gbrowse →
2.54+dfsg-4 →
armhf → 2015-06-22 06:19:06
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on bm-wb-03
╔══════════════════════════════════════════════════════════════════════════════╗
║ gbrowse 2.54+dfsg-4 (armhf) 22 Jun 2015 06:06 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: gbrowse
Version: 2.54+dfsg-4
Source Version: 2.54+dfsg-4
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/gbrowse-MHtkrg/gbrowse-2.54+dfsg' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/gbrowse-MHtkrg' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-96bc6626-8f03-4393-aa6f-f2e11a603c54' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 stretch-staging/main Sources [7974 kB]
Get:3 http://172.17.0.1 stretch-staging/main armhf Packages [9775 kB]
Ign http://172.17.0.1 stretch-staging/main Translation-en
Fetched 17.8 MB in 34s (515 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
─────────
Checking available source versions...
Download source files with APT
──────────────────────────────
Reading package lists...
Building dependency tree...
NOTICE: 'gbrowse' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/gmod/gbrowse/trunk/
Need to get 4054 kB of source archives.
Get:1 http://172.17.0.1/private/ stretch-staging/main gbrowse 2.54+dfsg-4 (dsc) [2569 B]
Get:2 http://172.17.0.1/private/ stretch-staging/main gbrowse 2.54+dfsg-4 (tar) [4031 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main gbrowse 2.54+dfsg-4 (diff) [19.6 kB]
Fetched 4054 kB in 1s (3846 kB/s)
Download complete and in download only mode
Check architectures
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Check dependencies
──────────────────
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-KyC0kb/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Ign file: ./ InRelease
Get:1 file: ./ Release.gpg [299 B]
Get:2 file: ./ Release [2119 B]
Ign file: ./ Translation-en
Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 76 not upgraded.
Need to get 0 B/818 B of archives.
After this operation, 0 B of additional disk space will be used.
Selecting previously unselected package sbuild-build-depends-core-dummy.
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(Reading database ... 11998 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), bioperl (>= 1.6.901), debhelper (>= 9), dh-apache2, apache2-dev, libbio-graphics-perl (>= 2.31), libcapture-tiny-perl, libcgi-session-perl, libgd-gd2-perl | libgd-gd2-noxpm-perl, libio-string-perl, libjson-perl, libstatistics-descriptive-perl, libwww-perl, libhttp-daemon-perl, perl, sqlite3, libdbd-sqlite3-perl, libterm-readkey-perl, libjs-prototype (>= 1.7), libjs-scriptaculous (>= 1.9), libvm-ec2-perl, libmodule-build-perl
Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), bioperl (>= 1.6.901), debhelper (>= 9), dh-apache2, apache2-dev, libbio-graphics-perl (>= 2.31), libcapture-tiny-perl, libcgi-session-perl, libgd-gd2-perl, libio-string-perl, libjson-perl, libstatistics-descriptive-perl, libwww-perl, libhttp-daemon-perl, perl, sqlite3, libdbd-sqlite3-perl, libterm-readkey-perl, libjs-prototype (>= 1.7), libjs-scriptaculous (>= 1.9), libvm-ec2-perl, libmodule-build-perl
dpkg-deb: building package `sbuild-build-depends-gbrowse-dummy' in `/«BUILDDIR»/resolver-Bq6WsT/apt_archive/sbuild-build-depends-gbrowse-dummy.deb'.
OK
Ign file: ./ InRelease
Get:1 file: ./ Release.gpg [299 B]
Get:2 file: ./ Release [2119 B]
Ign file: ./ Translation-en
Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install gbrowse build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
apache2-dev bioperl bsdmainutils ca-certificates debhelper file
fontconfig-config fonts-dejavu-core gettext gettext-base groff-base
intltool-debian libanyevent-cachedns-perl libanyevent-http-perl
libanyevent-perl libapr1 libapr1-dev libaprutil1 libaprutil1-dev
libasprintf0c2 libbio-graphics-perl libbio-perl-perl libcapture-tiny-perl
libcgi-pm-perl libcgi-session-perl libcommon-sense-perl libcpan-meta-perl
libcroco3 libdata-stag-perl libdbd-sqlite3-perl libdbi-perl
libencode-locale-perl libexpat1 libexpat1-dev libexporter-tiny-perl libffi6
libfile-listing-perl libfontconfig1 libfreetype6 libgd-gd2-perl libgd3
libglib2.0-0 libgnutls-deb0-28 libhogweed4 libhtml-parser-perl
libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl
libhttp-daemon-perl libhttp-date-perl libhttp-message-perl
libhttp-negotiate-perl libio-html-perl libio-socket-ssl-perl
libio-string-perl libjbig0 libjpeg62-turbo libjs-prototype
libjs-scriptaculous libjson-perl libldap-2.4-2 libldap2-dev
liblist-moreutils-perl liblwp-mediatypes-perl liblwp-protocol-https-perl
libmagic1 libmodule-build-perl libnet-http-perl libnet-ssleay-perl
libnettle6 libp11-kit0 libpipeline1 libsasl2-2 libsasl2-modules-db
libsctp-dev libsctp1 libsqlite3-0 libssl1.0.0 libstatistics-descriptive-perl
libstring-approx-perl libtasn1-6 libterm-readkey-perl libtiff5 libunistring0
liburi-perl libuuid1 libvm-ec2-perl libvpx2 libwww-perl
libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb1 libxdmcp6
libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl
libxml-sax-perl libxml-simple-perl libxml2 libxpm4 man-db netbase openssl
po-debconf sqlite3 ucf uuid-dev
Suggested packages:
wamerican wordlist whois vacation dh-make gettext-doc groff libev-perl
libevent-perl libio-async-perl libpoe-perl libtask-weaken-perl python
libxml-sax-expatxs-perl libnet-daemon-perl libsql-statement-perl libgd-tools
gnutls-bin libdata-dump-perl libcrypt-ssleay-perl libauthen-ntlm-perl less
www-browser libmail-box-perl sqlite3-doc
Recommended packages:
bioperl-run perl-doc libcache-cache-perl libbio-perl-run-perl
libapache-dbi-perl libyaml-perl libace-perl libxml-twig-perl
libset-scalar-perl curl wget lynx-cur autopoint libasprintf-dev
libgettextpo-dev libasync-interrupt-perl libguard-perl libbio-scf-perl
libgd-svg-perl libalgorithm-munkres-perl libarray-compare-perl
libbio-asn1-entrezgene-perl libclone-perl libconvert-binary-c-perl
libdbd-mysql-perl libdbd-pg-perl libgd-perl libgraph-perl libgraphviz-perl
libhtml-tableextract-perl libpostscript-perl libsoap-lite-perl
libsort-naturally-perl libspreadsheet-parseexcel-perl
libspreadsheet-writeexcel-perl libsvg-perl libsvg-graph-perl
libxml-dom-xpath-perl libxml-parser-perl libxml-sax-writer-perl
libxml-writer-perl libcgi-fast-perl libfreezethaw-perl perl-tk
libxml-libxslt-perl libmldbm-perl libxml-perl libglib2.0-data
shared-mime-info xdg-user-dirs libhtml-format-perl javascript-common
libjson-xs-perl libmodule-signature-perl libpod-readme-perl
libsoftware-license-perl libsasl2-modules lksctp-tools uuid-runtime
libhtml-form-perl libmailtools-perl libxml-sax-expat-perl xml-core ifupdown
libmail-sendmail-perl
The following NEW packages will be installed:
apache2-dev bioperl bsdmainutils ca-certificates debhelper file
fontconfig-config fonts-dejavu-core gettext gettext-base groff-base
intltool-debian libanyevent-cachedns-perl libanyevent-http-perl
libanyevent-perl libapr1 libapr1-dev libaprutil1 libaprutil1-dev
libasprintf0c2 libbio-graphics-perl libbio-perl-perl libcapture-tiny-perl
libcgi-pm-perl libcgi-session-perl libcommon-sense-perl libcpan-meta-perl
libcroco3 libdata-stag-perl libdbd-sqlite3-perl libdbi-perl
libencode-locale-perl libexpat1 libexpat1-dev libexporter-tiny-perl libffi6
libfile-listing-perl libfontconfig1 libfreetype6 libgd-gd2-perl libgd3
libglib2.0-0 libgnutls-deb0-28 libhogweed4 libhtml-parser-perl
libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl
libhttp-daemon-perl libhttp-date-perl libhttp-message-perl
libhttp-negotiate-perl libio-html-perl libio-socket-ssl-perl
libio-string-perl libjbig0 libjpeg62-turbo libjs-prototype
libjs-scriptaculous libjson-perl libldap-2.4-2 libldap2-dev
liblist-moreutils-perl liblwp-mediatypes-perl liblwp-protocol-https-perl
libmagic1 libmodule-build-perl libnet-http-perl libnet-ssleay-perl
libnettle6 libp11-kit0 libpipeline1 libsasl2-2 libsasl2-modules-db
libsctp-dev libsctp1 libsqlite3-0 libssl1.0.0 libstatistics-descriptive-perl
libstring-approx-perl libtasn1-6 libterm-readkey-perl libtiff5 libunistring0
liburi-perl libvm-ec2-perl libvpx2 libwww-perl libwww-robotrules-perl
libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxml-libxml-perl
libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl
libxml-simple-perl libxml2 libxpm4 man-db netbase openssl po-debconf
sbuild-build-depends-gbrowse-dummy sqlite3 ucf uuid-dev
The following packages will be upgraded:
libuuid1
1 upgraded, 109 newly installed, 0 to remove and 75 not upgraded.
