Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/g/gbrowse/gbrowse_2.56+dfsg-10+b1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/gbrowse-2.56+dfsg-10+b12133aurr/gbrowse_2.56+dfsg-10+b1_amd64.buildinfo Get source package info: gbrowse=2.56+dfsg-10 Source URL: http://snapshot.notset.fr/mr/package/gbrowse/2.56+dfsg-10/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=apache2-bin=2.4.52-1 apache2-dev=2.4.52-1 autoconf=2.71-2 automake=1:1.16.5-1.1 autopoint=0.21-4 autotools-dev=20220109.1 base-files=12.2 base-passwd=3.5.52 bash=5.1-6 binutils=2.37.90.20220130-2 binutils-common=2.37.90.20220130-2 binutils-x86-64-linux-gnu=2.37.90.20220130-2 bioperl=1.7.8-1 bsdextrautils=2.37.3-1+b1 bsdutils=1:2.37.3-1+b1 build-essential=12.9 bzip2=1.0.8-5 ca-certificates=20211016 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-16 dash=0.5.11+git20210903+057cd650a4ed-3 debconf=1.5.79 debhelper=13.6 debianutils=5.7-0.1 dh-autoreconf=20 dh-exec=0.23.4 dh-strip-nondeterminism=1.13.0-1 diffutils=1:3.7-5 dpkg=1.21.1 dpkg-dev=1.21.1 dwz=0.14-1 file=1:5.41-2 findutils=4.8.0-1 fontconfig-config=2.13.1-4.4 fonts-dejavu-core=2.37-2 g++=4:11.2.0-2 g++-11=11.2.0-16 gcc=4:11.2.0-2 gcc-11=11.2.0-16 gcc-11-base=11.2.0-16 gettext=0.21-4 gettext-base=0.21-4 grep=3.7-1 groff-base=1.22.4-8 gzip=1.10-4 hostname=3.23 init-system-helpers=1.61 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libalgorithm-diff-perl=1.201-1 libanyevent-cachedns-perl=0.08-2.1 libanyevent-http-perl=2.25-1 libanyevent-perl=7.170-2+b2 libapache-dbi-perl=1.12-2 libapache2-mod-perl2=2.0.12-1+b1 libapr1=1.7.0-8 libapr1-dev=1.7.0-8 libaprutil1=1.6.1-5 libaprutil1-dbd-sqlite3=1.6.1-5 libaprutil1-dev=1.6.1-5 libaprutil1-ldap=1.6.1-5 libarchive-zip-perl=1.68-1 libasan6=11.2.0-16 libatomic1=11.2.0-16 libattr1=1:2.5.1-1 libaudit-common=1:3.0.6-1 libaudit1=1:3.0.6-1+b1 libbinutils=2.37.90.20220130-2 libbio-coordinate-perl=1.7.1-4 libbio-db-biofetch-perl=1.7.3-4 libbio-db-gff-perl=1.7.4-1 libbio-db-seqfeature-perl=1.7.4-1 libbio-graphics-perl=2.40-6 libbio-perl-perl=1.7.8-1 libblkid1=2.37.3-1+b1 libbrotli1=1.0.9-2+b3 libbsd0=0.11.5-1+b1 libbz2-1.0=1.0.8-5 libc-bin=2.33-5 libc-dev-bin=2.33-5 libc6=2.33-5 libc6-dev=2.33-5 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcapture-tiny-perl=0.48-1 libcc1-0=11.2.0-16 libcgi-pm-perl=4.53-1 libcgi-session-perl=4.48-3 libclass-data-inheritable-perl=0.08-3 libcom-err2=1.46.5-2 libcommon-sense-perl=3.75-2+b1 libcrypt-dev=1:4.4.27-1.1 libcrypt1=1:4.4.27-1.1 libctf-nobfd0=2.37.90.20220130-2 libctf0=2.37.90.20220130-2 libcurl4=7.81.0-1 libdata-stag-perl=0.14-2 libdb5.3=5.3.28+dfsg1-0.8 libdbd-pg-perl=3.15.0-2+b1 libdbd-sqlite3-perl=1.70-3+b1 libdbi-perl=1.643-3+b2 libdebconfclient0=0.261 libdebhelper-perl=13.6 libdeflate0=1.9-1 libdevel-stacktrace-perl=2.0400-1 libdevel-symdump-perl=2.18-4 libdpkg-perl=1.21.1 libelf1=0.186-1 libencode-locale-perl=1.05-1.1 libexception-class-perl=1.45-1 libexpat1=2.4.4-1 libexpat1-dev=2.4.4-1 libexporter-tiny-perl=1.002002-1 libffi8=3.4.2-4 libfile-listing-perl=6.14-1 libfile-stripnondeterminism-perl=1.13.0-1 libfontconfig1=2.13.1-4.4 libfreetype6=2.11.1+dfsg-1 libgcc-11-dev=11.2.0-16 libgcc-s1=11.2.0-16 libgcrypt20=1.9.4-5 libgd-perl=2.76-2+b1 libgd3=2.3.0-2 libgdbm-compat4=1.22-1 libgdbm6=1.22-1 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.3-4+b1 libgomp1=11.2.0-16 libgpg-error0=1.43-3 libgssapi-krb5-2=1.18.3-7 libhogweed6=3.7.3-1 libhtml-parser-perl=3.76-1+b1 libhtml-tagset-perl=3.20-4 libhtml-tree-perl=5.07-2 libhttp-cookies-perl=6.10-1 libhttp-daemon-perl=6.12-1 libhttp-date-perl=6.05-1 libhttp-message-perl=6.36-1 libhttp-negotiate-perl=6.01-1 libicu67=67.1-7 libidn2-0=2.3.2-2 libio-html-perl=1.004-2 libio-socket-ssl-perl=2.074-2 libio-string-perl=1.08-3.1 libisl23=0.24-2 libitm1=11.2.0-16 libjansson4=2.13.1-1.1 libjbig0=2.1-3.1+b2 libjpeg62-turbo=1:2.1.2-1 libjs-prototype=1.7.1-3.1 libjs-scriptaculous=1.9.0-2.1 libjson-perl=4.04000-1 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 libldap-2.4-2=2.4.59+dfsg-1+b1 libldap2-dev=2.4.59+dfsg-1+b1 liblist-moreutils-perl=0.430-2 liblist-moreutils-xs-perl=0.430-2+b1 liblsan0=11.2.0-16 liblua5.3-0=5.3.6-1 liblwp-mediatypes-perl=6.04-1 liblwp-protocol-https-perl=6.10-1 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.41-2 libmagic1=1:5.41-2 libmd0=1.0.4-1 libmodule-build-perl=0.423100-1 libmount1=2.37.3-1+b1 libmpc3=1.2.1-1 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncursesw6=6.3-2 libnet-http-perl=6.22-1 libnet-ssleay-perl=1.92-1+b1 libnettle8=3.7.3-1 libnghttp2-14=1.43.