I: pbuilder: network access will be disabled during build
I: Current time: Mon Feb 17 20:38:17 -12 2025
I: pbuilder-time-stamp: 1739867897
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-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: using eatmydata during job
I: Copying source file
I: copying [gbrowse_2.56+dfsg-11.dsc]
I: copying [./gbrowse_2.56+dfsg.orig.tar.gz]
I: copying [./gbrowse_2.56+dfsg-11.debian.tar.xz]
I: Extracting source
gpgv: Signature made Fri Sep 30 09:31:20 2022
gpgv: using RSA key 5FB46F83D3B952046335D26D78DC68DB326D8438
gpgv: issuer "osallou@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./gbrowse_2.56+dfsg-11.dsc: no acceptable signature found
dpkg-source: info: extracting gbrowse in gbrowse-2.56+dfsg
dpkg-source: info: unpacking gbrowse_2.56+dfsg.orig.tar.gz
dpkg-source: info: unpacking gbrowse_2.56+dfsg-11.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying debian-packaging-patch
dpkg-source: info: applying gbrowse-slave-fix_defaults_path
dpkg-source: info: applying manpages.patch
dpkg-source: info: applying fix_pop_url
dpkg-source: info: applying skip_check_installed_test.patch
dpkg-source: info: applying source_init_functions
dpkg-source: info: applying init_script_dependency.patch
dpkg-source: info: applying fix_runlevel.patch
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying fix_whatis_entry.patch
dpkg-source: info: applying remove_copy_of_LoadHelper.pm.patch
dpkg-source: info: applying fix_gd2_deprecation
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/36273/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='i386'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 '
DISTRIBUTION='bookworm'
HOME='/root'
HOST_ARCH='i386'
IFS='
'
INVOCATION_ID='4e6af2774089469ab65b30d77c5776f1'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
LD_LIBRARY_PATH='/usr/lib/libeatmydata'
LD_PRELOAD='libeatmydata.so'
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='36273'
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.z18cz0R5/pbuilderrc_CcO4 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.z18cz0R5/b1 --logfile b1/build.log gbrowse_2.56+dfsg-11.dsc'
SUDO_GID='112'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://85.184.249.68:3128'
I: uname -a
Linux ionos6-i386 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 6036
-rwxr-xr-x 1 root root 1408088 Apr 23 2023 bash
-rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2
-rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep
-rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2
-rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore
-rwxr-xr-x 1 root root 42920 Sep 20 2022 cat
-rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp
-rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod
-rwxr-xr-x 1 root root 79816 Sep 20 2022 chown
-rwxr-xr-x 1 root root 162024 Sep 20 2022 cp
-rwxr-xr-x 1 root root 136916 Jan 5 2023 dash
-rwxr-xr-x 1 root root 137160 Sep 20 2022 date
-rwxr-xr-x 1 root root 100364 Sep 20 2022 dd
-rwxr-xr-x 1 root root 108940 Sep 20 2022 df
-rwxr-xr-x 1 root root 162152 Sep 20 2022 dir
-rwxr-xr-x 1 root root 87760 Mar 23 2023 dmesg
lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname
-rwxr-xr-x 1 root root 38760 Sep 20 2022 echo
-rwxr-xr-x 1 root root 41 Jan 24 2023 egrep
-rwxr-xr-x 1 root root 34664 Sep 20 2022 false
-rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep
-rwxr-xr-x 1 root root 84272 Mar 23 2023 findmnt
-rwsr-xr-x 1 root root 30240 Mar 23 2023 fusermount
-rwxr-xr-x 1 root root 218680 Jan 24 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 100952 Apr 10 2022 gzip
-rwxr-xr-x 1 root root 21916 Dec 19 2022 hostname
-rwxr-xr-x 1 root root 75756 Sep 20 2022 ln
-rwxr-xr-x 1 root root 55600 Mar 23 2023 login
-rwxr-xr-x 1 root root 162152 Sep 20 2022 ls
-rwxr-xr-x 1 root root 214568 Mar 23 2023 lsblk
-rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir
-rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod
-rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp
-rwxr-xr-x 1 root root 63016 Mar 23 2023 more
-rwsr-xr-x 1 root root 58912 Mar 23 2023 mount
-rwxr-xr-x 1 root root 13856 Mar 23 2023 mountpoint
-rwxr-xr-x 1 root root 157932 Sep 20 2022 mv
lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash
-rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink
-rwxr-xr-x 1 root root 75720 Sep 20 2022 rm
-rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir
-rwxr-xr-x 1 root root 22308 Jul 28 2023 run-parts
-rwxr-xr-x 1 root root 133224 Jan 5 2023 sed
lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash
-rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep
-rwxr-xr-x 1 root root 87976 Sep 20 2022 stty
-rwsr-xr-x 1 root root 83492 Mar 23 2023 su
-rwxr-xr-x 1 root root 38792 Sep 20 2022 sync
-rwxr-xr-x 1 root root 598456 Apr 6 2023 tar
-rwxr-xr-x 1 root root 13860 Jul 28 2023 tempfile
-rwxr-xr-x 1 root root 120776 Sep 20 2022 touch
-rwxr-xr-x 1 root root 34664 Sep 20 2022 true
-rwxr-xr-x 1 root root 17892 Mar 23 2023 ulockmgr_server
-rwsr-xr-x 1 root root 30236 Mar 23 2023 umount
-rwxr-xr-x 1 root root 38760 Sep 20 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress
-rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir
-rwxr-xr-x 1 root root 71216 Mar 23 2023 wdctl
lrwxrwxrwx 1 root root 8 Dec 19 2022 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 6460 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 8103 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/36273/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: i386
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: bioperl, debhelper-compat (= 13), dh-apache2, dh-exec, apache2-dev, libbio-graphics-perl, libbio-coordinate-perl, libbio-db-seqfeature-perl, libcapture-tiny-perl, libcgi-session-perl, libgd-gd2-perl | libgd-gd2-noxpm-perl, libio-string-perl, libjson-perl, libstatistics-descriptive-perl, libwww-perl, libhttp-daemon-perl, perl, sqlite3, libdbd-sqlite3-perl, libterm-readkey-perl, libjs-prototype, libjs-scriptaculous, libvm-ec2-perl, libmodule-build-perl, libcgi-pm-perl, rename
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 18156 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on bioperl; however:
Package bioperl is not installed.
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on dh-apache2; however:
Package dh-apache2 is not installed.
pbuilder-satisfydepends-dummy depends on dh-exec; however:
Package dh-exec is not installed.
pbuilder-satisfydepends-dummy depends on apache2-dev; however:
Package apache2-dev is not installed.
pbuilder-satisfydepends-dummy depends on libbio-graphics-perl; however:
Package libbio-graphics-perl is not installed.
pbuilder-satisfydepends-dummy depends on libbio-coordinate-perl; however:
Package libbio-coordinate-perl is not installed.
pbuilder-satisfydepends-dummy depends on libbio-db-seqfeature-perl; however:
Package libbio-db-seqfeature-perl is not installed.
pbuilder-satisfydepends-dummy depends on libcapture-tiny-perl; however:
Package libcapture-tiny-perl is not installed.
pbuilder-satisfydepends-dummy depends on libcgi-session-perl; however:
Package libcgi-session-perl is not installed.
pbuilder-satisfydepends-dummy depends on libgd-gd2-perl | libgd-gd2-noxpm-perl; however:
Package libgd-gd2-perl is not installed.