Need to get 29.9 MB/29.9 MB of archives.
After this operation, 92.9 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ stretch-staging/main libpipeline1 armhf 1.4.0-1 [24.0 kB]
Get:2 http://172.17.0.1/private/ stretch-staging/main groff-base armhf 1.22.3-1 [1085 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main bsdmainutils armhf 9.0.6 [177 kB]
Get:4 http://172.17.0.1/private/ stretch-staging/main man-db armhf 2.7.0.2-5 [972 kB]
Get:5 http://172.17.0.1/private/ stretch-staging/main libasprintf0c2 armhf 0.19.4-1 [31.5 kB]
Get:6 http://172.17.0.1/private/ stretch-staging/main libnettle6 armhf 3.1.1-3 [200 kB]
Get:7 http://172.17.0.1/private/ stretch-staging/main libhogweed4 armhf 3.1.1-3 [126 kB]
Get:8 http://172.17.0.1/private/ stretch-staging/main libffi6 armhf 3.1-2 [18.1 kB]
Get:9 http://172.17.0.1/private/ stretch-staging/main libp11-kit0 armhf 0.23.1-2 [94.1 kB]
Get:10 http://172.17.0.1/private/ stretch-staging/main libtasn1-6 armhf 4.5-2 [43.9 kB]
Get:11 http://172.17.0.1/private/ stretch-staging/main libgnutls-deb0-28 armhf 3.3.15-6 [645 kB]
Get:12 http://172.17.0.1/private/ stretch-staging/main libsasl2-modules-db armhf 2.1.26.dfsg1-13 [65.5 kB]
Get:13 http://172.17.0.1/private/ stretch-staging/main libsasl2-2 armhf 2.1.26.dfsg1-13 [97.2 kB]
Get:14 http://172.17.0.1/private/ stretch-staging/main libldap-2.4-2 armhf 2.4.40+dfsg-1+rpi1 [192 kB]
Get:15 http://172.17.0.1/private/ stretch-staging/main libmagic1 armhf 1:5.22+15-2 [244 kB]
Get:16 http://172.17.0.1/private/ stretch-staging/main libxml2 armhf 2.9.1+dfsg1-5 [703 kB]
Get:17 http://172.17.0.1/private/ stretch-staging/main libuuid1 armhf 2.26.2-6 [65.9 kB]
Get:18 http://172.17.0.1/private/ stretch-staging/main libapr1 armhf 1.5.1-3 [77.1 kB]
Get:19 http://172.17.0.1/private/ stretch-staging/main libexpat1 armhf 2.1.0-6 [60.2 kB]
Get:20 http://172.17.0.1/private/ stretch-staging/main libssl1.0.0 armhf 1.0.2c-1 [883 kB]
Get:21 http://172.17.0.1/private/ stretch-staging/main libaprutil1 armhf 1.5.4-1 [75.9 kB]
Get:22 http://172.17.0.1/private/ stretch-staging/main libglib2.0-0 armhf 2.44.1-1 [2314 kB]
Get:23 http://172.17.0.1/private/ stretch-staging/main libcroco3 armhf 0.6.8-3 [121 kB]
Get:24 http://172.17.0.1/private/ stretch-staging/main libfreetype6 armhf 2.5.2-4 [412 kB]
Get:25 http://172.17.0.1/private/ stretch-staging/main ucf all 3.0030 [69.7 kB]
Get:26 http://172.17.0.1/private/ stretch-staging/main fonts-dejavu-core all 2.35-1 [1064 kB]
Get:27 http://172.17.0.1/private/ stretch-staging/main fontconfig-config all 2.11.0-6.3 [273 kB]
Get:28 http://172.17.0.1/private/ stretch-staging/main libfontconfig1 armhf 2.11.0-6.3 [311 kB]
Get:29 http://172.17.0.1/private/ stretch-staging/main libjbig0 armhf 2.1-3.1 [27.5 kB]
Get:30 http://172.17.0.1/private/ stretch-staging/main libsctp1 armhf 1.0.16+dfsg-2 [27.1 kB]
Get:31 http://172.17.0.1/private/ stretch-staging/main libjpeg62-turbo armhf 1:1.4.0-7 [102 kB]
Get:32 http://172.17.0.1/private/ stretch-staging/main libtiff5 armhf 4.0.3-13 [193 kB]
Get:33 http://172.17.0.1/private/ stretch-staging/main libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:34 http://172.17.0.1/private/ stretch-staging/main libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:35 http://172.17.0.1/private/ stretch-staging/main libxdmcp6 armhf 1:1.1.2-1 [25.0 kB]
Get:36 http://172.17.0.1/private/ stretch-staging/main libxcb1 armhf 1.10-3 [38.1 kB]
Get:37 http://172.17.0.1/private/ stretch-staging/main libx11-data all 2:1.6.3-1 [128 kB]
Get:38 http://172.17.0.1/private/ stretch-staging/main libx11-6 armhf 2:1.6.3-1 [678 kB]
Get:39 http://172.17.0.1/private/ stretch-staging/main libxpm4 armhf 1:3.5.11-1 [41.7 kB]
Get:40 http://172.17.0.1/private/ stretch-staging/main netbase all 5.3 [19.0 kB]
Get:41 http://172.17.0.1/private/ stretch-staging/main file armhf 1:5.22+15-2 [59.9 kB]
Get:42 http://172.17.0.1/private/ stretch-staging/main gettext-base armhf 0.19.4-1 [117 kB]
Get:43 http://172.17.0.1/private/ stretch-staging/main libsqlite3-0 armhf 3.8.10.2-1 [389 kB]
Get:44 http://172.17.0.1/private/ stretch-staging/main openssl armhf 1.0.2c-1 [682 kB]
Get:45 http://172.17.0.1/private/ stretch-staging/main uuid-dev armhf 2.26.2-6 [79.3 kB]
Get:46 http://172.17.0.1/private/ stretch-staging/main libsctp-dev armhf 1.0.16+dfsg-2 [82.9 kB]
Get:47 http://172.17.0.1/private/ stretch-staging/main libapr1-dev armhf 1.5.1-3 [631 kB]
Get:48 http://172.17.0.1/private/ stretch-staging/main libldap2-dev armhf 2.4.40+dfsg-1+rpi1 [302 kB]
Get:49 http://172.17.0.1/private/ stretch-staging/main libexpat1-dev armhf 2.1.0-6 [117 kB]
Get:50 http://172.17.0.1/private/ stretch-staging/main libaprutil1-dev armhf 1.5.4-1 [356 kB]
Get:51 http://172.17.0.1/private/ stretch-staging/main gettext armhf 0.19.4-1 [1168 kB]
Get:52 http://172.17.0.1/private/ stretch-staging/main intltool-debian all 0.35.0+20060710.2 [25.9 kB]
Get:53 http://172.17.0.1/private/ stretch-staging/main po-debconf all 1.0.18 [248 kB]
Get:54 http://172.17.0.1/private/ stretch-staging/main debhelper all 9.20150507 [824 kB]
Get:55 http://172.17.0.1/private/ stretch-staging/main apache2-dev armhf 2.4.10-11 [280 kB]
Get:56 http://172.17.0.1/private/ stretch-staging/main libio-string-perl all 1.08-3 [12.3 kB]
