Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/g/gbrowse/gbrowse_2.56+dfsg-8_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/gbrowse-2.56+dfsg-8e1q3rxq_/gbrowse_2.56+dfsg-8_all.buildinfo Get source package info: gbrowse=2.56+dfsg-8 Source URL: http://snapshot.notset.fr/mr/package/gbrowse/2.56+dfsg-8/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=apache2-bin=2.4.41-4 apache2-dev=2.4.41-4 autoconf=2.69-11.1 automake=1:1.16.1-4 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.47 bash=5.0-5 binutils=2.34-2 binutils-common=2.34-2 binutils-x86-64-linux-gnu=2.34-2 bioperl=1.7.7-1 bsdmainutils=11.1.2+b1 bsdutils=1:2.34-0.1 build-essential=12.8 bzip2=1.0.8-2 ca-certificates=20190110 coreutils=8.30-3+b1 cpp=4:9.2.1-3.1 cpp-9=9.2.1-28 dash=0.5.10.2-6 debconf=1.5.73 debhelper=12.9 debianutils=4.9.1 dh-autoreconf=19 dh-exec=0.23.2 dh-strip-nondeterminism=1.6.3-2 diffutils=1:3.7-3 dpkg=1.19.7 dpkg-dev=1.19.7 dwz=0.13-5 fdisk=2.34-0.1 file=1:5.38-4 findutils=4.7.0-1 fontconfig-config=2.13.1-2 fonts-dejavu-core=2.37-1 g++=4:9.2.1-3.1 g++-9=9.2.1-28 gcc=4:9.2.1-3.1 gcc-10-base=10-20200211-1 gcc-9=9.2.1-28 gcc-9-base=9.2.1-28 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 grep=3.4-1 groff-base=1.22.4-4 gzip=1.9-3+b1 hostname=3.23 init-system-helpers=1.57 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-5 libalgorithm-diff-perl=1.19.03-2 libanyevent-cachedns-perl=0.08-2 libanyevent-http-perl=2.24-1 libanyevent-perl=7.170-1 libapache-dbi-perl=1.12-2 libapache2-mod-perl2=2.0.11-2 libapr1=1.6.5-1+b1 libapr1-dev=1.6.5-1+b1 libaprutil1=1.6.1-4+b1 libaprutil1-dbd-sqlite3=1.6.1-4+b1 libaprutil1-dev=1.6.1-4+b1 libaprutil1-ldap=1.6.1-4+b1 libarchive-zip-perl=1.67-1 libasan5=9.2.1-28 libatomic1=10-20200211-1 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-2 libaudit1=1:2.8.5-2+b1 libbinutils=2.34-2 libbio-coordinate-perl=1.7.1-3 libbio-db-biofetch-perl=1.7.3-3 libbio-db-gff-perl=1.7.4-1 libbio-db-seqfeature-perl=1.7.4-1 libbio-graphics-perl=2.40-6 libbio-perl-perl=1.7.7-1 libblkid1=2.34-0.1 libbrotli1=1.0.7-6 libbsd0=0.10.0-1 libbz2-1.0=1.0.8-2 libc-bin=2.29-10 libc-dev-bin=2.29-10 libc6=2.29-10 libc6-dev=2.29-10 libcap-ng0=0.7.9-2.1+b1 libcapture-tiny-perl=0.48-1 libcc1-0=10-20200211-1 libcgi-pm-perl=4.46-1 libcgi-session-perl=4.48-3 libclass-data-inheritable-perl=0.08-3 libcom-err2=1.45.5-2 libcommon-sense-perl=3.74-2+b8 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.10-10 libcrypt1=1:4.4.10-10 libctf-nobfd0=2.34-2 libctf0=2.34-2 libcurl4=7.67.0-2 libdata-stag-perl=0.14-2 libdb5.3=5.3.28+dfsg1-0.6 libdbd-pg-perl=3.10.4-1 libdbd-sqlite3-perl=1.64-1+b1 libdbi-perl=1.643-1 libdebconfclient0=0.251 libdebhelper-perl=12.9 libdevel-stacktrace-perl=2.0400-1 libdevel-symdump-perl=2.18-3 libdpkg-perl=1.19.7 libelf1=0.176-1.1 libencode-locale-perl=1.05-1 libexception-class-perl=1.44-1 libexpat1=2.2.9-1 libexpat1-dev=2.2.9-1 libexporter-tiny-perl=1.002001-1 libfdisk1=2.34-0.1 libffi7=3.3-3 libfile-listing-perl=6.04-1 libfile-stripnondeterminism-perl=1.6.3-2 libfontconfig1=2.13.1-2+b1 libfreetype6=2.10.1-2 libgcc-9-dev=9.2.1-28 libgcc-s1=10-20200211-1 libgcc1=1:10-20200211-1 libgcrypt20=1.8.5-3 libgd-perl=2.71-2+b1 libgd3=2.2.5-5.2 libgdbm-compat4=1.18.1-5 libgdbm6=1.18.1-5 libglib2.0-0=2.62.4-2 libgmp10=2:6.2.0+dfsg-3 libgnutls30=3.6.11.1-2 libgomp1=10-20200211-1 libgpg-error0=1.36-7 libgssapi-krb5-2=1.17-6 libhogweed5=3.5.1+really3.5.1-2 libhtml-parser-perl=3.72-3+b4 libhtml-tagset-perl=3.20-4 libhtml-tree-perl=5.07-2 libhttp-cookies-perl=6.08-1 libhttp-daemon-perl=6.06-1 libhttp-date-perl=6.05-1 libhttp-message-perl=6.18-1 libhttp-negotiate-perl=6.01-1 libicu63=63.2-2 libidn2-0=2.2.0-2 libio-html-perl=1.001-1 libio-socket-ssl-perl=2.067-1 libio-string-perl=1.08-3 libisl22=0.22-2 libitm1=10-20200211-1 libjansson4=2.12-1 libjbig0=2.1-3.1+b2 libjpeg62-turbo=1:1.5.2-2+b1 libjs-prototype=1.7.1-3 libjs-scriptaculous=1.9.0-2 libjson-perl=4.02000-2 libk5crypto3=1.17-6 libkeyutils1=1.6.1-2 libkrb5-3=1.17-6 libkrb5support0=1.17-6 libldap-2.4-2=2.4.49+dfsg-1 libldap-common=2.4.49+dfsg-1 libldap2-dev=2.4.49+dfsg-1 liblist-moreutils-perl=0.416-1+b5 liblsan0=10-20200211-1 liblua5.2-0=5.2.4-1.1+b3 liblwp-mediatypes-perl=6.04-1 liblwp-protocol-https-perl=6.07-2 