Package libgd-gd2-noxpm-perl is not installed.
pbuilder-satisfydepends-dummy depends on libio-string-perl; however:
Package libio-string-perl is not installed.
pbuilder-satisfydepends-dummy depends on libjson-perl; however:
Package libjson-perl is not installed.
pbuilder-satisfydepends-dummy depends on libstatistics-descriptive-perl; however:
Package libstatistics-descriptive-perl is not installed.
pbuilder-satisfydepends-dummy depends on libwww-perl; however:
Package libwww-perl is not installed.
pbuilder-satisfydepends-dummy depends on libhttp-daemon-perl; however:
Package libhttp-daemon-perl is not installed.
pbuilder-satisfydepends-dummy depends on sqlite3; however:
Package sqlite3 is not installed.
pbuilder-satisfydepends-dummy depends on libdbd-sqlite3-perl; however:
Package libdbd-sqlite3-perl is not installed.
pbuilder-satisfydepends-dummy depends on libterm-readkey-perl; however:
Package libterm-readkey-perl is not installed.
pbuilder-satisfydepends-dummy depends on libjs-prototype; however:
Package libjs-prototype is not installed.
pbuilder-satisfydepends-dummy depends on libjs-scriptaculous; however:
Package libjs-scriptaculous is not installed.
pbuilder-satisfydepends-dummy depends on libvm-ec2-perl; however:
Package libvm-ec2-perl is not installed.
pbuilder-satisfydepends-dummy depends on libmodule-build-perl; however:
Package libmodule-build-perl is not installed.
pbuilder-satisfydepends-dummy depends on libcgi-pm-perl; however:
Package libcgi-pm-perl is not installed.
pbuilder-satisfydepends-dummy depends on rename; however:
Package rename is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
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} libabsl20220623{a} libalgorithm-diff-perl{a} libanyevent-cachedns-perl{a} libanyevent-http-perl{a} libanyevent-perl{a} libaom3{a} libapache-dbi-perl{a} libapache2-mod-perl2{a} libapr1{a} libapr1-dev{a} libaprutil1{a} libaprutil1-dbd-sqlite3{a} libaprutil1-dev{a} libaprutil1-ldap{a} libarchive-zip-perl{a} libavif15{a} libbio-coordinate-perl{a} libbio-db-biofetch-perl{a} libbio-db-gff-perl{a} libbio-db-seqfeature-perl{a} libbio-graphics-perl{a} libbio-perl-perl{a} libbrotli1{a} libbsd0{a} libcapture-tiny-perl{a} libcgi-pm-perl{a} libcgi-session-perl{a} libclass-data-inheritable-perl{a} libclone-perl{a} libcommon-sense-perl{a} libcurl4{a} libdata-stag-perl{a} libdav1d6{a} libdbd-pg-perl{a} libdbd-sqlite3-perl{a} libdbi-perl{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libdevel-stacktrace-perl{a} libdevel-symdump-perl{a} 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} libgav1-1{a} libgd-perl{a} libgd3{a} libheif1{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-daemon-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libicu72{a} libio-html-perl{a} libio-socket-ssl-perl{a} libio-string-perl{a} libjbig0{a} libjpeg62-turbo{a} libjs-prototype{a} libjs-scriptaculous{a} libjson-perl{a} libldap-2.5-0{a} libldap-dev{a} libldap2-dev{a} liblerc4{a} liblist-moreutils-perl{a} liblist-moreutils-xs-perl{a} liblua5.3-0{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1{a} libmodule-build-perl{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnghttp2-14{a} libnuma1{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpipeline1{a} libpng16-16{a} libpq5{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} librav1e0{a} libreadline8{a} libregexp-ipv6-perl{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsctp-dev{a} libsctp1{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} libtiff6{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} liburi-perl{a} libvm-ec2-perl{a} libwebp7{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libx265-199{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} libyuv0{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} python3.11{a} python3.11-minimal{a} readline-common{a} rename{a} sensible-utils{a} sqlite3{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 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 libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libmailtools-perl libmldbm-perl libmodule-signature-perl libpod-readme-perl libpostscript-perl libsasl2-modules libset-scalar-perl libsoap-lite-perl libsoftware-license-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl libxml-dom-xpath-perl libxml-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, 181 newly installed, 0 to remove and 0 not upgraded.
Need to get 54.9 MB of archives. After unpacking 198 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main i386 libpython3.11-minimal i386 3.11.2-6 [813 kB]
Get: 2 http://deb.debian.org/debian bookworm/main i386 libexpat1 i386 2.5.0-1 [103 kB]
Get: 3 http://deb.debian.org/debian bookworm/main i386 python3.11-minimal i386 3.11.2-6 [2130 kB]
Get: 4 http://deb.debian.org/debian bookworm/main i386 python3-minimal i386 3.11.2-1+b1 [26.3 kB]
Get: 5 http://deb.debian.org/debian bookworm/main i386 media-types all 10.0.0 [26.1 kB]
Get: 6 http://deb.debian.org/debian bookworm/main i386 readline-common all 8.2-1.3 [69.0 kB]
Get: 7 http://deb.debian.org/debian bookworm/main i386 libreadline8 i386 8.2-1.3 [171 kB]
Get: 8 http://deb.debian.org/debian bookworm/main i386 libpython3.11-stdlib i386 3.11.2-6 [1799 kB]
Get: 9 http://deb.debian.org/debian bookworm/main i386 python3.11 i386 3.11.2-6 [572 kB]
Get: 10 http://deb.debian.org/debian bookworm/main i386 libpython3-stdlib i386 3.11.2-1+b1 [9308 B]
Get: 11 http://deb.debian.org/debian bookworm/main i386 python3 i386 3.11.2-1+b1 [26.3 kB]
Get: 12 http://deb.debian.org/debian bookworm/main i386 netbase all 6.4 [12.8 kB]
Get: 13 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 14 http://deb.debian.org/debian bookworm/main i386 openssl i386 3.0.11-1~deb12u2 [1423 kB]