Get:57 http://172.17.0.1/private/ stretch-staging/main libdata-stag-perl all 0.13-1 [476 kB]
Get:58 http://172.17.0.1/private/ stretch-staging/main libbio-perl-perl all 1.6.924-1 [4763 kB]
Get:59 http://172.17.0.1/private/ stretch-staging/main bioperl all 1.6.924-1 [419 kB]
Get:60 http://172.17.0.1/private/ stretch-staging/main ca-certificates all 20150426 [208 kB]
Get:61 http://172.17.0.1/private/ stretch-staging/main libanyevent-perl armhf 7.070-3 [404 kB]
Get:62 http://172.17.0.1/private/ stretch-staging/main libanyevent-cachedns-perl all 0.08-2 [7150 B]
Get:63 http://172.17.0.1/private/ stretch-staging/main libcommon-sense-perl armhf 3.73-3 [23.5 kB]
Get:64 http://172.17.0.1/private/ stretch-staging/main libanyevent-http-perl all 2.22-1 [35.0 kB]
Get:65 http://172.17.0.1/private/ stretch-staging/main libvpx2 armhf 1.4.0-3+rpi1 [397 kB]
Get:66 http://172.17.0.1/private/ stretch-staging/main libgd3 armhf 2.1.1-1+b1 [127 kB]
Get:67 http://172.17.0.1/private/ stretch-staging/main libgd-gd2-perl armhf 1:2.46-3.1+b2 [171 kB]
Get:68 http://172.17.0.1/private/ stretch-staging/main libbio-graphics-perl all 2.39-2 [606 kB]
Get:69 http://172.17.0.1/private/ stretch-staging/main libcapture-tiny-perl all 0.30-1 [24.6 kB]
Get:70 http://172.17.0.1/private/ stretch-staging/main libhtml-tagset-perl all 3.20-2 [13.5 kB]
Get:71 http://172.17.0.1/private/ stretch-staging/main liburi-perl all 1.64-1 [95.5 kB]
Get:72 http://172.17.0.1/private/ stretch-staging/main libhtml-parser-perl armhf 3.71-2 [105 kB]
Get:73 http://172.17.0.1/private/ stretch-staging/main libcgi-pm-perl all 4.15-1 [224 kB]
Get:74 http://172.17.0.1/private/ stretch-staging/main libcgi-session-perl all 4.48-2 [119 kB]
Get:75 http://172.17.0.1/private/ stretch-staging/main libcpan-meta-perl all 2.150001-1 [128 kB]
Get:76 http://172.17.0.1/private/ stretch-staging/main libdbi-perl armhf 1.633-1 [811 kB]
Get:77 http://172.17.0.1/private/ stretch-staging/main libdbd-sqlite3-perl armhf 1.46-1 [150 kB]
Get:78 http://172.17.0.1/private/ stretch-staging/main libencode-locale-perl all 1.03-1 [13.6 kB]
Get:79 http://172.17.0.1/private/ stretch-staging/main libexporter-tiny-perl all 0.042-1 [32.4 kB]
Get:80 http://172.17.0.1/private/ stretch-staging/main libhttp-date-perl all 6.02-1 [10.7 kB]
Get:81 http://172.17.0.1/private/ stretch-staging/main libfile-listing-perl all 6.04-1 [10.3 kB]
Get:82 http://172.17.0.1/private/ stretch-staging/main libhtml-tree-perl all 5.03-2 [210 kB]
Get:83 http://172.17.0.1/private/ stretch-staging/main libio-html-perl all 1.001-1 [17.6 kB]
Get:84 http://172.17.0.1/private/ stretch-staging/main liblwp-mediatypes-perl all 6.02-1 [22.1 kB]
Get:85 http://172.17.0.1/private/ stretch-staging/main libhttp-message-perl all 6.06-1 [80.1 kB]
Get:86 http://172.17.0.1/private/ stretch-staging/main libhttp-cookies-perl all 6.01-1 [17.4 kB]
Get:87 http://172.17.0.1/private/ stretch-staging/main libhttp-daemon-perl all 6.01-1 [17.3 kB]
Get:88 http://172.17.0.1/private/ stretch-staging/main libhttp-negotiate-perl all 6.00-2 [13.6 kB]
Get:89 http://172.17.0.1/private/ stretch-staging/main libnet-ssleay-perl armhf 1.68-1 [262 kB]
Get:90 http://172.17.0.1/private/ stretch-staging/main libio-socket-ssl-perl all 2.016-1 [179 kB]
Get:91 http://172.17.0.1/private/ stretch-staging/main libjs-prototype all 1.7.1-3 [44.3 kB]
Get:92 http://172.17.0.1/private/ stretch-staging/main libjs-scriptaculous all 1.9.0-2 [129 kB]
Get:93 http://172.17.0.1/private/ stretch-staging/main libjson-perl all 2.61-1 [84.7 kB]
Get:94 http://172.17.0.1/private/ stretch-staging/main liblist-moreutils-perl armhf 0.410-1 [65.6 kB]
Get:95 http://172.17.0.1/private/ stretch-staging/main libnet-http-perl all 6.07-1 [24.8 kB]
Get:96 http://172.17.0.1/private/ stretch-staging/main libwww-robotrules-perl all 6.01-1 [14.3 kB]
Get:97 http://172.17.0.1/private/ stretch-staging/main libwww-perl all 6.08-1 [194 kB]
Get:98 http://172.17.0.1/private/ stretch-staging/main liblwp-protocol-https-perl all 6.06-2 [9582 B]
Get:99 http://172.17.0.1/private/ stretch-staging/main libmodule-build-perl all 0.421100-2 [259 kB]
Get:100 http://172.17.0.1/private/ stretch-staging/main libstatistics-descriptive-perl all 3.0608-1 [41.5 kB]
Get:101 http://172.17.0.1/private/ stretch-staging/main libstring-approx-perl armhf 3.27-1+b2 [38.8 kB]
Get:102 http://172.17.0.1/private/ stretch-staging/main libterm-readkey-perl armhf 2.32-2 [26.2 kB]
Get:103 http://172.17.0.1/private/ stretch-staging/main libxml-namespacesupport-perl all 1.11-1 [14.8 kB]
Get:104 http://172.17.0.1/private/ stretch-staging/main libxml-sax-base-perl all 1.07-1 [23.1 kB]
Get:105 http://172.17.0.1/private/ stretch-staging/main libxml-sax-perl all 0.99+dfsg-2 [68.3 kB]
Get:106 http://172.17.0.1/private/ stretch-staging/main libxml-libxml-perl armhf 2.0116+dfsg-4 [341 kB]
Get:107 http://172.17.0.1/private/ stretch-staging/main libxml-simple-perl all 2.20-1 [74.7 kB]
Get:108 http://172.17.0.1/private/ stretch-staging/main libvm-ec2-perl all 1.28-1 [768 kB]
Get:109 http://172.17.0.1/private/ stretch-staging/main sqlite3 armhf 3.8.10.2-1 [106 kB]
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Preparing to unpack .../sbuild-build-depends-gbrowse-dummy.deb ...
Unpacking sbuild-build-depends-gbrowse-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.4.0-1) ...