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.38-4 libmagic1=1:5.38-4 libmodule-build-perl=0.423100-1 libmount1=2.34-0.1 libmpc3=1.1.0-1 libmpfr6=4.0.2-1 libncursesw6=6.1+20191019-1 libnet-http-perl=6.19-1 libnet-ssleay-perl=1.88-2 libnettle7=3.5.1+really3.5.1-2 libnghttp2-14=1.40.0-1 libp11-kit0=0.23.20-1 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpcre2-8-0=10.34-7 libpcre3=2:8.39-12+b1 libperl5.30=5.30.0-9 libpipeline1=1.5.2-2 libpng16-16=1.6.37-2 libpq5=12.2-1 libpsl5=0.20.2-2 libquadmath0=10-20200211-1 libreadline8=8.0-3 librtmp1=2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2=2.1.27+dfsg-2 libsasl2-modules-db=2.1.27+dfsg-2 libsctp-dev=1.0.18+dfsg-1 libsctp1=1.0.18+dfsg-1 libseccomp2=2.4.2-2 libselinux1=3.0-1 libsigsegv2=2.12-2 libsmartcols1=2.34-0.1 libsqlite3-0=3.31.1-2 libssh2-1=1.8.0-2.1 libssl1.1=1.1.1d-2 libstatistics-descriptive-perl=3.0702-1 libstdc++-9-dev=9.2.1-28 libstdc++6=10-20200211-1 libstring-approx-perl=3.28-1+b2 libsub-override-perl=0.09-2 libsub-uplevel-perl=0.2800-1 libsystemd0=244.2-1 libtasn1-6=4.15.0-2 libterm-readkey-perl=2.38-1+b1 libtest-deep-perl=1.128-1 libtest-differences-perl=0.67-1 libtest-exception-perl=0.43-1 libtest-most-perl=0.35-1 libtest-warn-perl=0.36-1 libtext-diff-perl=1.45-1 libtiff5=4.1.0+git191117-2 libtimedate-perl=2.3100-1 libtinfo6=6.1+20191019-1 libtool=2.4.6-12 libtry-tiny-perl=0.30-1 libtsan0=10-20200211-1 libubsan1=10-20200211-1 libuchardet0=0.0.6-3 libudev1=244.2-1 libunistring2=0.9.10-2 liburi-perl=1.76-2 libuuid1=2.34-0.1 libvm-ec2-perl=1.28-2 libwebp6=0.6.1-2+b1 libwww-perl=6.43-1 libwww-robotrules-perl=6.02-1 libx11-6=2:1.6.8-1 libx11-data=2:1.6.8-1 libxau6=1:1.0.8-1+b2 libxcb1=1.13.1-5 libxdmcp6=1:1.1.2-3 libxml-libxml-perl=2.0134+dfsg-1+b1 libxml-namespacesupport-perl=1.12-1 libxml-sax-base-perl=1.09-1 libxml-sax-perl=1.02+dfsg-1 libxml-simple-perl=2.25-1 libxml2=2.9.4+dfsg1-8 libxpm4=1:3.5.12-1 libzstd1=1.4.4+dfsg-1 linux-libc-dev=5.4.13-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.2.1-1.2 man-db=2.9.0-2 mawk=1.3.4.20200120-1 ncurses-base=6.1+20191019-1 ncurses-bin=6.1+20191019-1 netbase=6.0 openssl=1.1.1d-2 patch=2.7.6-6 perl=5.30.0-9 perl-base=5.30.0-9 perl-modules-5.30=5.30.0-9 perl-openssl-defaults=4 po-debconf=1.0.21 readline-common=8.0-3 rename=1.10-1 sed=4.7-1 sensible-utils=0.0.12+nmu1 sqlite3=3.31.1-2 sysvinit-utils=2.96-2.1 tar=1.30+dfsg-6+b1 ucf=3.0038+nmu1 util-linux=2.34-0.1 uuid-dev=2.34-0.1 xz-utils=5.2.4-1+b1 zlib1g=1:1.2.11.dfsg-1.2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20200308T090128Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20200213T035932Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d gbrowse=2.56+dfsg-8 && mkdir -p /build/gbrowse-sOFoU2 && dpkg-source --no-check -x /*.dsc /build/gbrowse-sOFoU2/gbrowse-2.56+dfsg && chown -R builduser:builduser /build/gbrowse-sOFoU2" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/gbrowse-sOFoU2/gbrowse-2.56+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1581851951" dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/gbrowse-sOFoU2 /tmp/gbrowse-2.56+dfsg-8e1q3rxq_ bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20200213T035932Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.tvcVLPcyKp as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.tvcVLPcyKp Reading package lists... Building dependency tree... util-linux is already the newest version (2.34-0.1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 132 kB of archives. After this operation, 393 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20200213T035932Z unstable/main amd64 libfakeroot amd64 1.24-1 [45.7 kB] Get:2 http://snapshot.notset.fr/archive/debian/20200213T035932Z unstable/main amd64 fakeroot amd64 1.24-1 [85.