sbuild (Debian sbuild) 0.62.6 (07 Dec 2011) on build01.raspbian.lan ╔══════════════════════════════════════════════════════════════════════════════╗ ║ gbrowse 2.48~dfsg-1 (armhf) 04 May 2012 20:50 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: gbrowse Version: 2.48~dfsg-1 Source Version: 2.48~dfsg-1 Distribution: testing Architecture: armhf I: NOTICE: Log filtering will replace 'build/gbrowse-BrZrXm/gbrowse-2.48~dfsg' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/gbrowse-BrZrXm' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/testing-armhf-sbuild-b2fd8fe9-45a1-4cc9-97cb-b6c867c07793' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Hit http://repo.raspbian.lan testing InRelease Hit http://repo.raspbian.lan testing/main Sources Hit http://repo.raspbian.lan testing/main armhf Packages Ign http://repo.raspbian.lan testing/main TranslationIndex Ign http://repo.raspbian.lan testing/main Translation-en Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'gbrowse' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/debian-med/trunk/packages/gmod/gbrowse/trunk/ Need to get 10.3 MB of source archives. Get:1 http://repo.raspbian.lan/raspbian/ testing/main gbrowse 2.48~dfsg-1 (dsc) [2597 B] Get:2 http://repo.raspbian.lan/raspbian/ testing/main gbrowse 2.48~dfsg-1 (tar) [10.3 MB] Get:3 http://repo.raspbian.lan/raspbian/ testing/main gbrowse 2.48~dfsg-1 (diff) [19.2 kB] Fetched 10.3 MB in 1s (10.1 MB/s) Download complete and in download only mode Check arch ────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-FXqYw4/apt_archive/sbuild-build-depends-core-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... 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 0 not upgraded. Need to get 0 B/704 B of archives. After this operation, 0 B of additional disk space will be used. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 10678 files and directories currently installed.) Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), bioperl (>= 1.6.901), debhelper (>= 8), libbio-graphics-perl (>= 2.26), libcapture-tiny-perl, libcgi-session-perl (>= 4.02), libgd-gd2-perl (>= 2.07) | libgd-gd2-noxpm-perl (>= 2.07), libio-string-perl, libjson-perl, libstatistics-descriptive-perl, libwww-perl, libhttp-daemon-perl, perl, perl (>= 5.10.0) | libextutils-cbuilder-perl, sqlite3, libdbd-sqlite3-perl, libterm-readkey-perl, libjs-prototype (>= 1.7), libjs-scriptaculous (>= 1.9) Filtered Build-Depends: libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), bioperl (>= 1.6.901), debhelper (>= 8), libbio-graphics-perl (>= 2.26), libcapture-tiny-perl, libcgi-session-perl (>= 4.02), libgd-gd2-perl (>= 2.07), libio-string-perl, libjson-perl, libstatistics-descriptive-perl, libwww-perl, libhttp-daemon-perl, perl, perl (>= 5.10.0), sqlite3, libdbd-sqlite3-perl, libterm-readkey-perl, libjs-prototype (>= 1.7), libjs-scriptaculous (>= 1.9) dpkg-deb: building package `sbuild-build-depends-gbrowse-dummy' in `/«BUILDDIR»/resolver-JdxgsJ/apt_archive/sbuild-build-depends-gbrowse-dummy.deb'. OK 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: bioperl bsdmainutils ca-certificates debhelper file fontconfig-config gettext gettext-base groff-base html2text intltool-debian libbio-graphics-perl libbio-perl-perl libcapture-tiny-perl libcgi-session-perl libcroco3 libdata-stag-perl libdbd-sqlite3-perl libdbi-perl libencode-locale-perl libexpat1 libffi5 libfile-listing-perl libfontconfig1 libfreetype6 libgd-gd2-perl libgd2-xpm libglib2.0-0 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-socket-ssl-perl libio-string-perl libjpeg8 libjs-prototype libjs-scriptaculous libjson-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic1 libnet-daemon-perl libnet-http-perl libnet-ssleay-perl libpcre3 libpipeline1 libplrpc-perl libpng12-0 libsqlite3-0 libssl1.0.0 libstatistics-descriptive-perl libterm-readkey-perl libunistring0 liburi-perl libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxml2 libxpm4 man-db netbase openssl po-debconf sqlite3 ttf-dejavu-core Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff libmath-random-perl libxml-sax-expatxs-perl libgd-tools 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 libxml-simple-perl libyaml-perl libace-perl liblist-moreutils-perl libxml-twig-perl libset-scalar-perl curl wget lynx-cur autopoint 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 libgraph-perl libgraphviz-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-perl libxml-sax-writer-perl libxml-writer-perl libxml-libxml-perl perl-tk libxml-libxslt-perl libmldbm-perl libglib2.0-data shared-mime-info libio-socket-inet6-perl javascript-common libjson-xs-perl libhtml-form-perl libhtml-format-perl libmailtools-perl xml-core ifupdown libmail-sendmail-perl The following NEW packages will be installed: bioperl bsdmainutils ca-certificates debhelper file fontconfig-config gettext gettext-base groff-base html2text intltool-debian libbio-graphics-perl libbio-perl-perl libcapture-tiny-perl libcgi-session-perl libcroco3 libdata-stag-perl libdbd-sqlite3-perl libdbi-perl libencode-locale-perl libexpat1 libffi5 libfile-listing-perl libfontconfig1 libfreetype6 libgd-gd2-perl libgd2-xpm libglib2.0-0 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-socket-ssl-perl libio-string-perl libjpeg8 libjs-prototype libjs-scriptaculous libjson-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic1 libnet-daemon-perl libnet-http-perl libnet-ssleay-perl libpcre3 libpipeline1 libplrpc-perl libpng12-0 libsqlite3-0 libssl1.0.0 