science optional gbrowse-data_2.56+dfsg-8_all.deb eb9baa0dc41a09e3520b84aea6497003 2374176 science optional gbrowse_2.56+dfsg-8_all.deb 2f69490a3a6396e0fef705e910683a39 10738 science optional gbrowse_2.56+dfsg-8_amd64.buildinfo Mon Jan 8 02:32:15 UTC 2024 I: diffoscope 240 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.33exSBP8/gbrowse_2.56+dfsg-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.33exSBP8/gbrowse_2.56+dfsg-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.33exSBP8/gbrowse_2.56+dfsg-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.33exSBP8/b1/gbrowse_2.56+dfsg-8_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.33exSBP8/b2/gbrowse_2.56+dfsg-8_amd64.changes ## close_archive (total time: 0.000s) 0.000s 4 calls diffoscope.comparators.deb.DebContainer 0.000s 10 calls diffoscope.comparators.xz.XzContainer 0.000s 6 calls diffoscope.comparators.tar.TarContainer 0.000s 4 calls diffoscope.comparators.deb.DebTarContainer ## command (total time: 1.305s) 0.873s 10 calls xz 0.360s 10 calls diff 0.032s 10 calls xxd 0.015s 1 call cmp 0.015s 1 call cmp (external) 0.007s 96 calls cmp (internal) 0.003s 10 calls db_dump ## compare_files (cumulative) (total time: 11.847s) 3.350s 1 call abc.DotChangesFile 3.183s 2 calls abc.DebFile 3.039s 3 calls abc.XzFile 2.068s 2 calls abc.DebDataTarFile 0.111s 1 call abc.BerkeleyDBFile 0.057s 1 call abc.TarFile 0.025s 1 call abc.TextFile 0.014s 1 call abc.Md5sumsFile ## container_extract (total time: 1.302s) 0.874s 10 calls diffoscope.comparators.xz.XzContainer 0.343s 1220 calls diffoscope.comparators.deb.DebTarContainer 0.070s 16 calls diffoscope.comparators.deb.DebContainer 0.016s 10 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 0.126s) 0.126s 8 calls linediff ## has_same_content_as (total time: 0.031s) 0.016s 2 calls abc.DebDataTarFile 0.011s 68 calls abc.TextFile 0.002s 13 calls abc.HtmlFile 0.001s 4 calls abc.DebFile 0.001s 4 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.000s 4 calls abc.XzFile 0.000s 2 calls abc.Md5sumsFile 0.000s 1 call abc.BerkeleyDBFile 0.000s 1 call abc.DotChangesFile 0.000s 1 call abc.TarFile ## main (total time: 6.534s) 6.532s 2 calls outputs 0.002s 1 call cleanup ## open_archive (total time: 0.000s) 0.000s 10 calls diffoscope.comparators.xz.XzContainer 0.000s 6 calls diffoscope.comparators.tar.TarContainer 0.000s 4 calls diffoscope.comparators.deb.DebContainer 0.000s 4 calls diffoscope.comparators.deb.DebTarContainer ## output (total time: 0.183s) 0.180s 1 call html 0.003s 1 call json 0.001s 1 call text ## recognizes (total time: 1.033s) 0.554s 4810 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.283s 12 calls diffoscope.comparators.binary.FilesystemFile 0.111s 216 calls diffoscope.comparators.debian.DebControlMember 0.085s 394 calls diffoscope.comparators.utils.archive.ArchiveMember 0.000s 10 calls abc.DotChangesFile 0.000s 16 calls abc.Md5sumsFile 0.000s 16 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink ## specialize (total time: 0.731s) 0.731s 100 calls specialize Mon Jan 8 02:32:23 UTC 2024 E: gbrowse failed to build reproducibly in bullseye on amd64. Mon Jan 8 02:32:23 UTC 2024 E: diffoscope 240 found issues, please check https://tests.reproducible-builds.org/debian/dbd/bullseye/amd64/gbrowse_2.56+dfsg-8.diffoscope.html Mon Jan 8 02:32:46 UTC 2024 I: Submitting .buildinfo files to external archives: Mon Jan 8 02:32:46 UTC 2024 I: Submitting 12K b1/gbrowse_2.56+dfsg-8_amd64.buildinfo.asc Mon Jan 8 02:32:47 UTC 2024 I: Submitting 12K b2/gbrowse_2.56+dfsg-8_amd64.buildinfo.asc Mon Jan 8 02:32:48 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Jan 8 02:32:48 UTC 2024 I: Done submitting .buildinfo files. Mon Jan 8 02:32:48 UTC 2024 I: Removing signed gbrowse_2.56+dfsg-8_amd64.buildinfo.asc files: removed './b1/gbrowse_2.56+dfsg-8_amd64.buildinfo.asc' removed './b2/gbrowse_2.56+dfsg-8_amd64.buildinfo.asc'