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 132 kB in 0s (870 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4509 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.24-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.24-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.24-1_amd64.deb ... Unpacking fakeroot (1.24-1) ... Setting up libfakeroot:amd64 (1.24-1) ... Setting up fakeroot (1.24-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.29-10) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20200308T090128Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20200213T035932Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.tvcVLPcyKp Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20200308T090128Z unstable InRelease [142 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20200213T035932Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20200308T090128Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20200308T090128Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20200308T090128Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20200308T090128Z unstable/main amd64 Packages [11.0 MB] Fetched 33.7 MB in 29s (1180 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.tvcVLPcyKp I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d gbrowse=2.56+dfsg-8 && mkdir -p /build/gbrowse-sOFoU2 && dpkg-source --no-check -x /*.dsc /build/gbrowse-sOFoU2/gbrowse-2.56+dfsg && chown -R builduser:builduser /build/gbrowse-sOFoU2"' exec /tmp/mmdebstrap.tvcVLPcyKp Reading package lists... NOTICE: 'gbrowse' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/gbrowse.git Please use: git clone https://salsa.debian.org/med-team/gbrowse.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 4382 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main gbrowse 2.56+dfsg-8 (dsc) [2670 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main gbrowse 2.56+dfsg-8 (tar) [4356 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main gbrowse 2.56+dfsg-8 (diff) [23.5 kB] Fetched 4382 kB in 3s (1260 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'gbrowse_2.56+dfsg-8.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting gbrowse in /build/gbrowse-sOFoU2/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: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/gbrowse-sOFoU2/gbrowse-2.56+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1581851951" dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.tvcVLPcyKp 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 . fakeroot debian/rules clean dh clean --with apache2 dh_clean debian/rules build-indep dh build-indep --with apache2 dh_update_autotools_config -i dh_autoreconf -i debian/rules override_dh_auto_configure make[1]: Entering directory '/build/gbrowse-sOFoU2/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/gbrowse-sOFoU2/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/gbrowse-sOFoU2/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/gbrowse-sOFoU2/gbrowse-2.56+dfsg' dh_auto_build -i perl Build NOTE: Run ./Build reconfig to change existing configuration. Building GBrowse x86_64-linux-gnu-gcc -I/build/gbrowse-sOFoU2/gbrowse-2.56+dfsg/libalign -I/usr/lib/x86_64-linux-gnu/perl/5.30/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/gbrowse-sOFoU2/gbrowse-2.56+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/gbrowse-sOFoU2/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/gbrowse-sOFoU2/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/gbrowse-sOFoU2/gbrowse-2.56+dfsg/install_util/GBrowseInstall.pm line 778. debian/rules override_dh_auto_test make[1]: Entering directory '/build/gbrowse-sOFoU2/gbrowse-2.56+dfsg' dh_auto_test -- TEST_FILES="t/02.rearchitecture.t t/05.deferredrendering.t t/00.compile.t t/01.yeast.t t/07.balancer.t t/08.calign.t" perl Build test --verbose 1 "TEST_FILES=t/02.rearchitecture.t t/05.deferredrendering.t t/00.compile.t t/01.yeast.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/gbrowse-sOFoU2/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. cannot remove directory for /tmp/gbrowse_testing/7tgQkNFgLA: No such file or directory at /usr/share/perl/5.30/File/Temp.pm line 916. 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/aaBrsj3EgJ: No such file or directory at /usr/share/perl/5.30/File/Temp.pm line 916. 