libstatistics-descriptive-perl libterm-readkey-perl libunistring0 liburi-perl libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxml2 libxpm4 man-db netbase openssl po-debconf sbuild-build-depends-gbrowse-dummy sqlite3 ttf-dejavu-core 0 upgraded, 74 newly installed, 0 to remove and 0 not upgraded. Need to get 9905 kB/26.9 MB of archives. After this operation, 66.5 MB of additional disk space will be used. Get:1 http://repo.raspbian.lan/raspbian/ testing/main libio-string-perl all 1.08-2 [12.0 kB] Get:2 http://repo.raspbian.lan/raspbian/ testing/main libdata-stag-perl all 0.11-2 [509 kB] Get:3 http://repo.raspbian.lan/raspbian/ testing/main libbio-perl-perl all 1.6.901-3 [6143 kB] Get:4 http://repo.raspbian.lan/raspbian/ testing/main bioperl all 1.6.901-3 [467 kB] Get:5 http://repo.raspbian.lan/raspbian/ testing/main libgd2-xpm armhf 2.0.36~rc1~dfsg-6 [222 kB] Get:6 http://repo.raspbian.lan/raspbian/ testing/main libgd-gd2-perl armhf 1:2.46-3 [200 kB] Get:7 http://repo.raspbian.lan/raspbian/ testing/main libbio-graphics-perl all 2.26-1 [669 kB] Get:8 http://repo.raspbian.lan/raspbian/ testing/main libcapture-tiny-perl all 0.17-1 [21.4 kB] Get:9 http://repo.raspbian.lan/raspbian/ testing/main libcgi-session-perl all 4.46-1 [123 kB] Get:10 http://repo.raspbian.lan/raspbian/ testing/main libnet-daemon-perl all 0.48-1 [46.2 kB] Get:11 http://repo.raspbian.lan/raspbian/ testing/main libplrpc-perl all 0.2020-2 [36.0 kB] Get:12 http://repo.raspbian.lan/raspbian/ testing/main libdbi-perl armhf 1.618-1 [894 kB] Get:13 http://repo.raspbian.lan/raspbian/ testing/main libdbd-sqlite3-perl armhf 1.35-1 [104 kB] Get:14 http://repo.raspbian.lan/raspbian/ testing/main libhttp-daemon-perl all 6.01-1 [17.3 kB] Get:15 http://repo.raspbian.lan/raspbian/ testing/main libjs-prototype all 1.7.0-2 [40.9 kB] Get:16 http://repo.raspbian.lan/raspbian/ testing/main libjs-scriptaculous all 1.9.0-2 [129 kB] Get:17 http://repo.raspbian.lan/raspbian/ testing/main libjson-perl all 2.53-1 [99.9 kB] Get:18 http://repo.raspbian.lan/raspbian/ testing/main libstatistics-descriptive-perl all 3.0400-1 [27.3 kB] Get:19 http://repo.raspbian.lan/raspbian/ testing/main libterm-readkey-perl armhf 2.30-4 [30.0 kB] Get:20 http://repo.raspbian.lan/raspbian/ testing/main sqlite3 armhf 3.7.11-2 [114 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 9905 kB in 1s (9628 kB/s) Selecting previously unselected package libpcre3:armhf. (Reading database ... 10678 files and directories currently installed.) Unpacking libpcre3:armhf (from .../libpcre3_1%3a8.30-4_armhf.deb) ... Selecting previously unselected package libpipeline1:armhf. Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.1-1_armhf.deb) ... Selecting previously unselected package libssl1.0.0:armhf. Unpacking libssl1.0.0:armhf (from .../libssl1.0.0_1.0.1b-1_armhf.deb) ... Selecting previously unselected package libmagic1:armhf. Unpacking libmagic1:armhf (from .../libmagic1_5.11-1_armhf.deb) ... Selecting previously unselected package libsqlite3-0:armhf. Unpacking libsqlite3-0:armhf (from .../libsqlite3-0_3.7.11-2_armhf.deb) ... Selecting previously unselected package libxml2:armhf. Unpacking libxml2:armhf (from .../libxml2_2.7.8.dfsg-9_armhf.deb) ... Selecting previously unselected package libffi5:armhf. Unpacking libffi5:armhf (from .../libffi5_3.0.10-3+b3_armhf.deb) ... Selecting previously unselected package libglib2.0-0:armhf. Unpacking libglib2.0-0:armhf (from .../libglib2.0-0_2.32.0-4_armhf.deb) ... Selecting previously unselected package libcroco3:armhf. Unpacking libcroco3:armhf (from .../libcroco3_0.6.5-1_armhf.deb) ... Selecting previously unselected package libexpat1:armhf. Unpacking libexpat1:armhf (from .../libexpat1_2.1.0-1_armhf.deb) ... Selecting previously unselected package libfreetype6:armhf. Unpacking libfreetype6:armhf (from .../libfreetype6_2.4.9-1_armhf.deb) ... Selecting previously unselected package ttf-dejavu-core. Unpacking ttf-dejavu-core (from .../ttf-dejavu-core_2.33-2_all.deb) ... Selecting previously unselected package fontconfig-config. Unpacking fontconfig-config (from .../fontconfig-config_2.8.0-3.1_all.deb) ... Selecting previously unselected package libfontconfig1:armhf. Unpacking libfontconfig1:armhf (from .../libfontconfig1_2.8.0-3.1_armhf.deb) ... Selecting previously unselected package libjpeg8:armhf. Unpacking libjpeg8:armhf (from .../libjpeg8_8d-1_armhf.deb) ... Selecting previously unselected package libpng12-0:armhf. Unpacking libpng12-0:armhf (from .../libpng12-0_1.2.49-1_armhf.deb) ... Selecting previously unselected package libunistring0:armhf. Unpacking libunistring0:armhf (from .../libunistring0_0.9.3-5_armhf.deb) ... Selecting previously unselected package libxau6:armhf. Unpacking libxau6:armhf (from .../libxau6_1%3a1.0.7-1_armhf.deb) ... Selecting previously unselected package libxdmcp6:armhf. Unpacking libxdmcp6:armhf (from .../libxdmcp6_1%3a1.1.1-1_armhf.deb) ... Selecting previously unselected package libxcb1:armhf. Unpacking libxcb1:armhf (from .../libxcb1_1.8.1-1_armhf.deb) ... Selecting previously unselected package libx11-data. Unpacking libx11-data (from .../libx11-data_2%3a1.4.4-4_all.deb) ... Selecting previously unselected package libx11-6:armhf. Unpacking libx11-6:armhf (from .../libx11-6_2%3a1.4.4-4_armhf.deb) ... Selecting previously unselected package libxpm4:armhf. Unpacking libxpm4:armhf (from .../libxpm4_1%3a3.5.10-1_armhf.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_9.0.1_armhf.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-7_armhf.