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libp11-kit0=0.24.0-6 libpam-modules=1.4.0-11 libpam-modules-bin=1.4.0-11 libpam-runtime=1.4.0-11 libpam0g=1.4.0-11 libpcre2-8-0=10.39-3 libpcre3=2:8.39-13 libperl5.34=5.34.0-3 libpipeline1=1.5.5-1 libpng16-16=1.6.37-3 libpq5=14.1-5+b1 libpsl5=0.21.0-1.2 libpython3-stdlib=3.9.8-1 libpython3.9-minimal=3.9.10-1 libpython3.9-stdlib=3.9.10-1 libquadmath0=11.2.0-16 libreadline8=8.1.2-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg2-3 libsasl2-modules-db=2.1.27+dfsg2-3 libsctp-dev=1.0.19+dfsg-1 libsctp1=1.0.19+dfsg-1 libseccomp2=2.5.3-2 libselinux1=3.3-1+b1 libsigsegv2=2.14-1 libsmartcols1=2.37.3-1+b1 libsqlite3-0=3.37.2-2 libssh2-1=1.10.0-2 libssl1.1=1.1.1m-1 libstatistics-descriptive-perl=3.0800-1 libstdc++-11-dev=11.2.0-16 libstdc++6=11.2.0-16 libstring-approx-perl=3.28-1+b4 libsub-override-perl=0.09-2 libsub-uplevel-perl=0.2800-1.1 libsystemd0=250.3-2 libtasn1-6=4.18.0-4 libterm-readkey-perl=2.38-1+b3 libtest-deep-perl=1.130-1 libtest-differences-perl=0.69-1 libtest-exception-perl=0.43-1 libtest-most-perl=0.37-1 libtest-warn-perl=0.36-1 libtext-diff-perl=1.45-1 libtiff5=4.3.0-3 libtimedate-perl=2.3300-2 libtinfo6=6.3-2 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtry-tiny-perl=0.31-1 libtsan0=11.2.0-16 libubsan1=11.2.0-16 libuchardet0=0.0.7-1 libudev1=250.3-2 libunistring2=0.9.10-6 liburi-perl=5.10-1 libuuid1=2.37.3-1+b1 libvm-ec2-perl=1.28-2 libwebp6=0.6.1-2.1 libwww-perl=6.61-1 libwww-robotrules-perl=6.02-1 libx11-6=2:1.7.2-2+b1 libx11-data=2:1.7.2-2 libxau6=1:1.0.9-1 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxml-libxml-perl=2.0207+dfsg-2+b1 libxml-namespacesupport-perl=1.12-1.1 libxml-sax-base-perl=1.09-1.1 libxml-sax-perl=1.02+dfsg-3 libxml-simple-perl=2.25-1 libxml2=2.9.12+dfsg-5+b1 libxpm4=1:3.5.12-1 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.15.15-2 login=1:4.11.1+dfsg1-1 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.10.0-2 mawk=1.3.4.20200120-3+b1 media-types=5.0.0 ncurses-base=6.3-2 ncurses-bin=6.3-2 netbase=6.3 openssl=1.1.1m-1 patch=2.7.6-7 perl=5.34.0-3 perl-base=5.34.0-3 perl-modules-5.34=5.34.0-3 perl-openssl-defaults=5 po-debconf=1.0.21+nmu1 python3=3.9.8-1 python3-minimal=3.9.8-1 python3.9=3.9.10-1 python3.9-minimal=3.9.10-1 readline-common=8.1.2-1 rename=1.30-1 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sqlite3=3.37.2-2 sysvinit-utils=3.01-1 tar=1.34+dfsg-1 tzdata=2021e-1 ucf=3.0043 util-linux=2.37.3-1+b1 uuid-dev=2.37.3-1+b1 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-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/20220130T030506Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220130T030506Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220210T102201Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220206T145153Z/ 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-10 && mkdir -p /build/gbrowse-u9k47r && dpkg-source --no-check -x /*.dsc /build/gbrowse-u9k47r/gbrowse-2.56+dfsg && cd /build/gbrowse-u9k47r/gbrowse-2.56+dfsg && { printf '%s' 'gbrowse (2.56+dfsg-10+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild against perl 5.34.0 -- amd64 / i386 Build Daemon (x86-csail-01) Sun, 06 Feb 2022 21:46:14 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/gbrowse-u9k47r" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/gbrowse-u9k47r/gbrowse-2.56+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1644183974" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/gbrowse-u9k47r /tmp/gbrowse-2.56+dfsg-10+b12133aurr bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220206T145153Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.pXqlXKqWhs 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.pXqlXKqWhs Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.3-1+b1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 136 kB of archives. After this operation, 406 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220206T145153Z unstable/main amd64 libfakeroot amd64 1.27-1 [48.5 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220206T145153Z unstable/main amd64 fakeroot amd64 1.27-1 [87.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 136 kB in 0s (1094 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 ... 4697 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.27-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.27-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.27-1_amd64.deb ... Unpacking fakeroot (1.27-1) ... Setting up libfakeroot:amd64 (1.27-1) ... Setting up fakeroot (1.27-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-5) ... 