Get: 15 http://deb.debian.org/debian bookworm/main i386 ca-certificates all 20230311 [153 kB]
Get: 16 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB]
Get: 17 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB]
Get: 18 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB]
Get: 19 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB]
Get: 20 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB]
Get: 21 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB]
Get: 22 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB]
Get: 23 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB]
Get: 24 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB]
Get: 25 http://deb.debian.org/debian bookworm/main i386 ucf all 3.0043+nmu1 [55.2 kB]
Get: 26 http://deb.debian.org/debian bookworm/main i386 libapr1 i386 1.7.2-3 [110 kB]
Get: 27 http://deb.debian.org/debian bookworm/main i386 libaprutil1 i386 1.6.3-1 [95.2 kB]
Get: 28 http://deb.debian.org/debian bookworm/main i386 libaprutil1-dbd-sqlite3 i386 1.6.3-1 [13.9 kB]
Get: 29 http://deb.debian.org/debian bookworm/main i386 libsasl2-modules-db i386 2.1.28+dfsg-10 [21.4 kB]
Get: 30 http://deb.debian.org/debian bookworm/main i386 libsasl2-2 i386 2.1.28+dfsg-10 [62.7 kB]
Get: 31 http://deb.debian.org/debian bookworm/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5 [196 kB]
Get: 32 http://deb.debian.org/debian bookworm/main i386 libaprutil1-ldap i386 1.6.3-1 [12.0 kB]
Get: 33 http://deb.debian.org/debian bookworm/main i386 libbrotli1 i386 1.0.9-2+b6 [275 kB]
Get: 34 http://deb.debian.org/debian bookworm/main i386 libnghttp2-14 i386 1.52.0-1+deb12u1 [80.7 kB]
Get: 35 http://deb.debian.org/debian bookworm/main i386 libpsl5 i386 0.21.2-1 [59.3 kB]
Get: 36 http://deb.debian.org/debian bookworm/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB]
Get: 37 http://deb.debian.org/debian bookworm/main i386 libssh2-1 i386 1.10.0-3+b1 [187 kB]
Get: 38 http://deb.debian.org/debian bookworm/main i386 libcurl4 i386 7.88.1-10+deb12u4 [424 kB]
Get: 39 http://deb.debian.org/debian bookworm/main i386 liblua5.3-0 i386 5.3.6-2 [144 kB]
Get: 40 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB]
Get: 41 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.3~deb12u1 [720 kB]
Get: 42 http://deb.debian.org/debian bookworm/main i386 apache2-bin i386 2.4.57-2 [1430 kB]
Get: 43 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 44 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB]
Get: 45 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB]
Get: 46 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 47 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB]
Get: 48 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 49 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB]
Get: 50 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 51 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 52 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B]
Get: 53 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 54 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 55 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB]
Get: 56 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB]
Get: 57 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB]
Get: 58 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 59 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 60 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB]
Get: 61 http://deb.debian.org/debian bookworm/main i386 uuid-dev i386 2.38.1-5+b1 [40.2 kB]
Get: 62 http://deb.debian.org/debian bookworm/main i386 libsctp1 i386 1.0.19+dfsg-2 [30.2 kB]
Get: 63 http://deb.debian.org/debian bookworm/main i386 libsctp-dev i386 1.0.19+dfsg-2 [72.9 kB]
Get: 64 http://deb.debian.org/debian bookworm/main i386 libapr1-dev i386 1.7.2-3 [764 kB]
Get: 65 http://deb.debian.org/debian bookworm/main i386 libldap-dev i386 2.5.13+dfsg-5 [318 kB]
Get: 66 http://deb.debian.org/debian bookworm/main i386 libldap2-dev all 2.5.13+dfsg-5 [22.6 kB]
Get: 67 http://deb.debian.org/debian bookworm/main i386 libexpat1-dev i386 2.5.0-1 [158 kB]
Get: 68 http://deb.debian.org/debian bookworm/main i386 libaprutil1-dev i386 1.6.3-1 [419 kB]
Get: 69 http://deb.debian.org/debian bookworm/main i386 libpcre2-16-0 i386 10.42-1 [243 kB]
Get: 70 http://deb.debian.org/debian bookworm/main i386 libpcre2-32-0 i386 10.42-1 [232 kB]
Get: 71 http://deb.debian.org/debian bookworm/main i386 libpcre2-posix3 i386 10.42-1 [55.4 kB]
Get: 72 http://deb.debian.org/debian bookworm/main i386 libpcre2-dev i386 10.42-1 [761 kB]
Get: 73 http://deb.debian.org/debian bookworm/main i386 apache2-dev i386 2.4.57-2 [306 kB]
Get: 74 http://deb.debian.org/debian bookworm/main i386 libio-string-perl all 1.08-4 [12.1 kB]
Get: 75 http://deb.debian.org/debian bookworm/main i386 libdata-stag-perl all 0.14-3 [448 kB]
Get: 76 http://deb.debian.org/debian bookworm/main i386 libbio-perl-perl all 1.7.8-1 [2603 kB]
Get: 77 http://deb.debian.org/debian bookworm/main i386 libclass-data-inheritable-perl all 0.08-3 [8588 B]
Get: 78 http://deb.debian.org/debian bookworm/main i386 libdevel-stacktrace-perl all 2.0400-2 [26.8 kB]
Get: 79 http://deb.debian.org/debian bookworm/main i386 libexception-class-perl all 1.45-1 [34.6 kB]
Get: 80 http://deb.debian.org/debian bookworm/main i386 libtest-deep-perl all 1.204-1 [52.9 kB]
Get: 81 http://deb.debian.org/debian bookworm/main i386 libcapture-tiny-perl all 0.48-2 [24.6 kB]
Get: 82 http://deb.debian.org/debian bookworm/main i386 libalgorithm-diff-perl all 1.201-1 [43.3 kB]
Get: 83 http://deb.debian.org/debian bookworm/main i386 libtext-diff-perl all 1.45-2 [27.2 kB]
Get: 84 http://deb.debian.org/debian bookworm/main i386 libtest-differences-perl all 0.69-1 [18.9 kB]
Get: 85 http://deb.debian.org/debian bookworm/main i386 libsub-uplevel-perl all 0.2800-3 [14.0 kB]