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.1-2_armhf.deb) ... Selecting previously unselected package netbase. Unpacking netbase (from .../archives/netbase_4.47_all.deb) ... Selecting previously unselected package file. Unpacking file (from .../archives/file_5.11-1_armhf.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-5+rpi1_armhf.deb) ... Selecting previously unselected package libio-string-perl. Unpacking libio-string-perl (from .../libio-string-perl_1.08-2_all.deb) ... Selecting previously unselected package libdata-stag-perl. Unpacking libdata-stag-perl (from .../libdata-stag-perl_0.11-2_all.deb) ... Selecting previously unselected package libbio-perl-perl. Unpacking libbio-perl-perl (from .../libbio-perl-perl_1.6.901-3_all.deb) ... Selecting previously unselected package bioperl. Unpacking bioperl (from .../bioperl_1.6.901-3_all.deb) ... Selecting previously unselected package openssl. Unpacking openssl (from .../openssl_1.0.1b-1_armhf.deb) ... Selecting previously unselected package ca-certificates. Unpacking ca-certificates (from .../ca-certificates_20120212_all.deb) ... Selecting previously unselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_armhf.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-5+rpi1_armhf.deb) ... Selecting previously unselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously unselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ... Selecting previously unselected package debhelper. Unpacking debhelper (from .../debhelper_9.20120419_all.deb) ... Selecting previously unselected package libgd2-xpm. Unpacking libgd2-xpm (from .../libgd2-xpm_2.0.36~rc1~dfsg-6_armhf.deb) ... Selecting previously unselected package libgd-gd2-perl. Unpacking libgd-gd2-perl (from .../libgd-gd2-perl_1%3a2.46-3_armhf.deb) ... Selecting previously unselected package libbio-graphics-perl. Unpacking libbio-graphics-perl (from .../libbio-graphics-perl_2.26-1_all.deb) ... Selecting previously unselected package libcapture-tiny-perl. Unpacking libcapture-tiny-perl (from .../libcapture-tiny-perl_0.17-1_all.deb) ... Selecting previously unselected package libcgi-session-perl. Unpacking libcgi-session-perl (from .../libcgi-session-perl_4.46-1_all.deb) ... Selecting previously unselected package libnet-daemon-perl. Unpacking libnet-daemon-perl (from .../libnet-daemon-perl_0.48-1_all.deb) ... Selecting previously unselected package libplrpc-perl. Unpacking libplrpc-perl (from .../libplrpc-perl_0.2020-2_all.deb) ... Selecting previously unselected package libdbi-perl. Unpacking libdbi-perl (from .../libdbi-perl_1.618-1_armhf.deb) ... Selecting previously unselected package libdbd-sqlite3-perl. Unpacking libdbd-sqlite3-perl (from .../libdbd-sqlite3-perl_1.35-1_armhf.deb) ... Selecting previously unselected package libencode-locale-perl. Unpacking libencode-locale-perl (from .../libencode-locale-perl_1.03-1_all.deb) ... Selecting previously unselected package libhttp-date-perl. Unpacking libhttp-date-perl (from .../libhttp-date-perl_6.02-1_all.deb) ... Selecting previously unselected package libfile-listing-perl. Unpacking libfile-listing-perl (from .../libfile-listing-perl_6.04-1_all.deb) ... Selecting previously unselected package liburi-perl. Unpacking liburi-perl (from .../liburi-perl_1.60-1_all.deb) ... Selecting previously unselected package libhtml-tagset-perl. Unpacking libhtml-tagset-perl (from .../libhtml-tagset-perl_3.20-2_all.deb) ... Selecting previously unselected package libhtml-parser-perl. Unpacking libhtml-parser-perl (from .../libhtml-parser-perl_3.69-2_armhf.deb) ... Selecting previously unselected package libhtml-tree-perl. Unpacking libhtml-tree-perl (from .../libhtml-tree-perl_4.2-1_all.deb) ... Selecting previously unselected package liblwp-mediatypes-perl. Unpacking liblwp-mediatypes-perl (from .../liblwp-mediatypes-perl_6.02-1_all.deb) ... Selecting previously unselected package libhttp-message-perl. Unpacking libhttp-message-perl (from .../libhttp-message-perl_6.03-1_all.deb) ... Selecting previously unselected package libhttp-cookies-perl. Unpacking libhttp-cookies-perl (from .../libhttp-cookies-perl_6.00-2_all.deb) ... Selecting previously unselected package libhttp-daemon-perl. Unpacking libhttp-daemon-perl (from .../libhttp-daemon-perl_6.01-1_all.deb) ... Selecting previously unselected package libhttp-negotiate-perl. Unpacking libhttp-negotiate-perl (from .../libhttp-negotiate-perl_6.00-2_all.deb) ... Selecting previously unselected package libnet-ssleay-perl. Unpacking libnet-ssleay-perl (from .../libnet-ssleay-perl_1.47-1_armhf.deb) ... Selecting previously unselected package libio-socket-ssl-perl. Unpacking libio-socket-ssl-perl (from .../libio-socket-ssl-perl_1.66-1_all.deb) ... Selecting previously unselected package libjs-prototype. Unpacking libjs-prototype (from .../libjs-prototype_1.7.0-2_all.deb) ... Selecting previously unselected package libjs-scriptaculous. Unpacking libjs-scriptaculous (from .../libjs-scriptaculous_1.9.0-2_all.deb) ... Selecting previously unselected package libjson-perl. Unpacking libjson-perl (from .../libjson-perl_2.53-1_all.deb) ... Selecting previously unselected package libnet-http-perl. Unpacking libnet-http-perl (from .../libnet-http-perl_6.03-1_all.deb) ... Selecting previously unselected package libwww-robotrules-perl. Unpacking libwww-robotrules-perl (from .../libwww-robotrules-perl_6.01-1_all.deb) ... Selecting previously unselected package libwww-perl. Unpacking libwww-perl (from .../libwww-perl_6.04-1_all.deb) ... Selecting