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/20220130T030506Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220130T030506Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220210T102201Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220206T145153Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.pXqlXKqWhs Get:1 http://snapshot.notset.fr/archive/debian/20220130T030506Z bookworm InRelease [129 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220210T102201Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20220206T145153Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20220130T030506Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220130T030506Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20220130T030506Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220130T030506Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20220130T030506Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220130T030506Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20220130T030506Z bookworm/main Sources [11.8 MB] Get:5 http://snapshot.notset.fr/archive/debian/20220130T030506Z bookworm/main amd64 Packages [11.2 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20220210T102201Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20220210T102201Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20220210T102201Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20220210T102201Z unstable/main amd64 Packages [12.1 MB] Fetched 35.3 MB in 28s (1254 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.pXqlXKqWhs I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d gbrowse=2.56+dfsg-10 && mkdir -p /build/gbrowse-u9k47r && dpkg-source --no-check -x /*.dsc /build/gbrowse-u9k47r/gbrowse-2.56+dfsg && cd /build/gbrowse-u9k47r/gbrowse-2.56+dfsg && { printf '%s' 'gbrowse (2.56+dfsg-10+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild against perl 5.34.0 -- amd64 / i386 Build Daemon (x86-csail-01) Sun, 06 Feb 2022 21:46:14 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/gbrowse-u9k47r"' exec /tmp/mmdebstrap.pXqlXKqWhs 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/20220130T030506Z bookworm/main gbrowse 2.56+dfsg-10 (dsc) [2674 B] Get:2 http://snapshot.notset.fr/archive/debian/20220130T030506Z bookworm/main gbrowse 2.56+dfsg-10 (tar) [4356 kB] Get:3 http://snapshot.notset.fr/archive/debian/20220130T030506Z bookworm/main gbrowse 2.56+dfsg-10 (diff) [23.7 kB] Fetched 4382 kB in 3s (1272 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'gbrowse_2.56+dfsg-10.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting gbrowse in /build/gbrowse-u9k47r/gbrowse-2.56+dfsg dpkg-source: info: unpacking gbrowse_2.56+dfsg.orig.tar.gz dpkg-source: info: unpacking gbrowse_2.56+dfsg-10.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-u9k47r/gbrowse-2.56+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1644183974" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.pXqlXKqWhs dpkg-buildpackage: info: source package gbrowse dpkg-buildpackage: info: source version 2.56+dfsg-10+b1 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by amd64 / i386 Build Daemon (x86-csail-01) dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with apache2 dh_clean debian/rules binary-arch dh binary-arch --with apache2 dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/build/gbrowse-u9k47r/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/gbrowse-u9k47r/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 -ffile-prefix-map=/build/gbrowse-u9k47r/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-u9k47r/gbrowse-2.56+dfsg' dh_auto_build -a /usr/bin/perl Build NOTE: Run ./Build reconfig to change existing configuration. Building GBrowse x86_64-linux-gnu-gcc -I/build/gbrowse-u9k47r/gbrowse-2.56+dfsg/libalign -I/usr/lib/x86_64-linux-gnu/perl/5.34/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/gbrowse-u9k47r/gbrowse-2.56+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/gbrowse-u9k47r/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 -ffile-prefix-map=/build/gbrowse-u9k47r/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-u9k47r/gbrowse-2.56+dfsg/install_util/GBrowseInstall.pm line 778. create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_installdirs make[1]: Entering directory '/build/gbrowse-u9k47r/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-u9k47r/gbrowse-2.56+dfsg' debian/rules override_dh_auto_install make[1]: Entering directory '/build/gbrowse-u9k47r/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-u9k47r/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.bs Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/auto/Bio/Graphics/Browser2/CAlign/CAlign.so Installing debian/gbrowse/man/man1/bed2gff3.