Setting up groff-base (1.22.3-1) ...
Setting up bsdmainutils (9.0.6) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up man-db (2.7.0.2-5) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libasprintf0c2:armhf (0.19.4-1) ...
Setting up libnettle6:armhf (3.1.1-3) ...
Setting up libhogweed4:armhf (3.1.1-3) ...
Setting up libffi6:armhf (3.1-2) ...
Setting up libp11-kit0:armhf (0.23.1-2) ...
Setting up libtasn1-6:armhf (4.5-2) ...
Setting up libgnutls-deb0-28:armhf (3.3.15-6) ...
Setting up libsasl2-modules-db:armhf (2.1.26.dfsg1-13) ...
Setting up libsasl2-2:armhf (2.1.26.dfsg1-13) ...
Setting up libldap-2.4-2:armhf (2.4.40+dfsg-1+rpi1) ...
Setting up libmagic1:armhf (1:5.22+15-2) ...
Setting up libxml2:armhf (2.9.1+dfsg1-5) ...
Setting up libapr1:armhf (1.5.1-3) ...
Setting up libexpat1:armhf (2.1.0-6) ...
Setting up libssl1.0.0:armhf (1.0.2c-1) ...
Setting up libaprutil1:armhf (1.5.4-1) ...
Setting up libglib2.0-0:armhf (2.44.1-1) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.8-3) ...
Setting up libfreetype6:armhf (2.5.2-4) ...
Setting up ucf (3.0030) ...
Setting up fonts-dejavu-core (2.35-1) ...
Setting up fontconfig-config (2.11.0-6.3) ...
Setting up libfontconfig1:armhf (2.11.0-6.3) ...
Setting up libjbig0:armhf (2.1-3.1) ...
Setting up libsctp1:armhf (1.0.16+dfsg-2) ...
Setting up libjpeg62-turbo:armhf (1:1.4.0-7) ...
Setting up libtiff5:armhf (4.0.3-13) ...
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up libxau6:armhf (1:1.0.8-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-1) ...
Setting up libxcb1:armhf (1.10-3) ...
Setting up libx11-data (2:1.6.3-1) ...
Setting up libx11-6:armhf (2:1.6.3-1) ...
Setting up libxpm4:armhf (1:3.5.11-1) ...
Setting up netbase (5.3) ...
Setting up file (1:5.22+15-2) ...
Setting up gettext-base (0.19.4-1) ...
Setting up libsqlite3-0:armhf (3.8.10.2-1) ...
Setting up openssl (1.0.2c-1) ...
Setting up uuid-dev:armhf (2.26.2-6) ...
Setting up libsctp-dev (1.0.16+dfsg-2) ...
Setting up libapr1-dev (1.5.1-3) ...
Setting up libldap2-dev:armhf (2.4.40+dfsg-1+rpi1) ...
Setting up libexpat1-dev:armhf (2.1.0-6) ...
Setting up libaprutil1-dev (1.5.4-1) ...
Setting up gettext (0.19.4-1) ...
Setting up intltool-debian (0.35.0+20060710.2) ...
Setting up po-debconf (1.0.18) ...
Setting up debhelper (9.20150507) ...
Setting up apache2-dev (2.4.10-11) ...
Setting up libio-string-perl (1.08-3) ...
Setting up libdata-stag-perl (0.13-1) ...
Setting up libbio-perl-perl (1.6.924-1) ...
Setting up bioperl (1.6.924-1) ...
Setting up ca-certificates (20150426) ...
Setting up libanyevent-perl (7.070-3) ...
Setting up libanyevent-cachedns-perl (0.08-2) ...
Setting up libcommon-sense-perl (3.73-3) ...
Setting up libanyevent-http-perl (2.22-1) ...
Setting up libvpx2:armhf (1.4.0-3+rpi1) ...
Setting up libgd3:armhf (2.1.1-1+b1) ...
Setting up libgd-gd2-perl (1:2.46-3.1+b2) ...
Setting up libbio-graphics-perl (2.39-2) ...
Setting up libcapture-tiny-perl (0.30-1) ...
Setting up libhtml-tagset-perl (3.20-2) ...
Setting up liburi-perl (1.64-1) ...
Setting up libhtml-parser-perl (3.71-2) ...
Setting up libcgi-pm-perl (4.15-1) ...
Setting up libcgi-session-perl (4.48-2) ...
Setting up libcpan-meta-perl (2.150001-1) ...
Setting up libdbi-perl (1.633-1) ...
Setting up libdbd-sqlite3-perl (1.46-1) ...
Setting up libencode-locale-perl (1.03-1) ...
Setting up libexporter-tiny-perl (0.042-1) ...
Setting up libhttp-date-perl (6.02-1) ...
Setting up libfile-listing-perl (6.04-1) ...
Setting up libhtml-tree-perl (5.03-2) ...
Setting up libio-html-perl (1.001-1) ...
Setting up liblwp-mediatypes-perl (6.02-1) ...
Setting up libhttp-message-perl (6.06-1) ...
Setting up libhttp-cookies-perl (6.01-1) ...
Setting up libhttp-daemon-perl (6.01-1) ...
Setting up libhttp-negotiate-perl (6.00-2) ...
Setting up libnet-ssleay-perl (1.68-1) ...
Setting up libio-socket-ssl-perl (2.016-1) ...
Setting up libjs-prototype (1.7.1-3) ...
Setting up libjs-scriptaculous (1.9.0-2) ...
Setting up libjson-perl (2.61-1) ...
Setting up liblist-moreutils-perl (0.410-1) ...
Setting up libnet-http-perl (6.07-1) ...
Setting up libwww-robotrules-perl (6.01-1) ...
Setting up libmodule-build-perl (0.421100-2) ...
Setting up libstatistics-descriptive-perl (3.0608-1) ...
Setting up libstring-approx-perl (3.27-1+b2) ...
Setting up libterm-readkey-perl (2.32-2) ...
Setting up libxml-namespacesupport-perl (1.11-1) ...
Setting up libxml-sax-base-perl (1.07-1) ...
Setting up libxml-sax-perl (0.99+dfsg-2) ...
update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...
Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version
Setting up libxml-libxml-perl (2.0116+dfsg-4) ...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...
Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version
Setting up libxml-simple-perl (2.20-1) ...
Setting up sqlite3 (3.8.10.2-1) ...
Setting up liblwp-protocol-https-perl (6.06-2) ...
Setting up libwww-perl (6.08-1) ...
Setting up libvm-ec2-perl (1.28-1) ...
Setting up sbuild-build-depends-gbrowse-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.19-18) ...
Processing triggers for ca-certificates (20150426) ...
Updating certificates in /etc/ssl/certs...