previously unselected package liblwp-protocol-https-perl. Unpacking liblwp-protocol-https-perl (from .../liblwp-protocol-https-perl_6.03-1_all.deb) ... Selecting previously unselected package libstatistics-descriptive-perl. Unpacking libstatistics-descriptive-perl (from .../libstatistics-descriptive-perl_3.0400-1_all.deb) ... Selecting previously unselected package libterm-readkey-perl. Unpacking libterm-readkey-perl (from .../libterm-readkey-perl_2.30-4_armhf.deb) ... Selecting previously unselected package sqlite3. Unpacking sqlite3 (from .../sqlite3_3.7.11-2_armhf.deb) ... Selecting previously unselected package sbuild-build-depends-gbrowse-dummy. Unpacking sbuild-build-depends-gbrowse-dummy (from .../sbuild-build-depends-gbrowse-dummy.deb) ... Setting up libpcre3:armhf (1:8.30-4) ... Setting up libpipeline1:armhf (1.2.1-1) ... Setting up libssl1.0.0:armhf (1.0.1b-1) ... Setting up libmagic1:armhf (5.11-1) ... Setting up libsqlite3-0:armhf (3.7.11-2) ... Setting up libxml2:armhf (2.7.8.dfsg-9) ... Setting up libffi5:armhf (3.0.10-3+b3) ... Setting up libglib2.0-0:armhf (2.32.0-4) ... No schema files found: doing nothing. Setting up libcroco3:armhf (0.6.5-1) ... Setting up libexpat1:armhf (2.1.0-1) ... Setting up libfreetype6:armhf (2.4.9-1) ... Setting up ttf-dejavu-core (2.33-2) ... Setting up fontconfig-config (2.8.0-3.1) ... Setting up libfontconfig1:armhf (2.8.0-3.1) ... Setting up libjpeg8:armhf (8d-1) ... Setting up libpng12-0:armhf (1.2.49-1) ... Setting up libunistring0:armhf (0.9.3-5) ... Setting up libxau6:armhf (1:1.0.7-1) ... Setting up libxdmcp6:armhf (1:1.1.1-1) ... Setting up libxcb1:armhf (1.8.1-1) ... Setting up libx11-data (2:1.4.4-4) ... Setting up libx11-6:armhf (2:1.4.4-4) ... Setting up libxpm4:armhf (1:3.5.10-1) ... Setting up bsdmainutils (9.0.1) ... 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 groff-base (1.21-7) ... Setting up man-db (2.6.1-2) ... Building database of manual pages ... Setting up netbase (4.47) ... Setting up file (5.11-1) ... Setting up gettext-base (0.18.1.1-5+rpi1) ... Setting up libio-string-perl (1.08-2) ... Setting up libdata-stag-perl (0.11-2) ... Setting up libbio-perl-perl (1.6.901-3) ... Setting up bioperl (1.6.901-3) ... Setting up openssl (1.0.1b-1) ... Setting up ca-certificates (20120212) ... Updating certificates in /etc/ssl/certs... 151 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d....done. Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5+rpi1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20120419) ... Setting up libgd2-xpm (2.0.36~rc1~dfsg-6) ... Setting up libgd-gd2-perl (1:2.46-3) ... Setting up libbio-graphics-perl (2.26-1) ... Setting up libcapture-tiny-perl (0.17-1) ... Setting up libcgi-session-perl (4.46-1) ... Setting up libnet-daemon-perl (0.48-1) ... Setting up libplrpc-perl (0.2020-2) ... Setting up libdbi-perl (1.618-1) ... Setting up libdbd-sqlite3-perl (1.35-1) ... Setting up libencode-locale-perl (1.03-1) ... Setting up libhttp-date-perl (6.02-1) ... Setting up libfile-listing-perl (6.04-1) ... Setting up liburi-perl (1.60-1) ... Setting up libhtml-tagset-perl (3.20-2) ... Setting up libhtml-parser-perl (3.69-2) ... Setting up libhtml-tree-perl (4.2-1) ... Setting up liblwp-mediatypes-perl (6.02-1) ... Setting up libhttp-message-perl (6.03-1) ... Setting up libhttp-cookies-perl (6.00-2) ... Setting up libhttp-daemon-perl (6.01-1) ... Setting up libhttp-negotiate-perl (6.00-2) ... Setting up libnet-ssleay-perl (1.47-1) ... Setting up libio-socket-ssl-perl (1.66-1) ... Setting up libjs-prototype (1.7.0-2) ... Setting up libjs-scriptaculous (1.9.0-2) ... Setting up libjson-perl (2.53-1) ... Setting up libnet-http-perl (6.03-1) ... Setting up libwww-robotrules-perl (6.01-1) ... Setting up libstatistics-descriptive-perl (3.0400-1) ... Setting up libterm-readkey-perl (2.30-4) ... Setting up sqlite3 (3.7.11-2) ... Setting up liblwp-protocol-https-perl (6.03-1) ... Setting up libwww-perl (6.04-1) ... Setting up sbuild-build-depends-gbrowse-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.2.0-2-mx5 armhf (armv7l) Toolchain package versions: binutils_2.22-6 dpkg-dev_1.16.2 g++-4.6_4.6.3-1.1+rpi2 gcc-4.6_4.6.3-1.1+rpi2 libc6-dev_2.13-30 libstdc++6_4.7.0-1.1+rpi libstdc++6-4.6-dev_4.6.3-1.1+rpi2 linux-libc-dev_3.2.12-1 Package versions: apt_0.8.15.10 base-files_6.7 base-passwd_3.5.24 bash_4.2-2 binutils_2.22-6 bioperl_1.6.901-3 bsdmainutils_9.0.1 bsdutils_1:2.20.1-4 build-essential_11.5+b1 bzip2_1.0.6-1 ca-certificates_20120212 coreutils_8.13-3.1 cpp_4:4.6.2-4 cpp-4.6_4.6.3-1.1+rpi2 dash_0.5.7-3 debconf_1.5.42 debfoster_2.7-1.1 debhelper_9.20120419 debian-archive-keyring_2010.08.28 debianutils_4.3 diffutils_1:3.2-2 dpkg_1.16.2 dpkg-dev_1.16.2 e2fslibs_1.42.2-2 e2fsprogs_1.42.2-2 fakeroot_1.18.3-1 file_5.11-1 findutils_4.4.2-4 fontconfig-config_2.8.0-3.1 g++_4:4.6.2-4 g++-4.6_4.6.3-1.1+rpi2 gcc_4:4.6.2-4 gcc-4.4-base_4.4.7-1 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.3-1.1+rpi2 gcc-4.6-base_4.6.3-1.1+rpi2 gcc-4.7-base_4.7.0-1.1+rpi gettext_0.18.1.1-5+rpi1 gettext-base_0.18.1.1-5+rpi1 gnupg_1.4.12-4 gpgv_1.4.12-4 grep_2.11-3 groff-base_1.21-7 gzip_1.4-5 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-22.1 insserv_1.14.0-3 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libbio-graphics-perl_2.26-1 libbio-perl-perl_1.6.901-3 libblkid1_2.20.1-4 libbz2-1.0_1.0.6-1 libc-bin_2.13-30 libc-dev-bin_2.13-30 libc6_2.13-30 libc6-dev_2.13-30 libcapture-tiny-perl_0.17-1 libcgi-session-perl_4.46-1 libclass-isa-perl_0.36-3 