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/gbrowse_sync_aws_slave.pl.1p Installing debian/gbrowse/man/man1/gtf2gff3.pl.1p Installing debian/gbrowse/man/man1/load_genbank.pl.1p Installing debian/gbrowse/man/man1/make_das_conf.pl.1p Installing debian/gbrowse/man/man1/ucsc_genes2gff.pl.1p Installing debian/gbrowse/man/man1/wiggle2gff3.pl.1p Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/das Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbgff Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_details Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_gmap Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_img Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_key_img Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_login Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_syn Installing debian/gbrowse/etc/gbrowse/aws_balancer.conf Installing debian/gbrowse/etc/gbrowse/detail_select_menu.conf Installing debian/gbrowse/etc/gbrowse/enzymes.txt Installing debian/gbrowse/etc/gbrowse/GBrowse.conf Installing debian/gbrowse/etc/gbrowse/log4perl.conf Installing debian/gbrowse/etc/gbrowse/pop_demo.conf Installing debian/gbrowse/etc/gbrowse/renderfarm.conf Installing debian/gbrowse/etc/gbrowse/slave_preload.conf Installing debian/gbrowse/etc/gbrowse/submitter_plugin.conf Installing debian/gbrowse/etc/gbrowse/volvox.conf Installing debian/gbrowse/etc/gbrowse/yeast_chr1+2.conf Installing debian/gbrowse/etc/gbrowse/yeast_renderfarm.conf Installing debian/gbrowse/etc/gbrowse/yeast_simple.conf Installing debian/gbrowse/etc/gbrowse/languages/de.pm Installing debian/gbrowse/etc/gbrowse/languages/en.pm Installing debian/gbrowse/etc/gbrowse/languages/es.pm Installing debian/gbrowse/etc/gbrowse/languages/fr.pm Installing debian/gbrowse/etc/gbrowse/languages/is.pm Installing debian/gbrowse/etc/gbrowse/languages/it.pm Installing debian/gbrowse/etc/gbrowse/languages/ja.pm Installing debian/gbrowse/etc/gbrowse/languages/ko.pm Installing debian/gbrowse/etc/gbrowse/languages/nl.pm Installing debian/gbrowse/etc/gbrowse/languages/pl.pm Installing debian/gbrowse/etc/gbrowse/languages/POSIX.pm Installing debian/gbrowse/etc/gbrowse/languages/ru.pm Installing debian/gbrowse/etc/gbrowse/languages/zh.pm Installing debian/gbrowse/etc/gbrowse/languages/zh_cn.pm Installing debian/gbrowse/etc/gbrowse/MobyServices/b64_encoded_gif_renderer.pm Installing debian/gbrowse/etc/gbrowse/MobyServices/b64_encoded_jpeg_renderer.pm Installing debian/gbrowse/etc/gbrowse/MobyServices/GbrowseServices.pm Installing debian/gbrowse/etc/gbrowse/MobyServices/GbrowseServices.PMS Installing debian/gbrowse/etc/gbrowse/MobyServices/moby.conf Installing debian/gbrowse/etc/gbrowse/MobyServices/text_formatted_renderer.pm Installing debian/gbrowse/etc/gbrowse/MobyServices/text_html_renderer.pm Installing debian/gbrowse/etc/gbrowse/MobyServices/text_plain_renderer.pm Installing debian/gbrowse/etc/gbrowse/MobyServices/text_xml_renderer.pm Installing debian/gbrowse/etc/gbrowse/plugins/Aligner.pm Installing debian/gbrowse/etc/gbrowse/plugins/AlignTwoSequences.pm Installing debian/gbrowse/etc/gbrowse/plugins/AttributeHiliter.pm Installing debian/gbrowse/etc/gbrowse/plugins/BatchDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/Blat.pm Installing debian/gbrowse/etc/gbrowse/plugins/CMapDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/CreateBlastDB.pm Installing debian/gbrowse/etc/gbrowse/plugins/FastaDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/FBTableDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/FilterTest.pm Installing debian/gbrowse/etc/gbrowse/plugins/GeneFinder.pm Installing debian/gbrowse/etc/gbrowse/plugins/LDAPAuthenticate.pm Installing debian/gbrowse/etc/gbrowse/plugins/OligoFinder.pm Installing debian/gbrowse/etc/gbrowse/plugins/PamAuthenticate.pm Installing debian/gbrowse/etc/gbrowse/plugins/PrimerDesigner.pm Installing debian/gbrowse/etc/gbrowse/plugins/ProteinDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/RandomGene.pm Installing debian/gbrowse/etc/gbrowse/plugins/RestrictionAnnotator.pm