https://launchpad.net/ubuntu/+source/gbrowse/2.56+dfsg-4build1/+build/17934572 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lgw01-amd64-004 4.4.0-166-generic #195-Ubuntu SMP Tue Oct 1 09:35:25 UTC 2019 x86_64 Buildd toolchain package versions: launchpad-buildd_178 python-lpbuildd_178 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.6 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 26 Oct 17:11:49 ntpdate[1902]: adjust time server 10.211.37.1 offset 0.000835 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=focal --arch=i386 PACKAGEBUILD-17934572 --image-type chroot /home/buildd/filecache-default/1990644b2ed835f25dcaa4fd2a2c1aec8ecd68bc Creating target for build PACKAGEBUILD-17934572 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=focal --arch=i386 PACKAGEBUILD-17934572 Starting target for build PACKAGEBUILD-17934572 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=focal --arch=i386 PACKAGEBUILD-17934572 'deb http://ftpmaster.internal/ubuntu focal main universe' 'deb http://ftpmaster.internal/ubuntu focal-security main universe' 'deb http://ftpmaster.internal/ubuntu focal-updates main universe' 'deb http://ftpmaster.internal/ubuntu focal-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-17934572 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=focal --arch=i386 PACKAGEBUILD-17934572 Updating target for build PACKAGEBUILD-17934572 Get:1 http://ftpmaster.internal/ubuntu focal InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu focal-security InRelease [79.7 kB] Get:3 http://ftpmaster.internal/ubuntu focal-updates InRelease [79.7 kB] Get:4 http://ftpmaster.internal/ubuntu focal-proposed InRelease [107 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main i386 Packages [954 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main Translation-en [505 kB] Get:7 http://ftpmaster.internal/ubuntu focal/universe i386 Packages [8725 kB] Get:8 http://ftpmaster.internal/ubuntu focal/universe Translation-en [5224 kB] Get:9 http://ftpmaster.internal/ubuntu focal-proposed/main i386 Packages [105 kB] Get:10 http://ftpmaster.internal/ubuntu focal-proposed/main Translation-en [64.4 kB] Get:11 http://ftpmaster.internal/ubuntu focal-proposed/universe i386 Packages [758 kB] Get:12 http://ftpmaster.internal/ubuntu focal-proposed/universe Translation-en [506 kB] Fetched 17.4 MB in 4s (4903 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libperl5.28 perl-modules-5.28 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libperl5.30 perl-modules-5.30 The following packages will be upgraded: base-files binutils binutils-common binutils-i686-linux-gnu bzip2 cpp-9 debianutils g++-9 gcc-9 gcc-9-base libacl1 libapparmor1 libasan5 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libbz2-1.0 libcap-ng0 libcc1-0 libcryptsetup12 libdebconfclient0 libgcc-9-dev libgcc1 libgcrypt20 libgomp1 libitm1 libjson-c4 libkmod2 liblockfile-bin liblockfile1 liblz4-1 libncurses6 libncursesw6 libp11-kit0 libquadmath0 libselinux1 libsemanage-common libsemanage1 libsqlite3-0 libstdc++-9-dev libstdc++6 libsystemd0 libtinfo6 libubsan1 libudev1 lsb-base ncurses-base ncurses-bin perl perl-base systemd systemd-sysv sysvinit-utils 55 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 52.1 MB of archives. After this operation, 41.2 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu focal/main i386 base-files i386 11ubuntu1 [60.6 kB] Get:2 http://ftpmaster.internal/ubuntu focal-proposed/main i386 debianutils i386 4.9 [86.6 kB] Get:3 http://ftpmaster.internal/ubuntu focal-proposed/main i386 ncurses-bin i386 6.1+20191019-1ubuntu1 [175 kB] Get:4 http://ftpmaster.internal/ubuntu focal-proposed/main i386 perl-modules-5.30 all 5.30.0-8 [2739 kB] Get:5 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libperl5.30 i386 5.30.0-8 [3582 kB] Get:6 http://ftpmaster.internal/ubuntu focal-proposed/main i386 perl i386 5.30.0-8 [224 kB] Get:7 