libcomerr2_1.42.2-2 libcroco3_0.6.5-1 libdata-stag-perl_0.11-2 libdb5.1_5.1.29-1 libdbd-sqlite3-perl_1.35-1 libdbi-perl_1.618-1 libdpkg-perl_1.16.2 libencode-locale-perl_1.03-1 libexpat1_2.1.0-1 libffi5_3.0.10-3+b3 libfile-fcntllock-perl_0.14-1 libfile-listing-perl_6.04-1 libfontconfig1_2.8.0-3.1 libfreetype6_2.4.9-1 libgc1c2_1:7.1-8 libgcc1_1:4.7.0-1.1+rpi libgd-gd2-perl_1:2.46-3 libgd2-xpm_2.0.36~rc1~dfsg-6 libgdbm3_1.8.3-10 libglib2.0-0_2.32.0-4 libgmp10_2:5.0.4+dfsg-1 libgomp1_4.7.0-1.1+rpi libhtml-parser-perl_3.69-2 libhtml-tagset-perl_3.20-2 libhtml-tree-perl_4.2-1 libhttp-cookies-perl_6.00-2 libhttp-daemon-perl_6.01-1 libhttp-date-perl_6.02-1 libhttp-message-perl_6.03-1 libhttp-negotiate-perl_6.00-2 libio-socket-ssl-perl_1.66-1 libio-string-perl_1.08-2 libjpeg8_8d-1 libjs-prototype_1.7.0-2 libjs-scriptaculous_1.9.0-2 libjson-perl_2.53-1 liblocale-gettext-perl_1.05-7 liblwp-mediatypes-perl_6.02-1 liblwp-protocol-https-perl_6.03-1 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.11-1 libmount1_2.20.1-4 libmpc2_0.9-4 libmpfr4_3.1.0-4 libncurses5_5.9-6 libncursesw5_5.9-6 libnet-daemon-perl_0.48-1 libnet-http-perl_6.03-1 libnet-ssleay-perl_1.47-1 libpam-modules_1.1.3-7 libpam-modules-bin_1.1.3-7 libpam-runtime_1.1.3-7 libpam0g_1.1.3-7 libpcre3_1:8.30-4 libpipeline1_1.2.1-1 libplrpc-perl_0.2020-2 libpng12-0_1.2.49-1 libreadline6_6.2-8 libselinux1_2.1.9-2 libsemanage-common_2.1.6-2 libsemanage1_2.1.6-2 libsepol1_2.1.4-1 libslang2_2.2.4-7 libsqlite3-0_3.7.11-2 libss2_1.42.2-2 libssl1.0.0_1.0.1b-1 libstatistics-descriptive-perl_3.0400-1 libstdc++6_4.7.0-1.1+rpi libstdc++6-4.6-dev_4.6.3-1.1+rpi2 libswitch-perl_2.16-2 libterm-readkey-perl_2.30-4 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-6 libunistring0_0.9.3-5 liburi-perl_1.60-1 libusb-0.1-4_2:0.1.12-20 libustr-1.0-1_1.0.4-2 libuuid1_2.20.1-4 libwww-perl_6.04-1 libwww-robotrules-perl_6.01-1 libx11-6_2:1.4.4-4 libx11-data_2:1.4.4-4 libxau6_1:1.0.7-1 libxcb1_1.8.1-1 libxdmcp6_1:1.1.1-1 libxml2_2.7.8.dfsg-9 libxpm4_1:3.5.10-1 linux-libc-dev_3.2.12-1 login_1:4.1.5-1 lsb-base_4.1+Debian0 make_3.81-8.1 man-db_2.6.1-2 mawk_1.3.3-17 mount_2.20.1-4 multiarch-support_2.13-30 ncurses-base_5.9-6 ncurses-bin_5.9-6 netbase_4.47 openssl_1.0.1b-1 passwd_1:4.1.5-1 patch_2.6.1-3 perl_5.14.2-9 perl-base_5.14.2-9 perl-modules_5.14.2-9 po-debconf_1.0.16+nmu2 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gbrowse-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sqlite3_3.7.11-2 sysv-rc_2.88dsf-22.1 sysvinit_2.88dsf-22.1 sysvinit-utils_2.88dsf-22.1 tar_1.26-4 ttf-dejavu-core_2.33-2 tzdata_2012b-1 ucf_3.0025+nmu3 util-linux_2.20.1-4 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-2 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Wed Mar 7 09:19:44 2012 UTC using RSA key ID 326D8438 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./gbrowse_2.48~dfsg-1.dsc dpkg-source: info: extracting gbrowse in gbrowse-2.48~dfsg dpkg-source: info: unpacking gbrowse_2.48~dfsg.orig.tar.bz2 dpkg-source: info: unpacking gbrowse_2.48~dfsg-1.debian.tar.gz 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 skipDeferedRenderingTests dpkg-source: info: applying skipRenderFarmTest_UpstreamBug12 Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── HOME=/sbuild-nonexistent LOGNAME=buildd PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin:/usr/games SCHROOT_CHROOT_NAME=testing-armhf-sbuild SCHROOT_COMMAND=env SCHROOT_GID=108 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=testing-armhf-sbuild-b2fd8fe9-45a1-4cc9-97cb-b6c867c07793 SCHROOT_UID=106 SCHROOT_USER=buildd SHELL=/bin/sh TERM=xterm USER=buildd dpkg-buildpackage ───────────────── dpkg-buildpackage: source package gbrowse dpkg-buildpackage: source version 2.48~dfsg-1 dpkg-source --before-build gbrowse-2.48~dfsg dpkg-buildpackage: host architecture armhf fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean dh_clean debian/rules build-arch dh build-arch dh_testdir -a debian/rules override_dh_auto_configure make[1]: Entering directory `/«PKGBUILDDIR»' 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 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 * 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 '2.48' make[1]: Leaving directory `/«PKGBUILDDIR»' dh_auto_build -a NOTE: Run ./Build reconfig to change existing configuration. Building GBrowse cc -I/«PKGBUILDDIR»/libalign -I/usr/lib/perl/5.14/CORE -DXS_VERSION="2.48" -DVERSION="2.48" -fPIC -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -O0 -g -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 -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/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/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 Use of uninitialized value in pattern match (m//) at /«PKGBUILDDIR»/install_util/GBrowseInstall.pm line 691. dh_auto_test -a NOTE: Run ./Build reconfig to change existing configuration. Use of uninitialized value in pattern match (m//) at /«PKGBUILDDIR»/install_util/GBrowseInstall.pm line 691. t/00.compile.t ............ ok t/01.yeast.t .............. ok t/02.rearchitecture.t ..... 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) t/05.deferredrendering.t .. skipped: (no reason given) t/06.featuresearch.t ...... skipped: (no reason given) t/07.karyotype.t .......... ok t/08.calign.t ............. ok All tests successful. Files=9, Tests=200, 135 wallclock secs ( 0.69 usr 0.09 sys + 123.41 cusr 4.39 csys = 128.58 CPU) Result: PASS fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_installdirs -a debian/rules override_dh_auto_install make[1]: Entering directory `/«PKGBUILDDIR»' ./Build --install_base=debian/gbrowse debianinstall NOTE: Run ./Build reconfig to change existing configuration. Use of uninitialized value in pattern match (m//) at /«PKGBUILDDIR»/install_util/GBrowseInstall.pm line 691. 