Installing debian/gbrowse/etc/gbrowse/plugins/SequenceDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/SimpleTrackFinder.pm Installing debian/gbrowse/etc/gbrowse/plugins/SinWave.pm Installing debian/gbrowse/etc/gbrowse/plugins/SourceTrackFinder.pm Installing debian/gbrowse/etc/gbrowse/plugins/Spectrogram.pm Installing debian/gbrowse/etc/gbrowse/plugins/Submitter.pm Installing debian/gbrowse/etc/gbrowse/plugins/test.pm Installing debian/gbrowse/etc/gbrowse/plugins/TestAuthenticator.pm Installing debian/gbrowse/etc/gbrowse/plugins/TestFinder.pm Installing debian/gbrowse/etc/gbrowse/plugins/TrackDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/TrackFinder.pm Installing debian/gbrowse/etc/gbrowse/synteny/oryza.synconf.disabled.conf Installing debian/gbrowse/etc/gbrowse/synteny/rice_synteny.conf Installing debian/gbrowse/etc/gbrowse/synteny/wild_rice_synteny.conf Installing debian/gbrowse/etc/gbrowse/themes/solid_gray_colors Installing debian/gbrowse/etc/gbrowse/themes/transparent_colors Installing debian/gbrowse/etc/gbrowse/themes/warm_colors Installing debian/gbrowse/var/lib/gbrowse/databases/admin_uploads/README Installing debian/gbrowse/var/lib/gbrowse/databases/gbrowse_syn/alignments/rice.aln.gz Installing debian/gbrowse/var/lib/gbrowse/databases/gbrowse_syn/rice/rice.gff3 Installing debian/gbrowse/var/lib/gbrowse/databases/gbrowse_syn/wild_rice/wild_rice.gff3 Installing debian/gbrowse/var/lib/gbrowse/databases/ideograms/human_cytobands.gff Installing debian/gbrowse/var/lib/gbrowse/databases/ideograms/mouse_cytobands.gff Installing debian/gbrowse/var/lib/gbrowse/databases/ideograms/rat_cytobands.gff Installing debian/gbrowse/var/lib/gbrowse/databases/pop_demo/pop_demo.gff3 Installing debian/gbrowse/var/lib/gbrowse/databases/yeast_chr1+2/dummy.fa Installing debian/gbrowse/var/lib/gbrowse/databases/yeast_chr1+2/yeast_chr1+2.gff3 Installing debian/gbrowse/var/lib/gbrowse/databases/yeast_scaffolds/chr1.fa Installing debian/gbrowse/var/lib/gbrowse/databases/yeast_scaffolds/chr2.fa Installing debian/gbrowse/var/lib/gbrowse/databases/yeast_scaffolds/chromosomes.gff3 Installing debian/gbrowse/usr/share/gbrowse/htdocs/annotation_help.html Installing debian/gbrowse/usr/share/gbrowse/htdocs/cloud_index.html Installing debian/gbrowse/usr/share/gbrowse/htdocs/gbrowse_karyotype_help.html Installing debian/gbrowse/usr/share/gbrowse/htdocs/gbrowse_syn_help.html Installing debian/gbrowse/usr/share/gbrowse/htdocs/general_help.html Installing debian/gbrowse/usr/share/gbrowse/htdocs/general_help.html.zh Installing debian/gbrowse/usr/share/gbrowse/htdocs/gmod_cog.jpeg Installing debian/gbrowse/usr/share/gbrowse/htdocs/index.html Installing debian/gbrowse/usr/share/gbrowse/htdocs/vbox_index.html Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/gbrowse.css Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/gbrowse_autocomplete.css Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/gbrowse_elements.css Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/gbrowse_solid.css Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/gbrowse_transparent.css Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/gbrowse_warm.css Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/karyotype.css Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/menulink.png Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/menulink_active.png Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/snapshots.css Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/subtracktable.css Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/titlebar-default.css Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/titlebar-safari.css Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/tracks.css Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/dropdown/default_theme.css Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/dropdown/dropdown.css Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/dropdown/helper.css Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/dropdown/images/favicon.ico Installing 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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/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/bigbed.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/featurefile.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/DataLoader/generic.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/DataLoader/gff.