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 5.030000 for linux # Current time local: Fri Oct 8 05:30:33 2021 # Current time GMT: Fri Oct 8 05:30:33 2021 # 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, 43 wallclock secs ( 0.10 usr 0.03 sys + 17.69 cusr 4.15 csys = 21.97 CPU) Result: PASS make[1]: Leaving directory '/build/gbrowse-sOFoU2/gbrowse-2.56+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-indep dh binary-indep --with apache2 dh_testroot -i dh_prep -i debian/rules override_dh_installdirs make[1]: Entering directory '/build/gbrowse-sOFoU2/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/gbrowse-sOFoU2/gbrowse-2.56+dfsg' debian/rules override_dh_auto_install make[1]: Entering directory '/build/gbrowse-sOFoU2/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/gbrowse-sOFoU2/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/make_das_conf.pl.1p Installing debian/gbrowse/man/man1/bed2gff3.pl.1p Installing debian/gbrowse/man/man1/gbrowse_sync_aws_slave.pl.1p Installing debian/gbrowse/man/man1/wiggle2gff3.pl.1p Installing debian/gbrowse/man/man1/load_genbank.pl.1p Installing debian/gbrowse/man/man1/ucsc_genes2gff.pl.1p Installing debian/gbrowse/man/man1/gbrowse_aws_balancer.pl.1p Installing debian/gbrowse/man/man1/gbrowse_clean.pl.1p Installing debian/gbrowse/man/man1/gbrowse_grow_cloud_vol.pl.1p Installing debian/gbrowse/man/man1/gtf2gff3.pl.1p Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_gmap Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_login Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_details Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_img Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_key_img Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_syn Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/das Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbgff Installing debian/gbrowse/etc/gbrowse/yeast_simple.conf Installing debian/gbrowse/etc/gbrowse/pop_demo.conf Installing debian/gbrowse/etc/gbrowse/renderfarm.conf Installing debian/gbrowse/etc/gbrowse/volvox.conf Installing debian/gbrowse/etc/gbrowse/yeast_chr1+2.conf Installing debian/gbrowse/etc/gbrowse/GBrowse.conf Installing debian/gbrowse/etc/gbrowse/yeast_renderfarm.conf Installing debian/gbrowse/etc/gbrowse/log4perl.conf Installing debian/gbrowse/etc/gbrowse/slave_preload.conf Installing 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debian/gbrowse/var/lib/gbrowse/databases/ideograms/mouse_cytobands.gff Installing debian/gbrowse/var/lib/gbrowse/databases/ideograms/rat_cytobands.gff Installing debian/gbrowse/var/lib/gbrowse/databases/ideograms/human_cytobands.gff Installing debian/gbrowse/var/lib/gbrowse/databases/admin_uploads/README Installing debian/gbrowse/var/lib/gbrowse/databases/yeast_scaffolds/chr1.fa 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_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/gbrowse_syn/wild_rice/wild_rice.gff3 Installing debian/gbrowse/var/lib/gbrowse/databases/gbrowse_syn/rice/rice.gff3 Installing 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debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Legacy/DB/SyntenyBlock.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Legacy/DB/SyntenyIO.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Legacy/Graphics/Browser.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Legacy/Graphics/Browser/PageSettings.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Legacy/Graphics/Browser/Synteny.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Legacy/Graphics/Browser/Util.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Legacy/Graphics/Browser/I18n.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/DB/Tagger.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/DB/GFF/Aggregator/waba_alignment.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/DB/GFF/Aggregator/wormbase_gene.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/DB/GFF/Aggregator/reftranscript.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/DB/GFF/Aggregator/match_gap.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/DB/SeqFeature/Store/Alias.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/DB/SeqFeature/Store/BedLoader.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/DB/Tagger/mysql.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/DB/Tagger/Tag.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/GBrowseFeature.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Karyotype.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/PluginSet.