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/load_genbank.pl.1p Installing debian/gbrowse/man/man1/gbrowse_clean.pl.1p Installing debian/gbrowse/man/man1/ucsc_genes2gff.pl.1p Installing debian/gbrowse/man/man1/make_das_conf.pl.1p Installing debian/gbrowse/man/man1/gtf2gff3.pl.1p Installing debian/gbrowse/man/man1/wiggle2gff3.pl.1p Installing debian/gbrowse/man/man1/bed2gff3.pl.1p Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_gmap Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbgff Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/das Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_key_img Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_details Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_img Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_syn Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_login Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse Installing debian/gbrowse/etc/gbrowse/submitter_plugin.conf Installing debian/gbrowse/etc/gbrowse/slave_preload.conf Installing debian/gbrowse/etc/gbrowse/log4perl.conf Installing debian/gbrowse/etc/gbrowse/volvox.conf Installing debian/gbrowse/etc/gbrowse/enzymes.txt Installing debian/gbrowse/etc/gbrowse/yeast_chr1+2.conf Installing debian/gbrowse/etc/gbrowse/yeast_simple.conf Installing debian/gbrowse/etc/gbrowse/detail_select_menu.conf Installing debian/gbrowse/etc/gbrowse/GBrowse.conf Installing debian/gbrowse/etc/gbrowse/yeast_renderfarm.conf Installing debian/gbrowse/etc/gbrowse/pop_demo.conf Installing debian/gbrowse/etc/gbrowse/themes/solid_gray_colors Installing debian/gbrowse/etc/gbrowse/themes/warm_colors Installing debian/gbrowse/etc/gbrowse/themes/transparent_colors Installing debian/gbrowse/etc/gbrowse/MobyServices/GbrowseServices.pm Installing debian/gbrowse/etc/gbrowse/MobyServices/moby.conf Installing debian/gbrowse/etc/gbrowse/MobyServices/b64_encoded_jpeg_renderer.pm Installing debian/gbrowse/etc/gbrowse/MobyServices/text_plain_renderer.pm 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/GbrowseServices.PMS Installing debian/gbrowse/etc/gbrowse/MobyServices/b64_encoded_gif_renderer.pm Installing debian/gbrowse/etc/gbrowse/MobyServices/text_xml_renderer.pm Installing debian/gbrowse/etc/gbrowse/plugins/SimpleTrackFinder.pm Installing debian/gbrowse/etc/gbrowse/plugins/Aligner.pm Installing debian/gbrowse/etc/gbrowse/plugins/TrackDumper.pm Installing 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debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::GFFhelper.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataSource.3pm Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataBase.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Plugin.3pm Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::match_gap.3pm Installing debian/gbrowse/man/man3/GBrowse::ConfigData.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render.3pm Installing debian/gbrowse/man/man3/Bio::DB::Tagger.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RegionSearch.3pm Installing debian/gbrowse/man/man3/CGI::Toggle.3pm Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::reftranscript.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::Graphics::Browser2::Plugin::AuthPlugin.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Realign.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RemoteSet.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Region.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::PadAlignment.3pm Installing debian/gbrowse/man/man3/Legacy::Graphics::Browser.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RenderPanels.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::AuthorizedFeatureFile.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::OptionPick.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Util.3pm Installing debian/gbrowse/bin/gtf2gff3.pl Installing debian/gbrowse/bin/make_das_conf.pl Installing debian/gbrowse/bin/load_genbank.pl Installing debian/gbrowse/bin/gbrowse_syn_load_alignments_msa.pl Installing debian/gbrowse/bin/gbrowse_metadb_config.pl Installing debian/gbrowse/bin/bed2gff3.pl Installing debian/gbrowse/bin/gbrowse_syn_load_alignment_database.pl Installing debian/gbrowse/bin/ucsc_genes2gff.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/scan_gbrowse.pl Installing debian/gbrowse/bin/wiggle2gff3.pl Installing debian/gbrowse/bin/gbrowse_slave Installing debian/gbrowse/bin/gbrowse_change_passwd.pl ./Build apache_conf > debian/gbrowse/etc/gbrowse/apache2.conf NOTE: Run ./Build reconfig to change existing configuration. INSTRUCTIONS: Paste the following into your Apache configuration file. You may wish to save it separately and include it using the Apache "Include /path/to/file" directive. Then restart Apache and point your browser to http://your.site/htdocs/ to start browsing the sample genomes. >>>>>> cut here <<<<< 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 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 * 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 '2.48' ./Build --install_base=debian/gbrowse install_slave 