http://ftpmaster.internal/ubuntu focal-proposed/main i386 perl-base i386 5.30.0-8 [1618 kB] Get:8 http://ftpmaster.internal/ubuntu focal-proposed/main i386 bzip2 i386 1.0.8-2 [34.6 kB] Get:9 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libbz2-1.0 i386 1.0.8-2 [33.0 kB] Get:10 http://ftpmaster.internal/ubuntu focal-proposed/main i386 ncurses-base all 6.1+20191019-1ubuntu1 [17.9 kB] Get:11 http://ftpmaster.internal/ubuntu focal/main i386 lsb-base all 11.1.0ubuntu1 [12.2 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main i386 sysvinit-utils i386 2.96~beta-3ubuntu2 [21.6 kB] Get:13 http://ftpmaster.internal/ubuntu focal-proposed/main i386 systemd-sysv i386 243-2ubuntu1 [9364 B] Get:14 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libacl1 i386 2.2.53-5 [20.3 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main i386 libapparmor1 i386 2.13.3-5ubuntu2 [36.6 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main i386 libaudit-common all 1:2.8.5-2ubuntu2 [4080 B] Get:17 http://ftpmaster.internal/ubuntu focal/main i386 libcap-ng0 i386 0.7.9-2.1 [11.3 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main i386 libaudit1 i386 1:2.8.5-2ubuntu2 [40.5 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main i386 libjson-c4 i386 0.13.1+dfsg-6 [31.0 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main i386 libcryptsetup12 i386 2:2.2.1-1ubuntu1 [206 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main i386 libkmod2 i386 26-3ubuntu1 [47.6 kB] Get:22 http://ftpmaster.internal/ubuntu focal-proposed/main i386 liblz4-1 i386 1.9.1-2 [56.6 kB] Get:23 http://ftpmaster.internal/ubuntu focal-proposed/main i386 systemd i386 243-2ubuntu1 [3780 kB] Get:24 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libsystemd0 i386 243-2ubuntu1 [282 kB] Get:25 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libubsan1 i386 9.2.1-14ubuntu1 [149 kB] Get:26 http://ftpmaster.internal/ubuntu focal-proposed/main i386 gcc-9-base i386 9.2.1-14ubuntu1 [19.4 kB] Get:27 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libstdc++6 i386 9.2.1-14ubuntu1 [548 kB] Get:28 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libgomp1 i386 9.2.1-14ubuntu1 [95.0 kB] Get:29 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libitm1 i386 9.2.1-14ubuntu1 [31.1 kB] Get:30 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libatomic1 i386 9.2.1-14ubuntu1 [9840 B] Get:31 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libasan5 i386 9.2.1-14ubuntu1 [411 kB] Get:32 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libquadmath0 i386 9.2.1-14ubuntu1 [230 kB] Get:33 http://ftpmaster.internal/ubuntu focal-proposed/main i386 cpp-9 i386 9.2.1-14ubuntu1 [8988 kB] Get:34 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libcc1-0 i386 9.2.1-14ubuntu1 [50.0 kB] Get:35 http://ftpmaster.internal/ubuntu focal/main i386 binutils-i686-linux-gnu i386 2.33.1-1ubuntu1 [1772 kB] Get:36 http://ftpmaster.internal/ubuntu focal/main i386 libbinutils i386 2.33.1-1ubuntu1 [512 kB] Get:37 http://ftpmaster.internal/ubuntu focal/main i386 binutils-common i386 2.33.1-1ubuntu1 [203 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main i386 binutils i386 2.33.1-1ubuntu1 [3400 B] Get:39 http://ftpmaster.internal/ubuntu focal-proposed/main i386 g++-9 i386 9.2.1-14ubuntu1 [10.2 MB] Get:40 http://ftpmaster.internal/ubuntu focal-proposed/main i386 gcc-9 i386 9.2.1-14ubuntu1 [9794 kB] Get:41 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libgcc-9-dev i386 9.2.1-14ubuntu1 [2360 kB] Get:42 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libstdc++-9-dev i386 9.2.1-14ubuntu1 [1754 kB] Get:43 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libgcc1 i386 1:9.2.1-14ubuntu1 [48.2 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main i386 libattr1 i386 1:2.4.48-5 [13.0 kB] Get:45 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libdebconfclient0 i386 0.250ubuntu1 [6456 B] Get:46 