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/RegionSearch.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/RemoteSet.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/DataBase.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/SubtrackTable.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/UserTracks.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/PadAlignment.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/UserDB.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Render.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Action.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Util.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Plugin.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/Session.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/TrackDumper.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/OptionPick.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Shellwords.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/SendMail.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/DataSource.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/I18n.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/AuthorizedFeatureFile.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/RenderPanels.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Plugin/AuthPlugin.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/DataLoader/wig2bigwig.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/DataLoader/generic.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/DataLoader/bam.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/archive.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/DataLoader/gff.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/DataLoader/gff3.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/DataLoader/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/sam.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/DataLoader/wiggle.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/DataLoader/useq.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/UserTracks/Filesystem.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/UserTracks/Database.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Render/SnapshotManager.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/Login.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/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 debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Render/HTML/TrackListing.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Render/HTML/TrackListing/Categories.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/TrackDumper/RichSeqMaker.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/CGI/Toggle.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/GBrowse/ConfigData.pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render::Slave::Status.3pm Installing debian/gbrowse/man/man3/Legacy::Graphics::Browser.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataLoader::useq.3pm Installing debian/gbrowse/man/man3/Bio::DB::Tagger.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataLoader::archive.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Realign.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::PadAlignment.3pm Installing debian/gbrowse/man/man3/Bio::DB::Tagger::Tag.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::DB::GFF::Aggregator::reftranscript.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::CAlign.3pm Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Markup.3pm Installing debian/gbrowse/man/man3/CGI::Toggle.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::OptionPick.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render::Slave::AWS_Balancer.3pm Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::AuthorizedFeatureFile.3pm Installing debian/gbrowse/man/man3/GBrowse::ConfigData.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RegionSearch.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RemoteSet.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataBase.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::GFFhelper.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RenderPanels.