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/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/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/etc/default/gbrowse-slave Performing variable substitutions in blib/etc/init.d/gbrowse-slave Use of uninitialized value $wwwuser in substitution (s///) at /«PKGBUILDDIR»/install_util/GBrowseInstall.pm line 796, line 20. Building GBrowse Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing debian/gbrowse/etc/init.d/gbrowse-slave Installing debian/gbrowse/etc/default/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/perl5/auto/Bio/Graphics/Browser2/CAlign/ mv debian/gbrowse/usr/share/perl5/Bio/Graphics/Browser2/CAlign.pm debian/gbrowse-calign/usr/lib/perl5/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 /«PKGBUILDDIR»/debian/gbrowse/etc -name '*.new' | xargs rename 's/.new//' rm -rf /«PKGBUILDDIR»/debian/gbrowse/usr/share/perl5/auto # Update conf files sed -i 's/gbrowse2/gbrowse/g' /«PKGBUILDDIR»/debian/gbrowse/etc/gbrowse/yeast*.conf sed -i 's/gbrowse2/gbrowse/g' /«PKGBUILDDIR»/debian/gbrowse/etc/gbrowse/slave*.conf make[1]: Leaving directory `/«PKGBUILDDIR»' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installexamples -a debian/rules override_dh_installman make[1]: Entering directory `/«PKGBUILDDIR»' #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 `/«PKGBUILDDIR»' dh_installcatalogs -a dh_installcron -a dh_installdebconf -a dh_installemacsen -a dh_installifupdown -a dh_installinfo -a dh_installinit -a dh_installmenu -a dh_installmime -a dh_installmodules -a dh_installlogcheck -a dh_installlogrotate -a dh_installpam -a dh_installppp -a dh_installudev -a dh_installwm -a dh_installxfonts -a dh_installgsettings -a dh_bugfiles -a dh_ucf -a dh_lintian -a dh_gconf -a dh_icons -a dh_perl -a dh_usrlocal -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 dh_md5sums -a debian/rules override_dh_builddeb make[1]: Entering directory `/«PKGBUILDDIR»' dh_builddeb -- -Zbzip2 dpkg-deb: building package `gbrowse-calign' in `../gbrowse-calign_2.48~dfsg-1_armhf.deb'. make[1]: Leaving directory `/«PKGBUILDDIR»' dpkg-genchanges -B -mbuildd >../gbrowse_2.48~dfsg-1_armhf.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build gbrowse-2.48~dfsg dpkg-buildpackage: binary only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120504-2057 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ gbrowse_2.48~dfsg-1_armhf.changes: ────────────────────────────────── Format: 1.8 Date: Sun, 19 Feb 2012 15:59:53 +0100 Source: gbrowse Binary: gbrowse gbrowse-data gbrowse-calign Architecture: armhf Version: 2.48~dfsg-1 Distribution: testing Urgency: low Maintainer: buildd Changed-By: Olivier Sallou Description: gbrowse - GMOD Generic Genome Browser gbrowse-calign - CAlign helper gbrowse-data - Sample data to use GBrowse Changes: gbrowse (2.48~dfsg-1) unstable; urgency=low . [ Olivier Sallou ] * new upstream release * debian/control: add libbiographics-perl dependency * debian/patches/skipRenderFarmTest_UpstreamBug12: fix an upstream test issue on renderfarm testing. . [ Charles Plessy ] * Updated VCS URLs (debian/control). Checksums-Sha1: e1f980eaf702292f6d8835bd7d5a5fbd0ad9b09e 35438 gbrowse-calign_2.48~dfsg-1_armhf.deb Checksums-Sha256: 1bfcb4a7288212a1a640af51385cfbcfd91400c61e7a716b1a7f9528cec6abc5 35438 gbrowse-calign_2.48~dfsg-1_armhf.deb Files: feed450847acfb22949d2ed8166b34bf 35438 science optional gbrowse-calign_2.48~dfsg-1_armhf.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ gbrowse-calign_2.48~dfsg-1_armhf.deb ──────────────────────────────────── new debian package, version 2.0. size 35438 bytes: control archive= 739 bytes. 459 bytes, 13 lines control 588 bytes, 7 lines md5sums Package: gbrowse-calign Source: gbrowse Version: 2.48~dfsg-1 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 122 Depends: perl (>= 5.14.2-9), perlapi-5.14.2, libc6 (>= 2.13-28), 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 2012-05-04 20:57 ./ drwxr-xr-x root/root 0 2012-05-04 20:57 ./usr/ drwxr-xr-x root/root 0 2012-05-04 20:57 ./usr/share/ drwxr-xr-x root/root 0 2012-05-04 20:57 ./usr/share/man/ drwxr-xr-x root/root 0 2012-05-04 20:57 ./usr/share/man/man3/ -rw-r--r-- root/root 2079 2012-05-04 20:57 ./usr/share/man/man3/Bio::Graphics::Browser2::CAlign.3pm.gz drwxr-xr-x root/root 0 2012-05-04 20:57 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-05-04 20:57 ./usr/share/doc/gbrowse-calign/ -rw-r--r-- root/root 780 2012-03-07 01:17 ./usr/share/doc/gbrowse-calign/changelog.Debian.gz -rw-r--r-- root/root 18227 2012-03-02 07:22 ./usr/share/doc/gbrowse-calign/copyright -rw-r--r-- root/root 18328 2012-02-24 13:04 ./usr/share/doc/gbrowse-calign/changelog.gz drwxr-xr-x root/root 0 2012-05-04 20:56 ./usr/lib/ drwxr-xr-x root/root 0 2012-05-04 20:56 ./usr/lib/perl5/ drwxr-xr-x root/root 0 2012-05-04 20:56 ./usr/lib/perl5/Bio/ drwxr-xr-x root/root 0 2012-05-04 20:56 ./usr/lib/perl5/Bio/Graphics/ drwxr-xr-x root/root 0 2012-05-04 20:57 ./usr/lib/perl5/Bio/Graphics/Browser2/ -rw-r--r-- root/root 1129 2012-05-04 20:54 ./usr/lib/perl5/Bio/Graphics/Browser2/CAlign.pm drwxr-xr-x root/root 0 2012-05-04 20:56 ./usr/lib/perl5/auto/ drwxr-xr-x root/root 0 2012-05-04 20:56 ./usr/lib/perl5/auto/Bio/ drwxr-xr-x root/root 0 2012-05-04 20:56 ./usr/lib/perl5/auto/Bio/Graphics/ drwxr-xr-x root/root 0 2012-05-04 20:56 ./usr/lib/perl5/auto/Bio/Graphics/Browser2/ drwxr-xr-x root/root 0 2012-05-04 20:57 ./usr/lib/perl5/auto/Bio/Graphics/Browser2/CAlign/ -rw-r--r-- root/root 0 2012-05-04 20:54 ./usr/lib/perl5/auto/Bio/Graphics/Browser2/CAlign/CAlign.bs -rw-r--r-- root/root 