http://ftpmaster.internal/ubuntu focal/main i386 libgcrypt20 i386 1.8.5-3ubuntu1 [402 kB] Get:47 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libncurses6 i386 6.1+20191019-1ubuntu1 [108 kB] Get:48 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libtinfo6 i386 6.1+20191019-1ubuntu1 [87.1 kB] Get:49 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libncursesw6 i386 6.1+20191019-1ubuntu1 [143 kB] Get:50 http://ftpmaster.internal/ubuntu focal/main i386 libselinux1 i386 2.9-2build1 [74.8 kB] Get:51 http://ftpmaster.internal/ubuntu focal/main i386 libsemanage-common all 2.9-3build1 [9736 B] Get:52 http://ftpmaster.internal/ubuntu focal/main i386 libsemanage1 i386 2.9-3build1 [94.8 kB] Get:53 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libudev1 i386 243-2ubuntu1 [81.9 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main i386 libp11-kit0 i386 0.23.18.1-2 [184 kB] Get:55 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libsqlite3-0 i386 3.30.1-1 [576 kB] Get:56 http://ftpmaster.internal/ubuntu focal/main i386 liblockfile-bin i386 1.16-1 [12.0 kB] Get:57 http://ftpmaster.internal/ubuntu focal/main i386 liblockfile1 i386 1.16-1 [7012 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 52.1 MB in 3s (18.4 MB/s) (Reading database ... 12732 files and directories currently installed.) Preparing to unpack .../base-files_11ubuntu1_i386.deb ... Unpacking base-files (11ubuntu1) over (10.2ubuntu7) ... Setting up base-files (11ubuntu1) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... Updating /root/.profile to current default. (Reading database ... 12732 files and directories currently installed.) Preparing to unpack .../debianutils_4.9_i386.deb ... Unpacking debianutils (4.9) over (4.8.6.3) ... Setting up debianutils (4.9) ... (Reading database ... 12732 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.1+20191019-1ubuntu1_i386.deb ... Unpacking ncurses-bin (6.1+20191019-1ubuntu1) over (6.1+20190803-1ubuntu1) ... Setting up ncurses-bin (6.1+20191019-1ubuntu1) ... (Reading database ... 12732 files and directories currently installed.) 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Setting up liblockfile1:i386 (1.16-1) ... Setting up libjson-c4:i386 (0.13.1+dfsg-6) ... Setting up libbinutils:i386 (2.33.1-1ubuntu1) ... Setting up libcc1-0:i386 (9.2.1-14ubuntu1) ... Setting up libitm1:i386 (9.2.1-14ubuntu1) ... Setting up libkmod2:i386 (26-3ubuntu1) ... Setting up binutils-i686-linux-gnu (2.33.1-1ubuntu1) ... Setting up binutils (2.33.1-1ubuntu1) ... Setting up libgcc-9-dev:i386 (9.2.1-14ubuntu1) ... Setting up perl (5.30.0-8) ... Setting up libcryptsetup12:i386 (2:2.2.1-1ubuntu1) ... Setting up gcc-9 (9.2.1-14ubuntu1) ... Setting up libstdc++-9-dev:i386 (9.2.1-14ubuntu1) ... Setting up systemd (243-2ubuntu1) ... Installing new version of config file /etc/systemd/networkd.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from KVM UUID. Setting up g++-9 (9.2.1-14ubuntu1) ... Setting up systemd-sysv (243-2ubuntu1) ... Processing triggers for libc-bin (2.30-0ubuntu2) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-17934572 i386 focal-proposed -c chroot:build-PACKAGEBUILD-17934572 --arch=i386 --dist=focal-proposed --nolog gbrowse_2.56+dfsg-4build1.dsc Initiating build PACKAGEBUILD-17934572 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-166-generic #195-Ubuntu SMP Tue Oct 1 09:35:25 UTC 2019 i686 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lgw01-amd64-004.buildd +==============================================================================+ | gbrowse 2.56+dfsg-4build1 (i386) 26 Oct 2019 17:12 | +==============================================================================+ Package: gbrowse Version: 2.56+dfsg-4build1 Source Version: 2.56+dfsg-4build1 Distribution: focal-proposed Machine Architecture: amd64 Host Architecture: i386 Build Architecture: i386 I: NOTICE: Log filtering will replace 'build/gbrowse-U5eVLK/gbrowse-2.56+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/gbrowse-U5eVLK' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-17934572/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- gbrowse_2.56+dfsg-4build1.