Get: 86 http://deb.debian.org/debian bookworm/main i386 libtest-exception-perl all 0.43-3 [16.9 kB]
Get: 87 http://deb.debian.org/debian bookworm/main i386 libtest-warn-perl all 0.37-2 [14.5 kB]
Get: 88 http://deb.debian.org/debian bookworm/main i386 libtest-most-perl all 0.38-1 [25.1 kB]
Get: 89 http://deb.debian.org/debian bookworm/main i386 bioperl all 1.7.8-1 [246 kB]
Get: 90 http://deb.debian.org/debian bookworm/main i386 dh-exec i386 0.27 [28.2 kB]
Get: 91 http://deb.debian.org/debian bookworm/main i386 fonts-dejavu-core all 2.37-6 [1068 kB]
Get: 92 http://deb.debian.org/debian bookworm/main i386 fontconfig-config i386 2.14.1-4 [315 kB]
Get: 93 http://deb.debian.org/debian bookworm/main i386 libabsl20220623 i386 20220623.1-1 [444 kB]
Get: 94 http://deb.debian.org/debian bookworm/main i386 libanyevent-perl i386 7.170-2+b3 [394 kB]
Get: 95 http://deb.debian.org/debian bookworm/main i386 libanyevent-cachedns-perl all 0.08-3 [7708 B]
Get: 96 http://deb.debian.org/debian bookworm/main i386 libcommon-sense-perl i386 3.75-3 [23.0 kB]
Get: 97 http://deb.debian.org/debian bookworm/main i386 libanyevent-http-perl all 2.25-2 [35.2 kB]
Get: 98 http://deb.debian.org/debian bookworm/main i386 libaom3 i386 3.6.0-1 [1895 kB]
Get: 99 http://deb.debian.org/debian bookworm/main i386 libdevel-symdump-perl all 2.18-5 [15.8 kB]
Get: 100 http://deb.debian.org/debian bookworm/main i386 libregexp-ipv6-perl all 0.03-3 [5212 B]
Get: 101 http://deb.debian.org/debian bookworm/main i386 liburi-perl all 5.17-1 [90.4 kB]
Get: 102 http://deb.debian.org/debian bookworm/main i386 libencode-locale-perl all 1.05-3 [12.9 kB]
Get: 103 http://deb.debian.org/debian bookworm/main i386 libtimedate-perl all 2.3300-2 [39.3 kB]
Get: 104 http://deb.debian.org/debian bookworm/main i386 libhttp-date-perl all 6.05-2 [10.5 kB]
Get: 105 http://deb.debian.org/debian bookworm/main i386 libfile-listing-perl all 6.15-1 [12.6 kB]
Get: 106 http://deb.debian.org/debian bookworm/main i386 libhtml-tagset-perl all 3.20-6 [11.7 kB]
Get: 107 http://deb.debian.org/debian bookworm/main i386 libhtml-parser-perl i386 3.81-1 [102 kB]
Get: 108 http://deb.debian.org/debian bookworm/main i386 libhtml-tree-perl all 5.07-3 [211 kB]
Get: 109 http://deb.debian.org/debian bookworm/main i386 libclone-perl i386 0.46-1 [13.8 kB]
Get: 110 http://deb.debian.org/debian bookworm/main i386 libio-html-perl all 1.004-3 [16.2 kB]
Get: 111 http://deb.debian.org/debian bookworm/main i386 liblwp-mediatypes-perl all 6.04-2 [20.2 kB]
Get: 112 http://deb.debian.org/debian bookworm/main i386 libhttp-message-perl all 6.44-1 [81.7 kB]
Get: 113 http://deb.debian.org/debian bookworm/main i386 libhttp-cookies-perl all 6.10-1 [19.6 kB]
Get: 114 http://deb.debian.org/debian bookworm/main i386 libhttp-negotiate-perl all 6.01-2 [13.1 kB]
Get: 115 http://deb.debian.org/debian bookworm/main i386 perl-openssl-defaults i386 7+b1 [7920 B]
Get: 116 http://deb.debian.org/debian bookworm/main i386 libnet-ssleay-perl i386 1.92-2+b1 [318 kB]
Get: 117 http://deb.debian.org/debian bookworm/main i386 libio-socket-ssl-perl all 2.081-2 [219 kB]
Get: 118 http://deb.debian.org/debian bookworm/main i386 libnet-http-perl all 6.22-1 [25.3 kB]
Get: 119 http://deb.debian.org/debian bookworm/main i386 liblwp-protocol-https-perl all 6.10-1 [12.2 kB]
Get: 120 http://deb.debian.org/debian bookworm/main i386 libtry-tiny-perl all 0.31-2 [22.6 kB]
Get: 121 http://deb.debian.org/debian bookworm/main i386 libwww-robotrules-perl all 6.02-1 [12.9 kB]
Get: 122 http://deb.debian.org/debian bookworm/main i386 libwww-perl all 6.68-1 [186 kB]
Get: 123 http://deb.debian.org/debian bookworm/main i386 libapache2-mod-perl2 i386 2.0.12-1+b2 [895 kB]
Get: 124 http://deb.debian.org/debian bookworm/main i386 libdbi-perl i386 1.643-4 [777 kB]
Get: 125 http://deb.debian.org/debian bookworm/main i386 libapache-dbi-perl all 1.12-3 [48.5 kB]
Get: 126 http://deb.debian.org/debian bookworm/main i386 libdav1d6 i386 1.0.0-2 [316 kB]
Get: 127 http://deb.debian.org/debian bookworm/main i386 libgav1-1 i386 0.18.0-1+b1 [307 kB]
Get: 128 http://deb.debian.org/debian bookworm/main i386 librav1e0 i386 0.5.1-6 [615 kB]
Get: 129 http://deb.debian.org/debian bookworm/main i386 libjpeg62-turbo i386 1:2.1.5-2 [169 kB]
Get: 130 http://deb.debian.org/debian bookworm/main i386 libyuv0 i386 0.0~git20230123.b2528b0-1 [108 kB]
Get: 131 http://deb.debian.org/debian bookworm/main i386 libavif15 i386 0.11.1-1 [101 kB]
Get: 132 http://deb.debian.org/debian bookworm/main i386 libbio-coordinate-perl all 1.7.1-4 [56.7 kB]
Get: 133 http://deb.debian.org/debian bookworm/main i386 libbio-db-biofetch-perl all 1.7.3-4 [17.5 kB]
Get: 134 http://deb.debian.org/debian bookworm/main i386 libcgi-pm-perl all 4.55-1 [220 kB]
Get: 135 http://deb.debian.org/debian bookworm/main i386 libbio-db-gff-perl all 1.7.4-1 [273 kB]
Get: 136 http://deb.debian.org/debian bookworm/main i386 libpq5 i386 15.5-0+deb12u1 [194 kB]
Get: 137 http://deb.debian.org/debian bookworm/main i386 libdbd-pg-perl i386 3.16.0-2 [213 kB]
Get: 138 http://deb.debian.org/debian bookworm/main i386 libdbd-sqlite3-perl i386 1.72-1 [182 kB]
Get: 139 http://deb.debian.org/debian bookworm/main i386 libbio-db-seqfeature-perl all 1.7.4-2 [169 kB]
Get: 140 http://deb.debian.org/debian bookworm/main i386 libpng16-16 i386 1.6.39-2 [283 kB]
Get: 141 http://deb.debian.org/debian bookworm/main i386 libfreetype6 i386 2.12.1+dfsg-5 [410 kB]
Get: 142 http://deb.debian.org/debian bookworm/main i386 libfontconfig1 i386 2.14.1-4 [398 kB]
Get: 143 http://deb.debian.org/debian bookworm/main i386 libde265-0 i386 1.0.11-1+deb12u1 [193 kB]
Get: 144 http://deb.debian.org/debian bookworm/main i386 libnuma1 i386 2.0.16-1 [22.7 kB]