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataSource.3pm Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::match_gap.3pm Installing debian/gbrowse/bin/gbrowse_clean.pl Installing debian/gbrowse/bin/load_genbank.pl Installing debian/gbrowse/bin/make_das_conf.pl Installing debian/gbrowse/bin/gbrowse_import_ucsc_db.pl Installing debian/gbrowse/bin/gtf2gff3.pl Installing debian/gbrowse/bin/ucsc_genes2gff.pl Installing debian/gbrowse/bin/gbrowse_syn_load_alignment_database.pl Installing debian/gbrowse/bin/gbrowse_grow_cloud_vol.pl Installing debian/gbrowse/bin/gbrowse_syn_load_alignments_msa.pl Installing debian/gbrowse/bin/gbrowse_change_passwd.pl Installing debian/gbrowse/bin/gbrowse_set_admin_passwd.pl Installing debian/gbrowse/bin/gbrowse_create_account.pl Installing debian/gbrowse/bin/gbrowse_slave Installing debian/gbrowse/bin/gbrowse_sync_aws_slave.pl Installing debian/gbrowse/bin/gbrowse_aws_balancer.pl Installing debian/gbrowse/bin/gbrowse_configure_slaves.pl Installing debian/gbrowse/bin/wiggle2gff3.pl Installing debian/gbrowse/bin/scan_gbrowse.pl Installing debian/gbrowse/bin/gbrowse_metadb_config.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/gbrowse-sOFoU2/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/gbrowse-sOFoU2/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/perl5/5.30/auto/Bio/Graphics/Browser2/CAlign/ mkdir -p debian/gbrowse-calign/usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/Graphics/Browser2/ mv debian/gbrowse/usr/share/perl5/auto/Bio/Graphics/Browser2/CAlign/* debian/gbrowse-calign/usr/lib/x86_64-linux-gnu/perl5/5.30/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/perl5/5.30/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/gbrowse-sOFoU2/gbrowse-2.56+dfsg/debian/gbrowse/etc -name '*.new' | xargs file-rename 's/.new//' rm -rf /build/gbrowse-sOFoU2/gbrowse-2.56+dfsg/debian/gbrowse/usr/share/perl5/auto # Update conf files sed -i 's/gbrowse2/gbrowse/g' /build/gbrowse-sOFoU2/gbrowse-2.56+dfsg/debian/gbrowse/etc/gbrowse/yeast*.conf sed -i 's/gbrowse2/gbrowse/g' /build/gbrowse-sOFoU2/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/gbrowse-sOFoU2/gbrowse-2.56+dfsg/debian/gbrowse/usr/share/perl5/GBrowse/ConfigData.pm /build/gbrowse-sOFoU2/gbrowse-2.56+dfsg/debian/gbrowse/etc/gbrowse/ConfigData.pm make[1]: Leaving directory '/build/gbrowse-sOFoU2/gbrowse-2.56+dfsg' dh_install -i dh_apache2 -i dh_installdocs -i dh_installchangelogs -i debian/rules override_dh_installman make[1]: Entering directory '/build/gbrowse-sOFoU2/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/gbrowse-sOFoU2/gbrowse-2.56+dfsg' dh_lintian -i dh_perl -i debian/rules override_dh_link make[1]: Entering directory '/build/gbrowse-sOFoU2/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/gbrowse-sOFoU2/gbrowse-2.56+dfsg' dh_strip_nondeterminism -i dh_compress -i dh_fixperms -i dh_missing -i dh_installdeb -i dh_gencontrol -i dh_md5sums -i dh_builddeb -i 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=all dpkg-genchanges --build=all >../gbrowse_2.56+dfsg-8_all.changes dpkg-genchanges: info: binary-only arch-indep upload (source code and arch-specific packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/gbrowse-sOFoU2 /tmp/gbrowse-2.56+dfsg-8e1q3rxq_ I: cleaning package lists and apt cache... W: deleting files in /tmp: gbslave_ccache W: deleting files in /tmp: bio_graphics_ff_cache_1000 I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.tvcVLPcyKp... I: success in 386.4987 seconds md5: Value of 'md5' differs for gbrowse-data_2.56+dfsg-8_all.deb md5: Size differs for gbrowse-data_2.56+dfsg-8_all.deb md5: Value of 'md5' differs for gbrowse_2.56+dfsg-8_all.deb md5: Size differs for gbrowse_2.56+dfsg-8_all.deb sha1: Value of 'sha1' differs for gbrowse-data_2.56+dfsg-8_all.deb sha1: Size differs for gbrowse-data_2.56+dfsg-8_all.deb sha1: Value of 'sha1' differs for gbrowse_2.56+dfsg-8_all.deb sha1: Size differs for gbrowse_2.56+dfsg-8_all.deb sha256: Value of 'sha256' differs for gbrowse-data_2.56+dfsg-8_all.deb sha256: Size differs for gbrowse-data_2.56+dfsg-8_all.deb sha256: Value of 'sha256' differs for gbrowse_2.56+dfsg-8_all.deb sha256: Size differs for gbrowse_2.56+dfsg-8_all.deb Checksums: FAIL diffoscope run passed diffoscope run passed