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-1ABOQk/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-1ABOQk/apt_archive ./ InRelease Get:2 copy:/<>/resolver-1ABOQk/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-1ABOQk/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-1ABOQk/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-1ABOQk/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libperl5.28 perl-modules-5.28 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-1ABOQk/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14652 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_i386.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: bioperl, debhelper (>= 11~), dh-apache2, dh-exec, apache2-dev, libbio-graphics-perl (>= 2.31), libbio-coordinate-perl, libcapture-tiny-perl, libcgi-session-perl, libgd-gd2-perl | libgd-gd2-noxpm-perl, libio-string-perl, libjson-perl, libstatistics-descriptive-perl, libwww-perl, libhttp-daemon-perl, perl, sqlite3, libdbd-sqlite3-perl, libterm-readkey-perl, libjs-prototype, libjs-scriptaculous, libvm-ec2-perl, libmodule-build-perl, libcgi-pm-perl | perl (<< 5.19), rename Filtered Build-Depends: bioperl, debhelper (>= 11~), dh-apache2, dh-exec, apache2-dev, libbio-graphics-perl (>= 2.31), libbio-coordinate-perl, libcapture-tiny-perl, libcgi-session-perl, libgd-gd2-perl | libgd-gd2-noxpm-perl, libio-string-perl, libjson-perl, libstatistics-descriptive-perl, libwww-perl, libhttp-daemon-perl, perl, sqlite3, libdbd-sqlite3-perl, libterm-readkey-perl, libjs-prototype, libjs-scriptaculous, libvm-ec2-perl, libmodule-build-perl, libcgi-pm-perl | perl (<< 5.19), rename dpkg-deb: building package 'sbuild-build-depends-gbrowse-dummy' in '/<>/resolver-k_vC1e/apt_archive/sbuild-build-depends-gbrowse-dummy.deb'. Ign:1 copy:/<>/resolver-k_vC1e/apt_archive ./ InRelease Get:2 copy:/<>/resolver-k_vC1e/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-k_vC1e/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-k_vC1e/apt_archive ./ Sources [414 B] Get:5 copy:/<>/resolver-k_vC1e/apt_archive ./ Packages [737 B] Fetched 3270 B in 0s (0 B/s) 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 packages were automatically installed and are no longer required: libperl5.28 perl-modules-5.28 Use 'apt autoremove' to remove them. The following additional packages will be installed: apache2-dev autoconf automake autopoint autotools-dev bioperl bsdmainutils debhelper dh-autoreconf dh-exec dh-strip-nondeterminism dwz file fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian libalgorithm-diff-perl libanyevent-cachedns-perl libanyevent-http-perl libanyevent-perl libapr1 libapr1-dev libaprutil1 libaprutil1-dev libarchive-zip-perl libasn1-8-heimdal libbio-coordinate-perl libbio-graphics-perl libbio-perl-perl libbsd0 libcapture-tiny-perl libcgi-pm-perl libcgi-session-perl libclass-data-inheritable-perl libcommon-sense-perl libcroco3 libdata-stag-perl libdbd-sqlite3-perl libdbi-perl libdebhelper-perl libdevel-stacktrace-perl libelf1 libencode-locale-perl libexception-class-perl libexpat1 libexpat1-dev libexporter-tiny-perl libfile-listing-perl libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgd-perl libgd3 libglib2.0-0 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-daemon-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libhx509-5-heimdal libicu63 libio-html-perl libio-socket-ssl-perl libio-string-perl libjbig0 libjpeg-turbo8 libjpeg8 libjs-prototype libjs-scriptaculous libjson-perl libkrb5-26-heimdal libldap-2.4-2 libldap-common libldap2-dev liblist-moreutils-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1 libmodule-build-perl libnet-http-perl