Get: 145 http://deb.debian.org/debian bookworm/main i386 libx265-199 i386 3.5-2+b1 [687 kB]
Get: 146 http://deb.debian.org/debian bookworm/main i386 libheif1 i386 1.15.1-1 [230 kB]
Get: 147 http://deb.debian.org/debian bookworm/main i386 libdeflate0 i386 1.14-1 [57.5 kB]
Get: 148 http://deb.debian.org/debian bookworm/main i386 libjbig0 i386 2.1-6.1 [31.6 kB]
Get: 149 http://deb.debian.org/debian bookworm/main i386 liblerc4 i386 4.0.0+ds-2 [181 kB]
Get: 150 http://deb.debian.org/debian bookworm/main i386 libwebp7 i386 1.2.4-0.2+deb12u1 [294 kB]
Get: 151 http://deb.debian.org/debian bookworm/main i386 libtiff6 i386 4.5.0-6+deb12u1 [332 kB]
Get: 152 http://deb.debian.org/debian bookworm/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB]
Get: 153 http://deb.debian.org/debian bookworm/main i386 libbsd0 i386 0.11.7-2 [121 kB]
Get: 154 http://deb.debian.org/debian bookworm/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB]
Get: 155 http://deb.debian.org/debian bookworm/main i386 libxcb1 i386 1.15-1 [148 kB]
Get: 156 http://deb.debian.org/debian bookworm/main i386 libx11-data all 2:1.8.4-2+deb12u2 [292 kB]
Get: 157 http://deb.debian.org/debian bookworm/main i386 libx11-6 i386 2:1.8.4-2+deb12u2 [782 kB]
Get: 158 http://deb.debian.org/debian bookworm/main i386 libxpm4 i386 1:3.5.12-1.1+deb12u1 [50.4 kB]
Get: 159 http://deb.debian.org/debian bookworm/main i386 libgd3 i386 2.3.3-9 [129 kB]
Get: 160 http://deb.debian.org/debian bookworm/main i386 libgd-perl i386 2.76-4+b1 [131 kB]
Get: 161 http://deb.debian.org/debian bookworm/main i386 libbio-graphics-perl all 2.40-6 [610 kB]
Get: 162 http://deb.debian.org/debian bookworm/main i386 libcgi-session-perl all 4.48-4 [118 kB]
Get: 163 http://deb.debian.org/debian bookworm/main i386 libexporter-tiny-perl all 1.006000-1 [38.6 kB]
Get: 164 http://deb.debian.org/debian bookworm/main i386 libhttp-daemon-perl all 6.16-1 [23.5 kB]
Get: 165 http://deb.debian.org/debian bookworm/main i386 libjs-prototype all 1.7.3-1 [44.3 kB]
Get: 166 http://deb.debian.org/debian bookworm/main i386 libjs-scriptaculous all 1.9.0-3 [110 kB]
Get: 167 http://deb.debian.org/debian bookworm/main i386 libjson-perl all 4.10000-1 [87.5 kB]
Get: 168 http://deb.debian.org/debian bookworm/main i386 liblist-moreutils-xs-perl i386 0.430-3+b1 [44.9 kB]
Get: 169 http://deb.debian.org/debian bookworm/main i386 liblist-moreutils-perl all 0.430-2 [46.9 kB]
Get: 170 http://deb.debian.org/debian bookworm/main i386 libmodule-build-perl all 0.423200-1 [253 kB]
Get: 171 http://deb.debian.org/debian bookworm/main i386 libstatistics-descriptive-perl all 3.0800-1 [65.6 kB]
Get: 172 http://deb.debian.org/debian bookworm/main i386 libstring-approx-perl i386 3.28-2+b1 [39.6 kB]
Get: 173 http://deb.debian.org/debian bookworm/main i386 libterm-readkey-perl i386 2.38-2+b1 [25.1 kB]
Get: 174 http://deb.debian.org/debian bookworm/main i386 libxml-namespacesupport-perl all 1.12-2 [15.1 kB]
Get: 175 http://deb.debian.org/debian bookworm/main i386 libxml-sax-base-perl all 1.09-3 [20.6 kB]
Get: 176 http://deb.debian.org/debian bookworm/main i386 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB]
Get: 177 http://deb.debian.org/debian bookworm/main i386 libxml-libxml-perl i386 2.0207+dfsg+really+2.0134-1+b1 [333 kB]
Get: 178 http://deb.debian.org/debian bookworm/main i386 libxml-simple-perl all 2.25-2 [69.8 kB]
Get: 179 http://deb.debian.org/debian bookworm/main i386 libvm-ec2-perl all 1.28-4 [760 kB]
Get: 180 http://deb.debian.org/debian bookworm/main i386 rename all 2.01-1 [21.0 kB]
Get: 181 http://deb.debian.org/debian bookworm/main i386 sqlite3 i386 3.40.1-2 [370 kB]
Fetched 54.9 MB in 1s (55.2 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libpython3.11-minimal:i386.
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Setting up libpython3.11-minimal:i386 (3.11.2-6) ...
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done.
Reading package lists...
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/gbrowse-2.56+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../gbrowse_2.56+dfsg-11_source.changes
dpkg-buildpackage: info: source package gbrowse
dpkg-buildpackage: info: source version 2.56+dfsg-11
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Olivier Sallou <osallou@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
debian/rules clean
dh clean --with apache2
dh_clean
debian/rules binary
dh binary --with apache2
dh_update_autotools_config
dh_autoreconf
debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/reproducible-path/gbrowse-2.56+dfsg'
dh_auto_configure -- --conf=/etc/gbrowse --htdocs=/usr/share/gbrowse/htdocs --tmp=/var/cache/gbrowse --databases=/var/lib/gbrowse/databases --cgibin=/usr/lib/cgi-bin/gbrowse --www-user=www-data --registration_done=1 --persistent=/var/lib/gbrowse
/usr/bin/perl Build.PL --installdirs vendor --config "optimize=-g -O2 -ffile-prefix-map=/build/reproducible-path/gbrowse-2.56+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" --config "ld=i686-linux-gnu-gcc -g -O2 -ffile-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
/usr/bin/perl Build
NOTE: Run ./Build reconfig to change existing configuration.
Building GBrowse
i686-linux-gnu-gcc -I/build/reproducible-path/gbrowse-2.56+dfsg/libalign -I/usr/lib/i386-linux-gnu/perl/5.36/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 -ffile-prefix-map=/build/reproducible-path/gbrowse-2.56+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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')
i686-linux-gnu-gcc -g -O2 -ffile-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"
/usr/bin/perl Build test --verbose 1 "TEST_FILES=t/00.compile.t t/01.yeast.t t/02.rearchitecture.t t/05.deferredrendering.t t/07.balancer.t t/08.calign.t"
NOTE: Run ./Build reconfig to change existing configuration.