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/DataLoader/gff3.pm Installing 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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/HTML/TrackListing.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Render/HTML/TrackListing/Categories.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Render/Slave/AWS_Balancer.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/Render/Slave/Status.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Bio/Graphics/Browser2/TrackDumper/RichSeqMaker.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/UserTracks/Filesystem.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/CGI/Toggle.pm Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/Legacy/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/I18n.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/GBrowse/ConfigData.pm Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::match_gap.3pm Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm Installing debian/gbrowse/man/man3/Bio::DB::SeqFeature::Store::Alias.3pm Installing debian/gbrowse/man/man3/Bio::DB::Tagger.3pm Installing debian/gbrowse/man/man3/Bio::DB::Tagger::Tag.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::AuthorizedFeatureFile.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::CAlign.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataBase.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataLoader::archive.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataLoader::useq.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::Markup.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::OptionPick.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::PadAlignment.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Plugin.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Plugin::AuthPlugin.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::PluginSet.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Realign.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Region.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::Render.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render::Slave::AWS_Balancer.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render::Slave::Status.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RenderPanels.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Util.3pm Installing debian/gbrowse/man/man3/CGI::Toggle.3pm Installing debian/gbrowse/man/man3/GBrowse::ConfigData.3pm Installing debian/gbrowse/man/man3/Legacy::Graphics::Browser.3pm Installing debian/gbrowse/bin/bed2gff3.pl Installing debian/gbrowse/bin/gbrowse_aws_balancer.pl Installing debian/gbrowse/bin/gbrowse_change_passwd.pl Installing debian/gbrowse/bin/gbrowse_clean.pl Installing debian/gbrowse/bin/gbrowse_configure_slaves.pl Installing debian/gbrowse/bin/gbrowse_create_account.pl Installing debian/gbrowse/bin/gbrowse_grow_cloud_vol.pl Installing debian/gbrowse/bin/gbrowse_import_ucsc_db.pl Installing debian/gbrowse/bin/gbrowse_metadb_config.pl Installing debian/gbrowse/bin/gbrowse_set_admin_passwd.pl Installing debian/gbrowse/bin/gbrowse_slave Installing debian/gbrowse/bin/gbrowse_syn_load_alignment_database.pl Installing debian/gbrowse/bin/gbrowse_syn_load_alignments_msa.pl Installing debian/gbrowse/bin/gbrowse_sync_aws_slave.pl Installing debian/gbrowse/bin/gtf2gff3.pl Installing debian/gbrowse/bin/load_genbank.pl Installing debian/gbrowse/bin/make_das_conf.pl Installing debian/gbrowse/bin/scan_gbrowse.pl Installing debian/gbrowse/bin/ucsc_genes2gff.pl Installing debian/gbrowse/bin/wiggle2gff3.pl #./Build apache_conf > debian/gbrowse/etc/gbrowse/gbrowse_apache2.conf perl Build.PL --conf=/etc/gbrowse --htdocs=/usr/share/gbrowse/htdocs --tmp=/var/cache/gbrowse --databases=/var/lib/gbrowse/databases --cgibin=/usr/lib/cgi-bin/gbrowse --www-user=www-data --registration_done=1 --persistent=/var/lib/gbrowse --installetc=y WARNING: the following files are missing in your kit: contrib/ace2gff.pl contrib/AxtPairwise_convert/axt2phy.pl contrib/blast2gff.pl contrib/conf_files/01.yeast.conf contrib/conf_files/02.wormbase.conf contrib/conf_files/03.fly.conf contrib/conf_files/04.human.conf contrib/conf_files/05.embl_proxy.conf contrib/conf_files/06.biosql.conf contrib/conf_files/07.chado.conf contrib/conf_files/08.genbank.conf contrib/conf_files/09.human_karyotype.conf contrib/conf_files/index.html contrib/conf_files/wormbase.syn contrib/Coverage/INSTALL contrib/Coverage/plugin/Coverage.pm contrib/Coverage/README contrib/gdump.pl contrib/GeneFinder/genefinder/gfcode.c