libnet-ssleay-perl libpipeline1 libroken18-heimdal libsasl2-2 libsasl2-modules-db libsctp-dev libsctp1 libsigsegv2 libstatistics-descriptive-perl libstring-approx-perl libsub-override-perl libsub-uplevel-perl libterm-readkey-perl libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl libtiff5 libtimedate-perl libtool libtry-tiny-perl libuchardet0 liburi-perl libvm-ec2-perl libwebp6 libwind0-heimdal 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 m4 man-db netbase perl-openssl-defaults po-debconf rename sqlite3 ucf uuid-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libev-perl libevent-perl libio-async-perl libpoe-perl libtask-weaken-perl python libxml-sax-expatxs-perl libclone-perl libmldbm-perl libnet-daemon-perl libsql-statement-perl libgd-tools libdata-dump-perl libcrypt-ssleay-perl lksctp-tools libtool-doc gfortran | fortran95-compiler gcj-jdk libauthen-ntlm-perl m4-doc apparmor 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 libalgorithm-diff-xs-perl libasync-interrupt-perl libev-perl | libevent-perl libguard-perl libbio-scf-perl libberkeleydb-perl libgd-svg-perl bioperl-run | libbio-perl-run-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 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 libarchive-cpio-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 libltdl-dev libdata-dump-perl libhtml-form-perl libmailtools-perl libxml-sax-expat-perl libmail-sendmail-perl The following NEW packages will be installed: apache2-dev autoconf automake autopoint autotools-dev bioperl bsdmainutils debhelper dh-autoreconf dh-exec dh-strip-nondeterminism dwz file fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian libalgorithm-diff-perl libanyevent-cachedns-perl libanyevent-http-perl libanyevent-perl libapr1 libapr1-dev libaprutil1 libaprutil1-dev libarchive-zip-perl libasn1-8-heimdal libbio-coordinate-perl libbio-graphics-perl libbio-perl-perl libbsd0 libcapture-tiny-perl libcgi-pm-perl libcgi-session-perl libclass-data-inheritable-perl libcommon-sense-perl libcroco3 libdata-stag-perl libdbd-sqlite3-perl libdbi-perl libdebhelper-perl libdevel-stacktrace-perl libelf1 libencode-locale-perl libexception-class-perl libexpat1 libexpat1-dev libexporter-tiny-perl libfile-listing-perl libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgd-perl libgd3 libglib2.0-0 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-daemon-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libhx509-5-heimdal libicu63 libio-html-perl libio-socket-ssl-perl libio-string-perl libjbig0 libjpeg-turbo8 libjpeg8 libjs-prototype libjs-scriptaculous libjson-perl libkrb5-26-heimdal libldap-2.4-2 libldap-common libldap2-dev liblist-moreutils-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1 libmodule-build-perl libnet-http-perl libnet-ssleay-perl libpipeline1 libroken18-heimdal libsasl2-2 libsasl2-modules-db libsctp-dev libsctp1 libsigsegv2 libstatistics-descriptive-perl libstring-approx-perl libsub-override-perl libsub-uplevel-perl libterm-readkey-perl libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl libtiff5 libtimedate-perl libtool libtry-tiny-perl libuchardet0 liburi-perl libvm-ec2-perl libwebp6 libwind0-heimdal 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 m4 man-db netbase perl-openssl-defaults po-debconf rename sbuild-build-depends-gbrowse-dummy sqlite3 ucf uuid-dev 0 upgraded, 143 newly installed, 0 to remove and 0 not upgraded. Need to get 35.7 MB of archives. After this operation, 137 MB of additional disk space will be used. Get:1 copy:/<>/resolver-k_vC1e/apt_archive ./ sbuild-build-depends-gbrowse-dummy 0.invalid.0 [1064 B] Get:2 http://ftpmaster.internal/ubuntu focal/main i386 libbsd0 i386 0.10.0-1 [49.8 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main i386 bsdmainutils i386 11.1.2ubuntu2 [183 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main i386 libuchardet0 i386 0.0.6-3 [65.2 