180 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.25-5 dpkg-dev_1.17.25 g++-4.9_4.9.2-10 gcc-4.9_4.9.2-10 libc6-dev_2.19-18 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 linux-libc-dev_3.16.7-ckt4-1+rpi1
Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apache2-dev_2.4.10-11 apt_1.0.9.8 base-files_8+rpi1 base-passwd_3.5.37 bash_4.3-11 binutils_2.25-5 bioperl_1.6.924-1 bsdmainutils_9.0.6 bsdutils_1:2.25.2-6 build-essential_11.7 bzip2_1.0.6-7 ca-certificates_20150426 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:4.9.2-2 cpp-4.9_4.9.2-10 dash_0.5.7-4 debconf_1.5.56 debconf-i18n_1.5.56 debfoster_2.7-2 debhelper_9.20150507 debianutils_4.4 diffutils_1:3.3-1 dmsetup_2:1.02.90-2.2 dpkg_1.17.25 dpkg-dev_1.17.25 e2fslibs_1.42.12-1.1 e2fsprogs_1.42.12-1.1 fakeroot_1.20.2-1 file_1:5.22+15-2 findutils_4.4.2-9 fontconfig-config_2.11.0-6.3 fonts-dejavu-core_2.35-1 g++_4:4.9.2-2 g++-4.9_4.9.2-10 gcc_4:4.9.2-2 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.4-1 gcc-4.9_4.9.2-10 gcc-4.9-base_4.9.2-10 gettext_0.19.4-1 gettext-base_0.19.4-1 gnupg_1.4.18-7 gpgv_1.4.18-7 grep_2.20-4.1 groff-base_1.22.3-1 gzip_1.6-4 hostname_3.15 init_1.22 init-system-helpers_1.22 initramfs-tools_0.120 initscripts_2.88dsf-59 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.2 klibc-utils_2.0.4-2+rpi1 kmod_18-3 libacl1_2.2.52-2 libanyevent-cachedns-perl_0.08-2 libanyevent-http-perl_2.22-1 libanyevent-perl_7.070-3 libapr1_1.5.1-3 libapr1-dev_1.5.1-3 libaprutil1_1.5.4-1 libaprutil1-dev_1.5.4-1 libapt-pkg4.12_1.0.9.8 libasan1_4.9.2-10 libasprintf0c2_0.19.4-1 libatomic1_4.9.2-10 libattr1_1:2.4.47-2 libaudit-common_1:2.4-1 libaudit1_1:2.4-1 libbio-graphics-perl_2.39-2 libbio-perl-perl_1.6.924-1 libblkid1_2.25.2-6 libbz2-1.0_1.0.6-7 libc-bin_2.19-18 libc-dev-bin_2.19-18 libc6_2.19-18 libc6-dev_2.19-18 libcap2_1:2.24-8 libcap2-bin_1:2.24-8 libcapture-tiny-perl_0.30-1 libcgi-pm-perl_4.15-1 libcgi-session-perl_4.48-2 libcloog-isl4_0.18.2-1 libcomerr2_1.42.12-1.1 libcommon-sense-perl_3.73-3 libcpan-meta-perl_2.150001-1 libcroco3_0.6.8-3 libcryptsetup4_2:1.6.6-5 libdata-stag-perl_0.13-1 libdb5.3_5.3.28-9 libdbd-sqlite3-perl_1.46-1 libdbi-perl_1.633-1 libdbus-1-3_1.8.16-1 libdebconfclient0_0.192 libdevmapper1.02.1_2:1.02.90-2.2 libdpkg-perl_1.17.25 libdrm2_2.4.58-2 libencode-locale-perl_1.03-1 libexpat1_2.1.0-6 libexpat1-dev_2.1.0-6 libexporter-tiny-perl_0.042-1 libfakeroot_1.20.2-1 libffi6_3.1-2 libfile-listing-perl_6.04-1 libfontconfig1_2.11.0-6.3 libfreetype6_2.5.2-4 libgc1c2_1:7.2d-6.4 libgcc-4.9-dev_4.9.2-10 libgcc1_1:4.9.2-10 libgcrypt20_1.6.3-2 libgd-gd2-perl_1:2.46-3.1+b2 libgd3_2.1.1-1+b1 libgdbm3_1.8.3-13.1 libglib2.0-0_2.44.1-1 libgmp10_2:6.0.0+dfsg-6+rpi1 libgnutls-deb0-28_3.3.15-6 libgomp1_4.9.2-10 libgpg-error0_1.17-3 libhogweed4_3.1.1-3 libhtml-parser-perl_3.71-2 libhtml-tagset-perl_3.20-2 libhtml-tree-perl_5.03-2 libhttp-cookies-perl_6.01-1 libhttp-daemon-perl_6.01-1 libhttp-date-perl_6.02-1 libhttp-message-perl_6.06-1 libhttp-negotiate-perl_6.00-2 libio-html-perl_1.001-1 libio-socket-ssl-perl_2.016-1 libio-string-perl_1.08-3 libisl10_0.12.2-2 libjbig0_2.1-3.1 libjpeg62-turbo_1:1.4.0-7 libjs-prototype_1.7.1-3 libjs-scriptaculous_1.9.0-2 libjson-perl_2.61-1 libklibc_2.0.4-2+rpi1 libkmod2_18-3 libldap-2.4-2_2.4.40+dfsg-1+rpi1 libldap2-dev_2.4.40+dfsg-1+rpi1 liblist-moreutils-perl_0.410-1 liblocale-gettext-perl_1.05-8+b1 liblwp-mediatypes-perl_6.02-1 liblwp-protocol-https-perl_6.06-2 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.22+15-2 libmodule-build-perl_0.421100-2 libmount1_2.25.2-6 libmpc3_1.0.2-1 libmpfr4_3.1.2-2 libncurses5_5.9+20140913-1 libncursesw5_5.9+20140913-1 libnet-http-perl_6.07-1 libnet-ssleay-perl_1.68-1 libnettle6_3.1.1-3 libnih-dbus1_1.0.3-4.3 libnih1_1.0.3-4.3 libp11-kit0_0.23.1-2 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam0g_1.1.8-3.1 libpcre3_2:8.35-3.3 libpipeline1_1.4.0-1 libpng12-0_1.2.50-2 libprocps3_2:3.3.9-9 libreadline6_6.3-8 libsasl2-2_2.1.26.dfsg1-13 libsasl2-modules-db_2.1.26.dfsg1-13 libsctp-dev_1.0.16+dfsg-2 libsctp1_1.0.16+dfsg-2 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-2 libslang2_2.3.0-2 libsmartcols1_2.25.2-6 libsqlite3-0_3.8.10.2-1 libss2_1.42.12-1.1 libssl1.0.0_1.0.2c-1 libstatistics-descriptive-perl_3.0608-1 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 libstring-approx-perl_3.27-1+b2 libsystemd0_215-17 libtasn1-6_4.5-2 libterm-readkey-perl_2.32-2 libtext-charwidth-perl_0.04-7+b4 libtext-iconv-perl_1.7-5+b5 libtext-wrapi18n-perl_0.06-7 libtiff5_4.0.3-13 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140913-1 libubsan0_4.9.2-10 libudev1_215-17 libunistring0_0.9.3-5.2 liburi-perl_1.64-1 libusb-0.1-4_2:0.1.12-25 libustr-1.0-1_1.0.4-3 libuuid1_2.26.2-6 libvm-ec2-perl_1.28-1 libvpx2_1.4.0-3+rpi1 libwww-perl_6.08-1 libwww-robotrules-perl_6.01-1 libx11-6_2:1.6.3-1 libx11-data_2:1.6.3-1 libxau6_1:1.0.8-1 libxcb1_1.10-3 libxdmcp6_1:1.1.2-1 libxml-libxml-perl_2.0116+dfsg-4 libxml-namespacesupport-perl_1.11-1 libxml-sax-base-perl_1.07-1 libxml-sax-perl_0.99+dfsg-2 libxml-simple-perl_2.20-1 libxml2_2.9.1+dfsg1-5 libxpm4_1:3.5.11-1 linux-libc-dev_3.16.7-ckt4-1+rpi1 login_1:4.2-3 lsb-base_4.1+Debian13+rpi1+nmu1 make_4.0-8.1 makedev_2.3.1-93 man-db_2.7.0.2-5 mawk_1.3.3-17 mount_2.25.2-6 mountall_2.54 multiarch-support_2.19-18 ncurses-base_5.9+20140913-1 ncurses-bin_5.9+20140913-1 netbase_5.3 openssl_1.0.2c-1 passwd_1:4.2-3 patch_2.7.5-1 perl_5.20.2-3 perl-base_5.20.2-3 perl-modules_5.20.2-3 plymouth_0.9.0-9 po-debconf_1.0.18 procps_2:3.3.9-9 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gbrowse-dummy_0.invalid.0 sed_4.2.2-4 sensible-utils_0.0.9 sqlite3_3.8.10.2-1 startpar_0.59-3 systemd_215-17 systemd-sysv_215-17 sysv-rc_2.88dsf-59 sysvinit-utils_2.88dsf-59 tar_1.27.1-2 tzdata_2015c-1 ucf_3.0030 udev_215-17 util-linux_2.25.2-6 uuid-dev_2.26.2-6 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-2
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Tue Jun 16 08:18:14 2015 UTC using RSA key ID 326D8438
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./gbrowse_2.54+dfsg-4.dsc
dpkg-source: info: extracting gbrowse in gbrowse-2.54+dfsg
dpkg-source: info: unpacking gbrowse_2.54+dfsg.orig.tar.bz2
dpkg-source: info: unpacking gbrowse_2.54+dfsg-4.debian.tar.xz
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 skipRenderFarmTest_UpstreamBug12
dpkg-source: info: applying skip_check_installed_test.patch
dpkg-source: info: applying source_init_functions
Check disc space
────────────────
Sufficient free space for build
User Environment
────────────────
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-96bc6626-8f03-4393-aa6f-f2e11a603c54
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package gbrowse
dpkg-buildpackage: source version 2.54+dfsg-4
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build gbrowse-2.54+dfsg
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean --with apache2
dh_testdir
dh_auto_clean
dh_clean
debian/rules build-arch
dh build-arch --with apache2
dh_testdir -a
debian/rules override_dh_auto_configure
make[1]: Entering directory '/«BUILDDIR»/gbrowse-2.54+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 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2" --config "ld=cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro" --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
Possible precedence issue with control flow operator at /«BUILDDIR»/gbrowse-2.54+dfsg/install_util/GBrowseInstall.pm line 1032.