contrib/GeneFinder/genefinder/README contrib/GeneFinder/genefinder/readseq.c contrib/GeneFinder/genefinder/readseq.h contrib/GeneFinder/nematode_gftables/cds.hex contrib/GeneFinder/nematode_gftables/gftables contrib/GeneFinder/nematode_gftables/newnem.atg contrib/GeneFinder/nematode_gftables/newnem.codon contrib/GeneFinder/nematode_gftables/newnem.gene contrib/GeneFinder/nematode_gftables/newnem.intron3 contrib/GeneFinder/nematode_gftables/newnem.intron5 contrib/GeneFinder/nematode_gftables/ref.hist contrib/GeneFinder/nematode_gftables/zk637.atg contrib/GeneFinder/nematode_gftables/zk637.intron3 contrib/GeneFinder/nematode_gftables/zk637.intron5 contrib/GeneFinder/nematode_gftables/zk637.trinuc contrib/import_ncbi_mv_hs.pl contrib/install_macosx/BuildConfig.pm contrib/install_macosx/README.html contrib/install_macosx/README.pod contrib/install_macosx/scripts/build-gbrowse.pl contrib/install_macosx/scripts/build-libraries.pl contrib/README contrib/SynView/cgi-lib/DAS/GUS.pm contrib/SynView/cgi-lib/DAS/GUS/Segment.pm contrib/SynView/cgi-lib/DAS/GUS/Segment/Feature.pm contrib/SynView/cgi-lib/DAS/Util/SqlParser.pm contrib/SynView/gbrowse.conf/plasmodb.conf contrib/SynView/gbrowse.conf/plasmodb.xml contrib/SynView/MAL11/MAL11.conf contrib/SynView/MAL11/MAL11.fa contrib/SynView/MAL11/MAL11.gff3 contrib/SynView/README contrib/TextDumper/README contrib/TextDumper/TextDumper.pm lib/Bio/DB/SeqFeature/Store/LoadHelper.pm Please inform the author. Checking prerequisites... recommends: * Bio::DB::BigFile is not installed * Bio::DB::Sam is not installed * Bio::Das is not installed * Crypt::SSLeay is not installed * DBD::mysql is not installed * DB_File::Lock is not installed * FCGI is not installed * File::NFSLock is not installed * GD::SVG is not installed * Net::OpenID::Consumer is not installed * Net::SMTP::SSL is not installed * Parse::Apache::ServerStatus is not installed * Template is not installed * Do not worry if some "recommended" prerequisites are missing. You can install * * them later if you need the features they provide. Do not proceed with the * * install if any of "REQUIRED" prerequisites are missing. * * * * The optional Safe::World module does not currently run on Perl 5.10 or * * higher, and so cannot be installed. * ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation Run 'Build installdeps' to install missing prerequisites. **** WARNING ***************************************************************************************** If you are upgrading from an earlier version of GBrowse and wish to use named user accounts, please set "user_accounts" to 1 in /etc/gbrowse2/GBrowse.conf and run bin/gbrowse_metadb_config.pl to create/update your user account database. See /etc/gbrowse2/GBrowse.conf.new for suggested settings. ****************************************************************************************************** NOTE: Run ./Build reconfig to change existing configuration. Now run: ./Build test ./Build demo (optional) ./Build install (as superuser/administrator) -or- ./Build install_slave (optional, for slave installations) Other useful targets: ./Build register (to register your copy of GBrowse) ./Build reconfig (to reconfigure install locations) ./Build demostop (to stop the demo) Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'GBrowse' version '2.56' ./Build --install_base=debian/gbrowse install_slave NOTE: Run ./Build reconfig to change existing configuration. Performing variable substitutions in blib/conf/aws_balancer.conf Performing variable substitutions in blib/conf/detail_select_menu.conf Performing variable substitutions in blib/conf/enzymes.txt Performing variable substitutions in blib/conf/GBrowse.conf Performing variable substitutions in blib/conf/log4perl.conf Performing variable substitutions in blib/conf/MobyServices/moby.conf Performing variable substitutions in blib/conf/pop_demo.conf Performing variable substitutions in blib/conf/renderfarm.conf Performing variable substitutions in blib/conf/slave_preload.conf Performing variable substitutions in blib/conf/submitter_plugin.conf Performing variable substitutions in blib/conf/synteny/oryza.synconf.disabled.conf Performing variable substitutions in blib/conf/synteny/rice_synteny.conf Performing variable substitutions in blib/conf/synteny/wild_rice_synteny.conf Performing variable substitutions in blib/conf/themes/solid_gray_colors Performing variable substitutions in blib/conf/themes/transparent_colors Performing