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main i386 groff-base i386 1.22.4-3 [879 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main i386 libpipeline1 i386 1.5.1-2 [28.0 kB] Get:7 http://ftpmaster.internal/ubuntu focal-proposed/main i386 man-db i386 2.9.0-1 [1128 kB] Get:8 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libmagic-mgc i386 1:5.37-6 [209 kB] Get:9 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libmagic1 i386 1:5.37-6 [81.9 kB] Get:10 http://ftpmaster.internal/ubuntu focal-proposed/main i386 file i386 1:5.37-6 [23.2 kB] Get:11 http://ftpmaster.internal/ubuntu focal/main i386 libelf1 i386 0.176-1.1 [50.1 kB] Get:12 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libexpat1 i386 2.2.9-1 [73.7 kB] Get:13 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libglib2.0-0 i386 2.62.2-1 [1334 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main i386 libicu63 i386 63.2-2 [8442 kB] Get:15 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libxml2 i386 2.9.4+dfsg1-7ubuntu5 [686 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main i386 netbase all 5.6 [13.0 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main i386 ucf all 3.0038+nmu1 [51.6 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main i386 gettext-base i386 0.19.8.1-9 [51.2 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main i386 libxau6 i386 1:1.0.9-0ubuntu1 [7804 B] Get:20 http://ftpmaster.internal/ubuntu focal/main i386 libxdmcp6 i386 1:1.1.3-0ubuntu1 [11.0 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main i386 libxcb1 i386 1.13.1-2 [49.9 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main i386 libx11-data all 2:1.6.8-1 [113 kB] Get:23 http://ftpmaster.internal/ubuntu focal/main i386 libx11-6 i386 2:1.6.8-1 [598 kB] Get:24 http://ftpmaster.internal/ubuntu focal/main i386 autotools-dev all 20180224.1 [39.6 kB] Get:25 http://ftpmaster.internal/ubuntu focal/main i386 libsigsegv2 i386 2.12-2 [14.2 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main i386 m4 i386 1.4.18-2 [202 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main i386 autoconf all 2.69-11ubuntu1 [321 kB] Get:28 http://ftpmaster.internal/ubuntu focal/main i386 automake all 1:1.16.1-4ubuntu3 [522 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main i386 autopoint all 0.19.8.1-9 [412 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main i386 libtool all 2.4.6-11 [194 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main i386 dh-autoreconf all 19 [16.1 kB] Get:32 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libarchive-zip-perl all 1.67-1 [90.4 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main i386 libsub-override-perl all 0.09-2 [9532 B] Get:34 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libfile-stripnondeterminism-perl all 1.6.1-1 [16.1 kB] Get:35 http://ftpmaster.internal/ubuntu focal-proposed/main i386 dh-strip-nondeterminism all 1.6.1-1 [5212 B] Get:36 http://ftpmaster.internal/ubuntu focal/main i386 dwz i386 0.13-1 [84.1 kB] Get:37 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libdebhelper-perl all 12.7.1ubuntu1 [52.0 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main i386 libcroco3 i386 0.6.13-1 [88.7 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main i386 gettext i386 0.19.8.1-9 [905 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main i386 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main i386 po-debconf all 1.0.21 [233 kB] Get:42 http://ftpmaster.internal/ubuntu focal-proposed/main i386 debhelper all 12.7.1ubuntu1 [875 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main i386 libapr1 i386 1.6.5-1 [100 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main i386 uuid-dev i386 2.34-0.1ubuntu2 [34.0 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main i386 libsctp1 i386 1.0.18+dfsg-1 [8260 B] Get:46 http://ftpmaster.internal/ubuntu focal/main i386 libsctp-dev i386 1.0.18+dfsg-1 [60.3 