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::Pg 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 '2.54'
make[1]: Leaving directory '/«BUILDDIR»/gbrowse-2.54+dfsg'
dh_auto_build -a
perl Build
Possible precedence issue with control flow operator at /«BUILDDIR»/gbrowse-2.54+dfsg/install_util/GBrowseInstall.pm line 1032.
NOTE: Run ./Build reconfig to change existing configuration.
Building GBrowse
cc -I/«BUILDDIR»/gbrowse-2.54+dfsg/libalign -I/usr/lib/arm-linux-gnueabihf/perl/5.20/CORE -DXS_VERSION="2.54" -DVERSION="2.54" -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 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -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')
cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -shared -L/usr/local/lib -fstack-protector -o blib/arch/auto/Bio/Graphics/Browser2/CAlign/CAlign.so lib/Bio/Graphics/Browser2/CAlign.o
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/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 /«BUILDDIR»/gbrowse-2.54+dfsg/install_util/GBrowseInstall.pm line 728.
dh_auto_test -a
perl Build test --verbose 1
Possible precedence issue with control flow operator at /«BUILDDIR»/gbrowse-2.54+dfsg/install_util/GBrowseInstall.pm line 1032.
NOTE: Run ./Build reconfig to change existing configuration.
Use of uninitialized value in pattern match (m//) at /«BUILDDIR»/gbrowse-2.54+dfsg/install_util/GBrowseInstall.pm line 728.
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 - bin/gbrowse_change_passwd.pl compiled ok
ok 36 - bin/gbrowse_change_passwd.pl stderr said "syntax OK"
ok 37 - bin/gbrowse_change_passwd.pl nothing on stdout
ok 38 - bin/gbrowse_clean.pl compiled ok
ok 39 - bin/gbrowse_clean.pl stderr said "syntax OK"
ok 40 - bin/gbrowse_clean.pl nothing on stdout
ok 41 - bin/gbrowse_configure_slaves.pl compiled ok
ok 42 - bin/gbrowse_configure_slaves.pl stderr said "syntax OK"
ok 43 - bin/gbrowse_configure_slaves.pl nothing on stdout
ok 44 - bin/gbrowse_create_account.pl compiled ok
ok 45 - bin/gbrowse_create_account.pl stderr said "syntax OK"
ok 46 - bin/gbrowse_create_account.pl nothing on stdout
ok 47 # skip explicitly skipping bin/gbrowse_grow_cloud_vol.pl
ok 48 - bin/gbrowse_import_ucsc_db.pl compiled ok
ok 49 - bin/gbrowse_import_ucsc_db.pl stderr said "syntax OK"
ok 50 - bin/gbrowse_import_ucsc_db.pl nothing on stdout
ok 51 # skip explicitly skipping bin/gbrowse_launch_aws_slaves.pl
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 - bin/gtf2gff3.pl compiled ok
ok 71 - bin/gtf2gff3.pl stderr said "syntax OK"
ok 72 - bin/gtf2gff3.pl nothing on stdout
ok 73 - bin/load_genbank.pl compiled ok
ok 74 - bin/load_genbank.pl stderr said "syntax OK"
ok 75 - bin/load_genbank.pl nothing on stdout
ok 76 # skip explicitly skipping bin/make_das_conf.pl
ok 77 - bin/process_bamfiles.pl compiled ok
ok 78 - bin/process_bamfiles.pl stderr said "syntax OK"
ok 79 - bin/process_bamfiles.pl nothing on stdout
ok 80 - bin/process_gadfly.pl compiled ok
ok 81 - bin/process_gadfly.pl stderr said "syntax OK"
ok 82 - bin/process_gadfly.pl nothing on stdout
ok 83 - bin/process_ncbi_human.pl compiled ok
ok 84 - bin/process_ncbi_human.pl stderr said "syntax OK"
ok 85 - bin/process_ncbi_human.pl nothing on stdout
ok 86 - bin/process_sgd.pl compiled ok
ok 87 - bin/process_sgd.pl stderr said "syntax OK"
ok 88 - bin/process_sgd.pl nothing on stdout
ok 89 - bin/report_missing_language_tags.pl compiled ok
ok 90 - bin/report_missing_language_tags.pl stderr said "syntax OK"
ok 91 - bin/report_missing_language_tags.pl nothing on stdout
ok 92 - bin/scan_gbrowse.pl compiled ok
ok 93 - bin/scan_gbrowse.pl stderr said "syntax OK"
ok 94 - bin/scan_gbrowse.pl nothing on stdout
ok 95 - bin/ucsc_genes2gff.pl compiled ok
ok 96 - bin/ucsc_genes2gff.pl stderr said "syntax OK"
ok 97 - bin/ucsc_genes2gff.pl nothing on stdout
ok 98 - bin/wiggle2gff3.pl compiled ok
ok 99 - bin/wiggle2gff3.pl stderr said "syntax OK"
ok 100 - bin/wiggle2gff3.pl nothing on stdout
1..100
ok
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
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ok 24
ok 25
ok 26
ok 27
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ok 29
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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
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ok 53
ok 54
ok 55
ok 56
ok 57
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ok 59
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ok 79
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ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok
t/03.render.t ............. skipped: (no reason given)
Sometimes this test gets 'stuck'. If this happens, kill the test and Build test again.
t/04.remoteserver.t ....... skipped: (no reason given)
CGI::param called in list context from /«BUILDDIR»/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/Render.pm line 2348, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /usr/share/perl5/CGI.pm line 408.
CGI::param called in list context from /«BUILDDIR»/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/Render.pm line 2357, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /usr/share/perl5/CGI.pm line 408.
CGI::param called in list context from /«BUILDDIR»/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/Render.pm line 2367, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /usr/share/perl5/CGI.pm line 408.
CGI::param called in list context from /«BUILDDIR»/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/Render.pm line 2384, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /usr/share/perl5/CGI.pm line 408.
CGI::param called in list context from /«BUILDDIR»/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/Render.pm line 2392, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /usr/share/perl5/CGI.pm line 408.
CGI::param called in list context from /«BUILDDIR»/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/Render.pm line 2395, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /usr/share/perl5/CGI.pm line 408.
CGI::param called in list context from /«BUILDDIR»/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/Render.pm line 2431, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /usr/share/perl5/CGI.pm line 408.
CGI::param called in list context from /«BUILDDIR»/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/Render.pm line 2435, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /usr/share/perl5/CGI.pm line 408.
CGI::param called in list context from /«BUILDDIR»/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 271, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /usr/share/perl5/CGI.pm line 408, <STDIN> line 1.
CGI::param called in list context from /«BUILDDIR»/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 271, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /usr/share/perl5/CGI.pm line 408, <STDIN> line 1.