Use of uninitialized value in pattern match (m//) at /build/reproducible-path/gbrowse-2.56+dfsg/install_util/GBrowseInstall.pm line 778.
t/00.compile.t ............
ok 1 - cgi-bin/das compiled ok
ok 2 - cgi-bin/das stderr said "syntax OK"
ok 3 - cgi-bin/das nothing on stdout
ok 4 - cgi-bin/gbgff compiled ok
ok 5 - cgi-bin/gbgff stderr said "syntax OK"
ok 6 - cgi-bin/gbgff nothing on stdout
ok 7 - cgi-bin/gbrowse compiled ok
ok 8 - cgi-bin/gbrowse stderr said "syntax OK"
ok 9 - cgi-bin/gbrowse nothing on stdout
ok 10 - cgi-bin/gbrowse_details compiled ok
ok 11 - cgi-bin/gbrowse_details stderr said "syntax OK"
ok 12 - cgi-bin/gbrowse_details nothing on stdout
ok 13 # skip explicitly skipping cgi-bin/gbrowse_gmap
ok 14 - cgi-bin/gbrowse_img compiled ok
ok 15 - cgi-bin/gbrowse_img stderr said "syntax OK"
ok 16 - cgi-bin/gbrowse_img nothing on stdout
ok 17 - cgi-bin/gbrowse_key_img compiled ok
ok 18 - cgi-bin/gbrowse_key_img stderr said "syntax OK"
ok 19 - cgi-bin/gbrowse_key_img nothing on stdout
ok 20 - cgi-bin/gbrowse_login compiled ok
ok 21 - cgi-bin/gbrowse_login stderr said "syntax OK"
ok 22 - cgi-bin/gbrowse_login nothing on stdout
ok 23 - cgi-bin/gbrowse_syn compiled ok
ok 24 - cgi-bin/gbrowse_syn stderr said "syntax OK"
ok 25 - cgi-bin/gbrowse_syn nothing on stdout
ok 26 - bin/auto_install_databases.pl compiled ok
ok 27 - bin/auto_install_databases.pl stderr said "syntax OK"
ok 28 - bin/auto_install_databases.pl nothing on stdout
ok 29 - bin/bed2gff3.pl compiled ok
ok 30 - bin/bed2gff3.pl stderr said "syntax OK"
ok 31 - bin/bed2gff3.pl nothing on stdout
ok 32 - bin/bp_load_gff.pl compiled ok
ok 33 - bin/bp_load_gff.pl stderr said "syntax OK"
ok 34 - bin/bp_load_gff.pl nothing on stdout
ok 35 # skip explicitly skipping bin/gbrowse_aws_balancer.pl
ok 36 - bin/gbrowse_change_passwd.pl compiled ok
ok 37 - bin/gbrowse_change_passwd.pl stderr said "syntax OK"
ok 38 - bin/gbrowse_change_passwd.pl nothing on stdout
ok 39 - bin/gbrowse_clean.pl compiled ok
ok 40 - bin/gbrowse_clean.pl stderr said "syntax OK"
ok 41 - bin/gbrowse_clean.pl nothing on stdout
ok 42 - bin/gbrowse_configure_slaves.pl compiled ok
ok 43 - bin/gbrowse_configure_slaves.pl stderr said "syntax OK"
ok 44 - bin/gbrowse_configure_slaves.pl nothing on stdout
ok 45 - bin/gbrowse_create_account.pl compiled ok
ok 46 - bin/gbrowse_create_account.pl stderr said "syntax OK"
ok 47 - bin/gbrowse_create_account.pl nothing on stdout
ok 48 # skip explicitly skipping bin/gbrowse_grow_cloud_vol.pl
ok 49 - bin/gbrowse_import_ucsc_db.pl compiled ok
ok 50 - bin/gbrowse_import_ucsc_db.pl stderr said "syntax OK"
ok 51 - bin/gbrowse_import_ucsc_db.pl nothing on stdout
ok 52 - bin/gbrowse_metadb_config.pl compiled ok
ok 53 - bin/gbrowse_metadb_config.pl stderr said "syntax OK"
ok 54 - bin/gbrowse_metadb_config.pl nothing on stdout
ok 55 # skip explicitly skipping bin/gbrowse_netinstall.pl
ok 56 # skip explicitly skipping bin/gbrowse_netinstall2.pl
ok 57 - bin/gbrowse_set_admin_passwd.pl compiled ok
ok 58 - bin/gbrowse_set_admin_passwd.pl stderr said "syntax OK"
ok 59 - bin/gbrowse_set_admin_passwd.pl nothing on stdout
ok 60 - bin/gbrowse_slave compiled ok
ok 61 - bin/gbrowse_slave stderr said "syntax OK"
ok 62 - bin/gbrowse_slave nothing on stdout
ok 63 # skip explicitly skipping bin/gbrowse_slave_start_aws.sh
ok 64 - bin/gbrowse_syn_load_alignment_database.pl compiled ok
ok 65 - bin/gbrowse_syn_load_alignment_database.pl stderr said "syntax OK"
ok 66 - bin/gbrowse_syn_load_alignment_database.pl nothing on stdout
ok 67 - bin/gbrowse_syn_load_alignments_msa.pl compiled ok
ok 68 - bin/gbrowse_syn_load_alignments_msa.pl stderr said "syntax OK"
ok 69 - bin/gbrowse_syn_load_alignments_msa.pl nothing on stdout
ok 70 # skip explicitly skipping bin/gbrowse_sync_aws_slave.pl
ok 71 - bin/gtf2gff3.pl compiled ok
ok 72 - bin/gtf2gff3.pl stderr said "syntax OK"
ok 73 - bin/gtf2gff3.pl nothing on stdout
ok 74 - bin/load_genbank.pl compiled ok
ok 75 - bin/load_genbank.pl stderr said "syntax OK"
ok 76 - bin/load_genbank.pl nothing on stdout
ok 77 # skip explicitly skipping bin/make_das_conf.pl
ok 78 - bin/process_bamfiles.pl compiled ok
ok 79 - bin/process_bamfiles.pl stderr said "syntax OK"
ok 80 - bin/process_bamfiles.pl nothing on stdout
ok 81 - bin/process_gadfly.pl compiled ok
ok 82 - bin/process_gadfly.pl stderr said "syntax OK"
ok 83 - bin/process_gadfly.pl nothing on stdout
ok 84 - bin/process_ncbi_human.pl compiled ok
ok 85 - bin/process_ncbi_human.pl stderr said "syntax OK"
ok 86 - bin/process_ncbi_human.pl nothing on stdout
ok 87 - bin/process_sgd.pl compiled ok
ok 88 - bin/process_sgd.pl stderr said "syntax OK"
ok 89 - bin/process_sgd.pl nothing on stdout
ok 90 - bin/report_missing_language_tags.pl compiled ok
ok 91 - bin/report_missing_language_tags.pl stderr said "syntax OK"
ok 92 - bin/report_missing_language_tags.pl nothing on stdout
ok 93 - bin/scan_gbrowse.pl compiled ok
ok 94 - bin/scan_gbrowse.pl stderr said "syntax OK"
ok 95 - bin/scan_gbrowse.pl nothing on stdout
ok 96 - bin/split_wig.pl compiled ok
ok 97 - bin/split_wig.pl stderr said "syntax OK"
ok 98 - bin/split_wig.pl nothing on stdout
ok 99 - bin/ucsc_genes2gff.pl compiled ok
ok 100 - bin/ucsc_genes2gff.pl stderr said "syntax OK"
ok 101 - bin/ucsc_genes2gff.pl nothing on stdout
ok 102 - bin/wiggle2gff3.pl compiled ok
ok 103 - bin/wiggle2gff3.pl stderr said "syntax OK"
ok 104 - bin/wiggle2gff3.pl nothing on stdout
1..104
ok
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781.
t/01.yeast.t ..............