variable substitutions in blib/conf/themes/warm_colors Performing variable substitutions in blib/conf/volvox.conf Performing variable substitutions in blib/conf/yeast_chr1+2.conf Performing variable substitutions in blib/conf/yeast_renderfarm.conf Performing variable substitutions in blib/conf/yeast_simple.conf Performing variable substitutions in blib/htdocs/annotation_help.html Performing variable substitutions in blib/htdocs/cloud_index.html Performing variable substitutions in blib/htdocs/example_scripts/index.html Performing variable substitutions in blib/htdocs/example_scripts/README Performing variable substitutions in blib/htdocs/gbrowse_karyotype_help.html Performing variable substitutions in blib/htdocs/gbrowse_syn_help.html Performing variable substitutions in blib/htdocs/general_help.html Performing variable substitutions in blib/htdocs/index.html Performing variable substitutions in blib/htdocs/tutorial/conf_files/elegans_core.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/elegans_extra.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/HEADER.html Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_final.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_final_withPhylo.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_halfway.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_Phylo.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_quarter.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_refactored.conf Performing variable substitutions in blib/htdocs/tutorial/data_files/HEADER.html Performing variable substitutions in blib/htdocs/tutorial/tutorial.html Performing variable substitutions in blib/htdocs/tutorial/tutorial.phyTreeEdit.html Performing variable substitutions in blib/htdocs/vbox_index.html Performing variable substitutions in blib/etc/default/gbrowse-aws-balancer Use of uninitialized value $wwwuser in substitution (s///) at /build/gbrowse-u9k47r/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-u9k47r/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/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/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/perl5/5.34/auto/Bio/Graphics/Browser2/CAlign/ mkdir -p debian/gbrowse-calign/usr/lib/x86_64-linux-gnu/perl5/5.34/Bio/Graphics/Browser2/ mv debian/gbrowse/usr/share/perl5/auto/Bio/Graphics/Browser2/CAlign/* debian/gbrowse-calign/usr/lib/x86_64-linux-gnu/perl5/5.34/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/perl5/5.34/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-u9k47r/gbrowse-2.56+dfsg/debian/gbrowse/etc -name '*.new' | xargs file-rename 's/.new//' rm -rf /build/gbrowse-u9k47r/gbrowse-2.56+dfsg/debian/gbrowse/usr/share/perl5/auto # Update conf files sed -i 's/gbrowse2/gbrowse/g' /build/gbrowse-u9k47r/gbrowse-2.56+dfsg/debian/gbrowse/etc/gbrowse/yeast*.conf sed -i 's/gbrowse2/gbrowse/g' /build/gbrowse-u9k47r/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-u9k47r/gbrowse-2.56+dfsg/debian/gbrowse/usr/share/perl5/GBrowse/ConfigData.pm /build/gbrowse-u9k47r/gbrowse-2.56+dfsg/debian/gbrowse/etc/gbrowse/ConfigData.pm make[1]: Leaving directory '/build/gbrowse-u9k47r/gbrowse-2.56+dfsg' dh_install -a dh_apache2 -a dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installman make[1]: Entering directory '/build/gbrowse-u9k47r/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-u9k47r/gbrowse-2.56+dfsg' dh_lintian -a dh_perl -a debian/rules override_dh_link make[1]: Entering directory '/build/gbrowse-u9k47r/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-u9k47r/gbrowse-2.56+dfsg' dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'gbrowse-calign-dbgsym' in '../gbrowse-calign-dbgsym_2.56+dfsg-10+b1_amd64.deb'. dpkg-deb: building package 'gbrowse-calign' in '../gbrowse-calign_2.56+dfsg-10+b1_amd64.deb'. dpkg-genbuildinfo --build=any -O../gbrowse_2.56+dfsg-10+b1_amd64.buildinfo dpkg-genchanges --build=any -O../gbrowse_2.56+dfsg-10+b1_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/gbrowse-u9k47r /tmp/gbrowse-2.56+dfsg-10+b12133aurr I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.pXqlXKqWhs... I: success in 376.8334 seconds md5: gbrowse-calign-dbgsym_2.56+dfsg-10+b1_amd64.deb: OK md5: gbrowse-calign_2.56+dfsg-10+b1_amd64.deb: OK sha1: gbrowse-calign-dbgsym_2.56+dfsg-10+b1_amd64.deb: OK sha1: gbrowse-calign_2.56+dfsg-10+b1_amd64.deb: OK sha256: gbrowse-calign-dbgsym_2.56+dfsg-10+b1_amd64.deb: OK sha256: gbrowse-calign_2.56+dfsg-10+b1_amd64.deb: OK Checksums: OK