CGI::param called in list context from /«BUILDDIR»/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 278, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /usr/share/perl5/CGI.pm line 408, <STDIN> line 1.
CGI::param called in list context from /«BUILDDIR»/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 279, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /usr/share/perl5/CGI.pm line 408, <STDIN> line 1.
CGI::param called in list context from /«BUILDDIR»/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 278, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /usr/share/perl5/CGI.pm line 408, <STDIN> line 1.
CGI::param called in list context from /«BUILDDIR»/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 279, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /usr/share/perl5/CGI.pm line 408, <STDIN> line 1.
CGI::param called in list context from /«BUILDDIR»/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 501, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /usr/share/perl5/CGI.pm line 408, <> line 132.
CGI::param called in list context from /«BUILDDIR»/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 501, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /usr/share/perl5/CGI.pm line 408, <> line 132.
cannot remove directory for /tmp/gbrowse_testing/4MVms0BAXZ: No such file or directory at /usr/share/perl/5.20/File/Temp.pm line 778.
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
t/06.featuresearch.t ...... skipped: (no reason given)
t/07.karyotype.t ..........
1..3
ok 1
ok 2
ok 3
ok
t/08.calign.t .............
1..6
# Running under perl version 5.020002 for linux
# Current time local: Mon Jun 22 06:17:54 2015
# Current time GMT: Mon Jun 22 06:17:54 2015
# Using Test.pm version 1.26
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok
All tests successful.
Files=9, Tests=225, 93 wallclock secs ( 0.39 usr 0.06 sys + 79.94 cusr 5.94 csys = 86.33 CPU)
Result: PASS
fakeroot debian/rules binary-arch
dh binary-arch --with apache2
dh_testroot -a
dh_prep -a
debian/rules override_dh_installdirs
make[1]: Entering directory '/«BUILDDIR»/gbrowse-2.54+dfsg'
# svn(-buildpackage) seems to ignore the x bit
chmod +x debian/gbrowse-calign.dirs
dh_installdirs
make[1]: Leaving directory '/«BUILDDIR»/gbrowse-2.54+dfsg'
debian/rules override_dh_auto_install
make[1]: Entering directory '/«BUILDDIR»/gbrowse-2.54+dfsg'
./Build --install_base=debian/gbrowse debianinstall
Possible precedence issue with control flow operator at /«BUILDDIR»/gbrowse-2.54+dfsg/install_util/GBrowseInstall.pm line 1032.
NOTE: Run ./Build reconfig to change existing configuration.
Use of uninitialized value in pattern match (m//) at /«BUILDDIR»/gbrowse-2.54+dfsg/install_util/GBrowseInstall.pm line 728.
Building GBrowse
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/auto/Bio/Graphics/Browser2/CAlign/CAlign.bs
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/auto/Bio/Graphics/Browser2/CAlign/CAlign.so
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_clean.pl.1p
Installing debian/gbrowse/man/man1/bed2gff3.pl.1p
Installing debian/gbrowse/man/man1/gtf2gff3.pl.1p
Installing debian/gbrowse/man/man1/make_das_conf.pl.1p
Installing debian/gbrowse/man/man1/gbrowse_grow_cloud_vol.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/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
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Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_trace.scf
Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/dbgff/data_files/elegans_acceptor.gff
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Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/figures/wiggle_density.png
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Legacy/Graphics/Browser.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Legacy/Graphics/Browser/Synteny.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Legacy/Graphics/Browser/I18n.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Legacy/Graphics/Browser/Util.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Legacy/Graphics/Browser/PageSettings.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Legacy/DB/SyntenyIO.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Legacy/DB/SyntenyBlock.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/GBrowseFeature.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Karyotype.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Plugin.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataBase.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Shellwords.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Util.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/OptionPick.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataSource.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Markup.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/PluginSet.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataLoader.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/PadAlignment.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/CachedTrack.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Realign.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/SendMail.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Render.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/TrackDumper.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Session.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/SubtrackTable.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/RenderPanels.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/RegionSearch.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/I18n.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/CAlign.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Region.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/UserDB.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Action.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/RemoteSet.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/GFFhelper.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/UserTracks.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/ExternalData.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/gff3.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/wiggle.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/generic.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/featurefile.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/wig2bigwig.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/bigwig.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/bed.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/gff.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/bam.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/sam.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Render/Slave.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Render/TrackConfig.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Render/SnapshotManager.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Render/HTML.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Render/Login.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Render/Slave/Status.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Render/HTML/TrackListing.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Render/HTML/TrackListing/Categories.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/UserTracks/Database.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/UserTracks/Filesystem.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Plugin/AuthPlugin.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/TrackDumper/RichSeqMaker.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/DB/Tagger.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/DB/SeqFeature/Store/BedLoader.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/DB/SeqFeature/Store/Alias.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/DB/GFF/Aggregator/wormbase_gene.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/DB/GFF/Aggregator/waba_alignment.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/DB/GFF/Aggregator/reftranscript.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/DB/GFF/Aggregator/match_gap.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/DB/Tagger/Tag.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/DB/Tagger/mysql.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/CGI/Toggle.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/GBrowse/ConfigData.pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataSource.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/CGI::Toggle.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RegionSearch.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RenderPanels.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::CAlign.3pm
Installing debian/gbrowse/man/man3/GBrowse::ConfigData.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Plugin.3pm
Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Plugin::AuthPlugin.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Markup.3pm
Installing debian/gbrowse/man/man3/Bio::DB::Tagger::Tag.3pm
Installing debian/gbrowse/man/man3/Bio::DB::SeqFeature::Store::Alias.3pm
Installing debian/gbrowse/man/man3/Legacy::Graphics::Browser.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::PadAlignment.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Util.3pm
Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::AuthorizedFeatureFile.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::GFFhelper.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RemoteSet.3pm
Installing debian/gbrowse/man/man3/Bio::DB::Tagger.3pm
Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataBase.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::OptionPick.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Region.3pm
Installing debian/gbrowse/bin/gbrowse_launch_aws_slaves.pl
Installing debian/gbrowse/bin/ucsc_genes2gff.pl
Installing debian/gbrowse/bin/gbrowse_configure_slaves.pl
Installing debian/gbrowse/bin/gbrowse_slave
Installing debian/gbrowse/bin/make_das_conf.pl
Installing debian/gbrowse/bin/wiggle2gff3.pl
Installing debian/gbrowse/bin/scan_gbrowse.pl
Installing debian/gbrowse/bin/gbrowse_change_passwd.pl
Installing debian/gbrowse/bin/gtf2gff3.pl
Installing debian/gbrowse/bin/gbrowse_metadb_config.pl
Installing debian/gbrowse/bin/gbrowse_import_ucsc_db.pl
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_grow_cloud_vol.pl
Installing debian/gbrowse/bin/load_genbank.pl
Installing debian/gbrowse/bin/gbrowse_set_admin_passwd.pl
Installing debian/gbrowse/bin/gbrowse_clean.pl
Installing debian/gbrowse/bin/gbrowse_create_account.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
Possible precedence issue with control flow operator at /«BUILDDIR»/gbrowse-2.54+dfsg/install_util/GBrowseInstall.pm line 1032.
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::Pg 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 '2.54'
./Build --install_base=debian/gbrowse install_slave
Possible precedence issue with control flow operator at /«BUILDDIR»/gbrowse-2.54+dfsg/install_util/GBrowseInstall.pm line 1032.
NOTE: Run ./Build reconfig to change existing configuration.