1..7
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ok
t/02.rearchitecture.t .....
1..90
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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, <GEN171> line 2.
Use of uninitialized value $_[5] in pack at /usr/share/perl5/Bio/DB/IndexedBase.pm line 1005, <GEN176> line 2.
cannot unlink file for /tmp/gbrowse_testing/NvDdemtCaM/sequence.42755.fasta: No such file or directory at t/03.render.t line 40.
cannot restore permissions to 0100666 for /tmp/gbrowse_testing/NvDdemtCaM/sequence.42755.fasta: No such file or directory at t/03.render.t line 40.
cannot remove directory for /tmp/gbrowse_testing/NvDdemtCaM: No such file or directory at t/03.render.t line 40.
t/03.render.t .............
1..150
ok 1
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ok
Sometimes this test gets 'stuck'. If this happens, kill the test and Build test again.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781.
Can't locate object method "png" via package "�PNG
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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
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ok 30
ok 31
ok 32
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ok 34
ok 35
ok 36
ok 37
ok 38
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ok 40
ok 41
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Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781.
Can't locate object method "png" via package "�PNG
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Can't locate object method "png" via package "�PNG
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�E��z(��s��]u��%%a����IEND�B`�"?) at /build/reproducible-path/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/CachedTrack.pm line 154, <> line 45.
t/05.deferredrendering.t ..
1..19
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 778.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 781.
t/06.featuresearch.t ......
1..26
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok
t/07.balancer.t ........... skipped: Optional module Parse::Apache::ServerStatus not installed
t/07.karyotype.t ..........
1..3
ok 1
ok 2
ok 3
ok
t/08.calign.t .............
1..6
# Running under perl version 5.036000 for linux
# Current time local: Tue Feb 18 08:39:10 2025
# Current time GMT: Tue Feb 18 08:39:10 2025
# Using Test.pm version 1.31
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok
All tests successful.
Files=10, Tests=448, 26 wallclock secs ( 0.08 usr 0.02 sys + 11.84 cusr 2.48 csys = 14.42 CPU)
Result: PASS
make[1]: Leaving directory '/build/reproducible-path/gbrowse-2.56+dfsg'
create-stamp debian/debhelper-build-stamp
dh_prep
debian/rules override_dh_installdirs
make[1]: Entering directory '/build/reproducible-path/gbrowse-2.56+dfsg'
# svn(-buildpackage) seems to ignore the x bit
chmod +x debian/gbrowse-calign.dirs
dh_installdirs
make[1]: Leaving directory '/build/reproducible-path/gbrowse-2.56+dfsg'
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/reproducible-path/gbrowse-2.56+dfsg'
./Build --install_base=debian/gbrowse debianinstall
NOTE: Run ./Build reconfig to change existing configuration.
Use of uninitialized value in pattern match (m//) at /build/reproducible-path/gbrowse-2.56+dfsg/install_util/GBrowseInstall.pm line 778.
Building GBrowse
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/auto/Bio/Graphics/Browser2/CAlign/CAlign.so
Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/auto/Bio/Graphics/Browser2/CAlign/CAlign.bs
Installing debian/gbrowse/man/man1/load_genbank.pl.1p
Installing debian/gbrowse/man/man1/gbrowse_aws_balancer.pl.1p
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Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/UserTracks/Filesystem.pm
Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/UserTracks/Database.pm
Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/DB/Tagger.pm
Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/DB/Tagger/mysql.pm
Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/DB/Tagger/Tag.pm
Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/DB/GFF/Aggregator/match_gap.pm
Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/DB/GFF/Aggregator/waba_alignment.pm
Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/DB/GFF/Aggregator/wormbase_gene.pm
Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/DB/GFF/Aggregator/reftranscript.pm
Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/DB/SeqFeature/Store/BedLoader.pm
Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/DB/SeqFeature/Store/Alias.pm
Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Legacy/Graphics/Browser.pm
Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Legacy/Graphics/Browser/Synteny.pm
Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Legacy/Graphics/Browser/I18n.pm
Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Legacy/Graphics/Browser/Util.pm
Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Legacy/Graphics/Browser/PageSettings.pm
Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Legacy/DB/SyntenyIO.pm
Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Legacy/DB/SyntenyBlock.pm
Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/GBrowse/ConfigData.pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataLoader::archive.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::CAlign.3pm
Installing debian/gbrowse/man/man3/Bio::DB::Tagger::Tag.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataLoader::useq.3pm
Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Util.3pm
Installing debian/gbrowse/man/man3/Bio::DB::SeqFeature::Store::Alias.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Realign.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Plugin::AuthPlugin.3pm
Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Installing debian/gbrowse/man/man3/CGI::Toggle.3pm
Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RegionSearch.3pm
Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataSource.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::GFFhelper.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render.3pm
Installing debian/gbrowse/man/man3/GBrowse::ConfigData.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataBase.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RenderPanels.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RemoteSet.3pm
Installing debian/gbrowse/man/man3/Bio::DB::Tagger.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::AuthorizedFeatureFile.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Markup.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render::Slave::AWS_Balancer.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Region.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/Legacy::Graphics::Browser.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render::Slave::Status.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::OptionPick.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::PluginSet.3pm
Installing debian/gbrowse/bin/gbrowse_grow_cloud_vol.pl
Installing debian/gbrowse/bin/gbrowse_change_passwd.pl
Installing debian/gbrowse/bin/gtf2gff3.pl
Installing debian/gbrowse/bin/gbrowse_aws_balancer.pl
Installing debian/gbrowse/bin/gbrowse_create_account.pl
Installing debian/gbrowse/bin/gbrowse_sync_aws_slave.pl
Installing debian/gbrowse/bin/wiggle2gff3.pl
Installing debian/gbrowse/bin/scan_gbrowse.pl
Installing debian/gbrowse/bin/bed2gff3.pl
Installing debian/gbrowse/bin/gbrowse_syn_load_alignment_database.pl
Installing debian/gbrowse/bin/gbrowse_slave
Installing debian/gbrowse/bin/gbrowse_import_ucsc_db.pl
Installing debian/gbrowse/bin/make_das_conf.pl
Installing debian/gbrowse/bin/gbrowse_metadb_config.pl
Installing debian/gbrowse/bin/load_genbank.pl
Installing debian/gbrowse/bin/gbrowse_clean.pl
Installing debian/gbrowse/bin/gbrowse_set_admin_passwd.pl
Installing debian/gbrowse/bin/gbrowse_syn_load_alignments_msa.pl
Installing debian/gbrowse/bin/gbrowse_configure_slaves.pl
Installing debian/gbrowse/bin/ucsc_genes2gff.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, <GEN91> 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, <GEN97> line 20.