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main i386 libapr1-dev i386 1.6.5-1 [701 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main i386 libaprutil1 i386 1.6.1-4build1 [93.1 kB] Get:49 http://ftpmaster.internal/ubuntu focal/main i386 libroken18-heimdal i386 7.5.0+dfsg-3build1 [45.4 kB] Get:50 http://ftpmaster.internal/ubuntu focal/main i386 libasn1-8-heimdal i386 7.5.0+dfsg-3build1 [187 kB] Get:51 http://ftpmaster.internal/ubuntu focal/main i386 libheimbase1-heimdal i386 7.5.0+dfsg-3build1 [32.5 kB] Get:52 http://ftpmaster.internal/ubuntu focal/main i386 libhcrypto4-heimdal i386 7.5.0+dfsg-3build1 [94.6 kB] Get:53 http://ftpmaster.internal/ubuntu focal/main i386 libwind0-heimdal i386 7.5.0+dfsg-3build1 [48.3 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main i386 libhx509-5-heimdal i386 7.5.0+dfsg-3build1 [117 kB] Get:55 http://ftpmaster.internal/ubuntu focal/main i386 libkrb5-26-heimdal i386 7.5.0+dfsg-3build1 [232 kB] Get:56 http://ftpmaster.internal/ubuntu focal/main i386 libheimntlm0-heimdal i386 7.5.0+dfsg-3build1 [16.4 kB] Get:57 http://ftpmaster.internal/ubuntu focal/main i386 libgssapi3-heimdal i386 7.5.0+dfsg-3build1 [108 kB] Get:58 http://ftpmaster.internal/ubuntu focal/main i386 libsasl2-modules-db i386 2.1.27+dfsg-1build3 [15.7 kB] Get:59 http://ftpmaster.internal/ubuntu focal/main i386 libsasl2-2 i386 2.1.27+dfsg-1build3 [53.0 kB] Get:60 http://ftpmaster.internal/ubuntu focal/main i386 libldap-common all 2.4.48+dfsg-1ubuntu2 [17.3 kB] Get:61 http://ftpmaster.internal/ubuntu focal/main i386 libldap-2.4-2 i386 2.4.48+dfsg-1ubuntu2 [168 kB] Get:62 http://ftpmaster.internal/ubuntu focal/main i386 libldap2-dev i386 2.4.48+dfsg-1ubuntu2 [281 kB] Get:63 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libexpat1-dev i386 2.2.9-1 [121 kB] Get:64 http://ftpmaster.internal/ubuntu focal/main i386 libaprutil1-dev i386 1.6.1-4build1 [403 kB] Get:65 http://ftpmaster.internal/ubuntu focal/main i386 apache2-dev i386 2.4.41-1ubuntu1 [179 kB] Get:66 http://ftpmaster.internal/ubuntu focal/main i386 libio-string-perl all 1.08-3 [11.1 kB] Get:67 http://ftpmaster.internal/ubuntu focal/universe i386 libdata-stag-perl all 0.14-2 [369 kB] Get:68 http://ftpmaster.internal/ubuntu focal/universe i386 libbio-perl-perl all 1.7.2-3 [4545 kB] Get:69 http://ftpmaster.internal/ubuntu focal/main i386 libclass-data-inheritable-perl all 0.08-3 [8084 B] Get:70 http://ftpmaster.internal/ubuntu focal/main i386 libdevel-stacktrace-perl all 2.0400-1 [22.7 kB] Get:71 http://ftpmaster.internal/ubuntu focal/main i386 libexception-class-perl all 1.44-1 [25.9 kB] Get:72 http://ftpmaster.internal/ubuntu focal/universe i386 libtest-deep-perl all 1.128-1 [41.3 kB] Get:73 http://ftpmaster.internal/ubuntu focal/main i386 libcapture-tiny-perl all 0.48-1 [20.4 kB] Get:74 http://ftpmaster.internal/ubuntu focal/main i386 libalgorithm-diff-perl all 1.19.03-2 [46.6 kB] Get:75 http://ftpmaster.internal/ubuntu focal/universe i386 libtext-diff-perl all 1.45-1 [25.7 kB] Get:76 http://ftpmaster.internal/ubuntu focal/universe i386 libtest-differences-perl all 0.67-1 [16.3 kB] Get:77 http://ftpmaster.internal/ubuntu focal/universe i386 libsub-uplevel-perl all 0.2800-1 [13.5 kB] Get:78 http://ftpmaster.internal/ubuntu focal/universe i386 libtest-exception-perl all 0.43-1 [14.7 kB] Get:79 http://ftpmaster.internal/ubuntu focal/universe i386 libtest-warn-perl all 0.36-1 [14.0 kB] Get:80 http://ftpmaster.internal/ubuntu focal/universe i386 libtest-most-perl all 0.35-1 [22.1 kB] Get:81 http://ftpmaster.internal/ubuntu focal/universe i386 bioperl all 1.7.2-3 [384 kB] Get:82 http://ftpmaster.internal/ubuntu focal/main i386 fonts-dejavu-core all 2.37-1 [1041 kB] Get:83 http://ftpmaster.internal/ubuntu focal/main i386 fontconfig-config all 2.13.1-2ubuntu2 [28.9 kB] Get:84 http://ftpmaster.internal/ubuntu focal/universe i386 libanyevent-perl i386 7.160-1build1 [369 kB] Get:85 