10580 2012-05-04 20:57 ./usr/lib/perl5/auto/Bio/Graphics/Browser2/CAlign/CAlign.so ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bioperl* bsdmainutils* ca-certificates* debhelper* file* fontconfig-config* gettext* gettext-base* groff-base* html2text* intltool-debian* libbio-graphics-perl* libbio-perl-perl* libcapture-tiny-perl* libcgi-session-perl* libcroco3* libdata-stag-perl* libdbd-sqlite3-perl* libdbi-perl* libencode-locale-perl* libexpat1* libffi5* libfile-listing-perl* libfontconfig1* libfreetype6* libgd-gd2-perl* libgd2-xpm* libglib2.0-0* 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-socket-ssl-perl* libio-string-perl* libjpeg8* libjs-prototype* libjs-scriptaculous* libjson-perl* liblwp-mediatypes-perl* liblwp-protocol-https-perl* libmagic1* libnet-daemon-perl* libnet-http-perl* libnet-ssleay-perl* libpcre3* libpipeline1* libplrpc-perl* libpng12-0* libsqlite3-0* libssl1.0.0* libstatistics-descriptive-perl* libterm-readkey-perl* libunistring0* liburi-perl* libwww-perl* libwww-robotrules-perl* libx11-6* libx11-data* libxau6* libxcb1* libxdmcp6* libxml2* libxpm4* man-db* netbase* openssl* po-debconf* sbuild-build-depends-core-dummy* sbuild-build-depends-gbrowse-dummy* sqlite3* ttf-dejavu-core* 0 upgraded, 0 newly installed, 75 to remove and 0 not upgraded. After this operation, 66.5 MB disk space will be freed. (Reading database ... 16140 files and directories currently installed.) Removing sbuild-build-depends-gbrowse-dummy ... Removing libbio-graphics-perl ... Removing bioperl ... Removing debhelper ... Removing man-db ... Purging configuration files for man-db ... Removing bsdmainutils ... Purging configuration files for bsdmainutils ... Removing file ... Removing libgd-gd2-perl ... Removing libgd2-xpm ... Purging configuration files for libgd2-xpm ... Removing libfontconfig1:armhf ... Purging configuration files for libfontconfig1:armhf ... Removing fontconfig-config ... Purging configuration files for fontconfig-config ... Removing po-debconf ... Removing intltool-debian ... Removing gettext ... Removing gettext-base ... Removing groff-base ... Purging configuration files for groff-base ... Removing html2text ... Purging configuration files for html2text ... Removing libbio-perl-perl ... Removing libcapture-tiny-perl ... Removing libcgi-session-perl ... Removing libcroco3:armhf ... Purging configuration files for libcroco3:armhf ... Removing libdata-stag-perl ... Removing libdbd-sqlite3-perl ... Removing libdbi-perl ... Removing libhttp-daemon-perl ... Removing libexpat1:armhf ... Purging configuration files for libexpat1:armhf ... Removing libglib2.0-0:armhf ... Purging configuration files for libglib2.0-0:armhf ... Removing libffi5:armhf ... Purging configuration files for libffi5:armhf ... Removing libfreetype6:armhf ... Purging configuration files for libfreetype6:armhf ... Removing libio-string-perl ... Removing libjpeg8:armhf ... Removing libjs-scriptaculous ... Removing libjs-prototype ... Removing libjson-perl ... Removing libmagic1:armhf ... Purging configuration files for libmagic1:armhf ... Removing libplrpc-perl ... Removing libnet-daemon-perl ... Removing libpcre3:armhf ... Purging configuration files for libpcre3:armhf ... Removing libpipeline1:armhf ... Purging configuration files for libpipeline1:armhf ... Removing libpng12-0:armhf ... Purging configuration files for libpng12-0:armhf ... Removing sqlite3 ... Removing libsqlite3-0:armhf ... Purging configuration files for libsqlite3-0:armhf ... Removing libstatistics-descriptive-perl ... Removing libterm-readkey-perl ... Removing libunistring0:armhf ... Purging configuration files for libunistring0:armhf ... Removing libxpm4:armhf ... Purging configuration files for libxpm4:armhf ... Removing libx11-6:armhf ... Purging configuration files for libx11-6:armhf ... Removing libx11-data ... Removing libxcb1:armhf ... Purging configuration files for libxcb1:armhf ... Removing libxau6:armhf ... Purging configuration files for libxau6:armhf ... Removing libxdmcp6:armhf ... Purging configuration files for libxdmcp6:armhf ... Removing libxml2:armhf ... Purging configuration files for libxml2:armhf ... Removing sbuild-build-depends-core-dummy ... Removing ttf-dejavu-core ... Removing libwww-perl ... Removing liblwp-protocol-https-perl ... Removing ca-certificates ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for ca-certificates ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libhttp-negotiate-perl ... Removing libhttp-cookies-perl ... Removing libhttp-message-perl ... Removing libencode-locale-perl ... Removing libfile-listing-perl ... Removing libhtml-tree-perl ... Removing libhtml-parser-perl ... Removing libhtml-tagset-perl ... Removing libhttp-date-perl ... Removing libio-socket-ssl-perl ... Removing liblwp-mediatypes-perl ... Removing libnet-http-perl ... Removing libnet-ssleay-perl ... Removing openssl ... Purging configuration files for openssl ... Removing libssl1.0.0:armhf ... Purging configuration files for libssl1.0.0:armhf ... Removing libwww-robotrules-perl ... Removing liburi-perl ... Removing netbase ... Purging configuration files for netbase ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: armhf Build-Space: 50400 Build-Time: 251 Distribution: testing Install-Time: 143 Job: gbrowse_2.48~dfsg-1 Package: gbrowse Package-Time: 423 Source-Version: 2.48~dfsg-1 Space: 50400 Status: successful Version: 2.48~dfsg-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120504-2057 Build needed 00:07:03, 50400k disc space