Building GBrowse
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing debian/gbrowse/etc/default/gbrowse-aws-balancer
Installing debian/gbrowse/etc/default/gbrowse-slave
Installing debian/gbrowse/etc/init.d/gbrowse-aws-balancer
Installing debian/gbrowse/etc/init.d/gbrowse-slave
Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/GBrowse/ConfigData.pm
mv debian/gbrowse/lib/perl5/* debian/gbrowse/usr/share/perl5
# Remove arch dependant data
mkdir -p debian/gbrowse-calign/usr/lib/i386-linux-gnu/perl5/5.36/auto/Bio/Graphics/Browser2/CAlign/
mkdir -p debian/gbrowse-calign/usr/lib/i386-linux-gnu/perl5/5.36/Bio/Graphics/Browser2/
mv debian/gbrowse/usr/share/perl5/auto/Bio/Graphics/Browser2/CAlign/* debian/gbrowse-calign/usr/lib/i386-linux-gnu/perl5/5.36/auto/Bio/Graphics/Browser2/CAlign/
mv debian/gbrowse/usr/share/perl5/Bio/Graphics/Browser2/CAlign.pm debian/gbrowse-calign/usr/lib/i386-linux-gnu/perl5/5.36/Bio/Graphics/Browser2/CAlign.pm
rm -rf debian/gbrowse/lib
rm -f debian/gbrowse/usr/share/doc/gbrowse/INSTALL
rm -f debian/gbrowse/usr/share/perl5/auto/GBrowse/.packlist
rm -f debian/gbrowse/usr/share/gbrowse/htdocs/js/prototype.js
rm -f debian/gbrowse/usr/share/gbrowse/htdocs/js/scriptaculous.js
chmod 644 debian/gbrowse/etc/gbrowse/MobyServices/text_xml_renderer.pm
chmod 644 debian/gbrowse/etc/gbrowse/synteny/oryza.synconf.disabled.conf
#Remove database (kept as separate package)
rm -rf debian/gbrowse/var/lib/gbrowse/databases/*
#Rename pl scripts in bin
file-rename 's/\.pl//' debian/gbrowse/bin/*.pl
mv debian/gbrowse/bin debian/gbrowse/usr/bin
# Activate configuration files.
find /build/reproducible-path/gbrowse-2.56+dfsg/debian/gbrowse/etc -name '*.new' | xargs file-rename 's/.new//'
rm -rf /build/reproducible-path/gbrowse-2.56+dfsg/debian/gbrowse/usr/share/perl5/auto
# Update conf files
sed -i 's/gbrowse2/gbrowse/g' /build/reproducible-path/gbrowse-2.56+dfsg/debian/gbrowse/etc/gbrowse/yeast*.conf
sed -i 's/gbrowse2/gbrowse/g' /build/reproducible-path/gbrowse-2.56+dfsg/debian/gbrowse/etc/gbrowse/slave*.conf
# move OpenID constumer secret to /etc/gbrowse to make it system admin configurable
mv /build/reproducible-path/gbrowse-2.56+dfsg/debian/gbrowse/usr/share/perl5/GBrowse/ConfigData.pm /build/reproducible-path/gbrowse-2.56+dfsg/debian/gbrowse/etc/gbrowse/ConfigData.pm
make[1]: Leaving directory '/build/reproducible-path/gbrowse-2.56+dfsg'
dh_install
dh_apache2
dh_installdocs
dh_installchangelogs
debian/rules override_dh_installman
make[1]: Entering directory '/build/reproducible-path/gbrowse-2.56+dfsg'
#Rename due to perl extension seen as polish
file-rename 's/\.pl\.1p/\.1p/' debian/gbrowse/man/man1/*.pl.1p
mkdir -p debian/gbrowse-calign/man/man3/
mv debian/gbrowse/man/man3/Bio::Graphics::Browser2::CAlign.3pm debian/gbrowse-calign/man/man3/Bio::Graphics::Browser2::CAlign.3pm
dh_installman
rm -rf debian/gbrowse/man
rm -rf debian/gbrowse-calign/man
make[1]: Leaving directory '/build/reproducible-path/gbrowse-2.56+dfsg'
dh_lintian
dh_perl
debian/rules override_dh_link
make[1]: Entering directory '/build/reproducible-path/gbrowse-2.56+dfsg'
dh_link
# Fix broken link ... even if I habe no idea what a link to a not existing dir should serve for
ln -sf /var/cache/gbrowse/images debian/gbrowse/usr/share/gbrowse/htdocs/i
make[1]: Leaving directory '/build/reproducible-path/gbrowse-2.56+dfsg'
dh_strip_nondeterminism
dh_strip_nondeterminism: warning: Ignoring unwritable file: dna1.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: trace2.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: categorytable.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: setting_popup.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: trace1.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: config_editing.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: dna2.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: wiggle_density.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: balloon.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: balloon_ie.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: down_right.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: close.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: up_right.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: down_left.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: up_left.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: balloon.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: down_right.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: close.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: up_right.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: down_left.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: up_left.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: menu.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: minus.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: grey.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: blue_peaks.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: share.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: tools.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: snap_share.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: download.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: mminus.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: mplus.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: snap_down.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: pop_out.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: opacity_thumb.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: grey_0.4_pixel.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: dark_0.4_pixel.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: red_peaks.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: empty.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: ruler-icon.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: panleft.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: fmini_2.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: panright.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: ex.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: minus12.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: check.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: snap_ex.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: open_open.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: pop_in.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: ficon.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: ficon_2.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: panright2.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: panleft2.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: snap_mail.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: snap_check.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: square.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: query.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: trash.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: plus.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: ruler.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: upload_list.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: landmark.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: sugarcane_sorghum_synteny.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: worm_exons_spec.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: upload.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: detail.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: upload_field.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: detail_scale.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: yeast_I_genes_spec.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: multiple_hits.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: remote.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: worm_telomeric_spec.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: navbar.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: overview+detail.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: blogspot-logo.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: livejournal-logo.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: myopenid-logo.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: aim-logo.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: yahoo-logo.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: menulink.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: menulink_active.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-up-open.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-left-on.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: pattern1.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-left-open.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: pattern2.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-right.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-up.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-left.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: pattern3.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-right-open.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: icon.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-up-on.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-down.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-right-on.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-down-on.png
dh_strip_nondeterminism: warning: Ignoring unwritable file: nav-arrow-down-open.png
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'gbrowse-data' in '../gbrowse-data_2.56+dfsg-11_all.deb'.
dpkg-deb: building package 'gbrowse' in '../gbrowse_2.56+dfsg-11_all.deb'.
dpkg-deb: building package 'gbrowse-calign' in '../gbrowse-calign_2.56+dfsg-11_i386.deb'.
dpkg-deb: building package 'gbrowse-calign-dbgsym' in '../gbrowse-calign-dbgsym_2.56+dfsg-11_i386.deb'.
dpkg-genbuildinfo --build=binary -O../gbrowse_2.56+dfsg-11_i386.buildinfo
dpkg-genchanges --build=binary -O../gbrowse_2.56+dfsg-11_i386.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/36273 and its subdirectories
I: Current time: Mon Feb 17 20:39:20 -12 2025
I: pbuilder-time-stamp: 1739867960