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/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-slave
Performing variable substitutions in blib/etc/init.d/gbrowse-slave
Use of uninitialized value $wwwuser in substitution (s///) at /«BUILDDIR»/gbrowse-2.54+dfsg/install_util/GBrowseInstall.pm line 821, <GEN89> 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-slave
Installing debian/gbrowse/etc/init.d/gbrowse-slave
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/GBrowse/ConfigData.pm
mv debian/gbrowse/lib/perl5/* debian/gbrowse/usr/share/perl5
# Remove arch dependant data
mv debian/gbrowse/usr/share/perl5/auto/Bio/Graphics/Browser2/CAlign/* debian/gbrowse-calign/usr/lib/arm-linux-gnueabihf/perl5/5.20/auto/Bio/Graphics/Browser2/CAlign/
mv debian/gbrowse/usr/share/perl5/Bio/Graphics/Browser2/CAlign.pm debian/gbrowse-calign/usr/lib/arm-linux-gnueabihf/perl5/5.20/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
#Remove database (kept as separate package)
rm -rf debian/gbrowse/var/lib/gbrowse/databases/*
#Rename pl scripts in bin
rename 's/\.pl//' debian/gbrowse/bin/*.pl
mv debian/gbrowse/bin debian/gbrowse/usr/bin
# Activate configuration files.
find /«BUILDDIR»/gbrowse-2.54+dfsg/debian/gbrowse/etc -name '*.new' | xargs rename 's/.new//'
rm -rf /«BUILDDIR»/gbrowse-2.54+dfsg/debian/gbrowse/usr/share/perl5/auto
# Update conf files
sed -i 's/gbrowse2/gbrowse/g' /«BUILDDIR»/gbrowse-2.54+dfsg/debian/gbrowse/etc/gbrowse/yeast*.conf
sed -i 's/gbrowse2/gbrowse/g' /«BUILDDIR»/gbrowse-2.54+dfsg/debian/gbrowse/etc/gbrowse/slave*.conf
make[1]: Leaving directory '/«BUILDDIR»/gbrowse-2.54+dfsg'
dh_apache2 -a
dh_installdocs -a
dh_installchangelogs -a
debian/rules override_dh_installman
make[1]: Entering directory '/«BUILDDIR»/gbrowse-2.54+dfsg'
#Rename due to perl extension seen as polish
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 '/«BUILDDIR»/gbrowse-2.54+dfsg'
dh_perl -a
dh_link -a
dh_compress -a
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package `gbrowse-calign' in `../gbrowse-calign_2.54+dfsg-4_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../gbrowse_2.54+dfsg-4_armhf.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build gbrowse-2.54+dfsg
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20150622-0618
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
gbrowse_2.54+dfsg-4_armhf.changes:
──────────────────────────────────
Format: 1.8
Date: Tue, 16 Jun 2015 10:12:37 +0200
Source: gbrowse
Binary: gbrowse gbrowse-data gbrowse-calign
Architecture: armhf
Version: 2.54+dfsg-4
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Olivier Sallou <osallou@debian.org>
Description:
gbrowse - GMOD Generic Genome Browser
gbrowse-calign - CAlign helper
gbrowse-data - Sample data to use GBrowse
Closes: 788642
Changes:
gbrowse (2.54+dfsg-4) unstable; urgency=medium
.
* d/control: add libmodule-build-perl dependency for perl 5.22 transition
(Closes: #788642).
Checksums-Sha1:
f5d4b77a4f40aa6c4d03ad1ca776e6719d3c6b6b 34138 gbrowse-calign_2.54+dfsg-4_armhf.deb
Checksums-Sha256:
1169917f9b58027b70c5a5de5c457fb0f86710ddae63a7dbd94294c62683d5cd 34138 gbrowse-calign_2.54+dfsg-4_armhf.deb
Files:
276d821c3251f690682dca969257943e 34138 science optional gbrowse-calign_2.54+dfsg-4_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
gbrowse-calign_2.54+dfsg-4_armhf.deb
────────────────────────────────────
new debian package, version 2.0.
size 34138 bytes: control archive=813 bytes.
454 bytes, 13 lines control
663 bytes, 7 lines md5sums
Package: gbrowse-calign
Source: gbrowse
Version: 2.54+dfsg-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 51
Depends: perl (>= 5.20.2-3), perlapi-5.20.2, libc6 (>= 2.4), gbrowse
Section: science
Priority: optional
Homepage: http://www.gbrowse.org/
Description: CAlign helper
This package provides the CAlign helper
for use with Realign. It speeds up Smith-Waterman alignment.
drwxr-xr-x root/root 0 2015-06-22 06:18 ./
drwxr-xr-x root/root 0 2015-06-22 06:18 ./usr/
drwxr-xr-x root/root 0 2015-06-22 06:17 ./usr/lib/
drwxr-xr-x root/root 0 2015-06-22 06:17 ./usr/lib/arm-linux-gnueabihf/
drwxr-xr-x root/root 0 2015-06-22 06:17 ./usr/lib/arm-linux-gnueabihf/perl5/
drwxr-xr-x root/root 0 2015-06-22 06:17 ./usr/lib/arm-linux-gnueabihf/perl5/5.20/
drwxr-xr-x root/root 0 2015-06-22 06:17 ./usr/lib/arm-linux-gnueabihf/perl5/5.20/Bio/
drwxr-xr-x root/root 0 2015-06-22 06:17 ./usr/lib/arm-linux-gnueabihf/perl5/5.20/Bio/Graphics/
drwxr-xr-x root/root 0 2015-06-22 06:18 ./usr/lib/arm-linux-gnueabihf/perl5/5.20/Bio/Graphics/Browser2/
-rw-r--r-- root/root 1129 2015-06-22 06:16 ./usr/lib/arm-linux-gnueabihf/perl5/5.20/Bio/Graphics/Browser2/CAlign.pm
drwxr-xr-x root/root 0 2015-06-22 06:17 ./usr/lib/arm-linux-gnueabihf/perl5/5.20/auto/
drwxr-xr-x root/root 0 2015-06-22 06:17 ./usr/lib/arm-linux-gnueabihf/perl5/5.20/auto/Bio/
drwxr-xr-x root/root 0 2015-06-22 06:17 ./usr/lib/arm-linux-gnueabihf/perl5/5.20/auto/Bio/Graphics/
drwxr-xr-x root/root 0 2015-06-22 06:17 ./usr/lib/arm-linux-gnueabihf/perl5/5.20/auto/Bio/Graphics/Browser2/
drwxr-xr-x root/root 0 2015-06-22 06:18 ./usr/lib/arm-linux-gnueabihf/perl5/5.20/auto/Bio/Graphics/Browser2/CAlign/
-rw-r--r-- root/root 0 2015-06-22 06:16 ./usr/lib/arm-linux-gnueabihf/perl5/5.20/auto/Bio/Graphics/Browser2/CAlign/CAlign.bs
-rw-r--r-- root/root 9556 2015-06-22 06:18 ./usr/lib/arm-linux-gnueabihf/perl5/5.20/auto/Bio/Graphics/Browser2/CAlign/CAlign.so
drwxr-xr-x root/root 0 2015-06-22 06:18 ./usr/share/
drwxr-xr-x root/root 0 2015-06-22 06:18 ./usr/share/doc/
drwxr-xr-x root/root 0 2015-06-22 06:18 ./usr/share/doc/gbrowse-calign/
-rw-r--r-- root/root 1318 2015-06-16 08:14 ./usr/share/doc/gbrowse-calign/changelog.Debian.gz
-rw-r--r-- root/root 18924 2012-12-11 15:44 ./usr/share/doc/gbrowse-calign/changelog.gz
-rw-r--r-- root/root 18223 2015-06-16 08:11 ./usr/share/doc/gbrowse-calign/copyright
drwxr-xr-x root/root 0 2015-06-22 06:18 ./usr/share/man/
drwxr-xr-x root/root 0 2015-06-22 06:18 ./usr/share/man/man3/
-rw-r--r-- root/root 2160 2015-06-22 06:18 ./usr/share/man/man3/Bio::Graphics::Browser2::CAlign.3pm.gz
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 31448
Build-Time: 167
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 525
Job: gbrowse_2.54+dfsg-4
Machine Architecture: armhf
Package: gbrowse
Package-Time: 758
Source-Version: 2.54+dfsg-4
Space: 31448
Status: successful
Version: 2.54+dfsg-4
────────────────────────────────────────────────────────────────────────────────
Finished at 20150622-0618
Build needed 00:12:38, 31448k disc space