http://ftpmaster.internal/ubuntu focal/universe i386 libanyevent-cachedns-perl all 0.08-2 [6698 B] Get:86 http://ftpmaster.internal/ubuntu focal/main i386 libcommon-sense-perl i386 3.74-2build6 [20.1 kB] Get:87 http://ftpmaster.internal/ubuntu focal/universe i386 libanyevent-http-perl all 2.24-1 [30.4 kB] Get:88 http://ftpmaster.internal/ubuntu focal/universe i386 libbio-coordinate-perl all 1.7.1-3 [56.3 kB] Get:89 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libfreetype6 i386 2.10.1-2 [356 kB] Get:90 http://ftpmaster.internal/ubuntu focal/main i386 libfontconfig1 i386 2.13.1-2ubuntu2 [124 kB] Get:91 http://ftpmaster.internal/ubuntu focal/main i386 libjpeg-turbo8 i386 2.0.3-0ubuntu1 [127 kB] Get:92 http://ftpmaster.internal/ubuntu focal/main i386 libjpeg8 i386 8c-2ubuntu8 [2188 B] Get:93 http://ftpmaster.internal/ubuntu focal/main i386 libjbig0 i386 2.1-3.1build1 [27.3 kB] Get:94 http://ftpmaster.internal/ubuntu focal/main i386 libwebp6 i386 0.6.1-2 [197 kB] Get:95 http://ftpmaster.internal/ubuntu focal/main i386 libtiff5 i386 4.0.10+git191003-1 [175 kB] Get:96 http://ftpmaster.internal/ubuntu focal/main i386 libxpm4 i386 1:3.5.12-1 [35.8 kB] Get:97 http://ftpmaster.internal/ubuntu focal/main i386 libgd3 i386 2.2.5-5.2 [123 kB] Get:98 http://ftpmaster.internal/ubuntu focal/main i386 libgd-perl i386 2.71-2build1 [133 kB] Get:99 http://ftpmaster.internal/ubuntu focal/universe i386 libbio-graphics-perl all 2.40-3 [604 kB] Get:100 http://ftpmaster.internal/ubuntu focal/main i386 libhtml-tagset-perl all 3.20-3 [12.1 kB] Get:101 http://ftpmaster.internal/ubuntu focal/main i386 liburi-perl all 1.76-1 [77.3 kB] Get:102 http://ftpmaster.internal/ubuntu focal/main i386 libhtml-parser-perl i386 3.72-3build3 [87.2 kB] Get:103 http://ftpmaster.internal/ubuntu focal/main i386 libcgi-pm-perl all 4.44-1 [186 kB] Get:104 http://ftpmaster.internal/ubuntu focal/universe i386 libcgi-session-perl all 4.48-3 [108 kB] Get:105 http://ftpmaster.internal/ubuntu focal/main i386 libdbi-perl i386 1.642-1build1 [729 kB] Get:106 http://ftpmaster.internal/ubuntu focal/universe i386 libdbd-sqlite3-perl i386 1.64-1build1 [158 kB] Get:107 http://ftpmaster.internal/ubuntu focal/main i386 libencode-locale-perl all 1.05-1 [12.3 kB] Get:108 http://ftpmaster.internal/ubuntu focal/main i386 libexporter-tiny-perl all 1.002001-1 [35.5 kB] Get:109 http://ftpmaster.internal/ubuntu focal/main i386 libtimedate-perl all 2.3000-2 [37.5 kB] Get:110 http://ftpmaster.internal/ubuntu focal/main i386 libhttp-date-perl all 6.02-1 [10.4 kB] Get:111 http://ftpmaster.internal/ubuntu focal/main i386 libfile-listing-perl all 6.04-1 [9774 B] Get:112 http://ftpmaster.internal/ubuntu focal/main i386 libhtml-tree-perl all 5.07-2 [200 kB] Get:113 http://ftpmaster.internal/ubuntu focal/main i386 libio-html-perl all 1.001-1 [14.9 kB] Get:114 http://ftpmaster.internal/ubuntu focal/main i386 liblwp-mediatypes-perl all 6.04-1 [19.5 kB] Get:115 http://ftpmaster.internal/ubuntu focal/main i386 libhttp-message-perl all 6.18-1 [75.3 kB] Get:116 http://ftpmaster.internal/ubuntu focal-proposed/main i386 libhttp-cookies-perl all 6.04-2 [17.5 kB] Get:117 http://ftpmaster.internal/ubuntu focal/main i386 libhttp-daemon-perl all 6.06-1 [21.4 kB] Get:118 http://ftpmaster.internal/ubuntu focal/main i386 libhttp-negotiate-perl all 6.01-1 [12.5 kB] Get:119 http://ftpmaster.internal/ubuntu focal/main i386 perl-openssl-defaults i386 3build1 [7008 B] Get:120 http://ftpmaster.internal/ubuntu focal/main i386 libnet-ssleay-perl i386 1.88-0ubuntu2 [301 kB] Get:121 http://ftpmaster.internal/ubuntu focal/main i386 libio-socket-ssl-perl all 2.066-0ubuntu4 [177 kB] Get:122 http://ftpmaster.internal/ubuntu focal/universe i386 libjs-prototype all 1.7.1-3 [44.2 kB] Get:123 http://ftpmaster.internal/ubuntu focal/universe i386 libjs-scriptaculous all 1.9.0-2 [107 kB] Get:124 http://ftpmaster.internal/ubuntu focal/main i386 libjson-perl all 4.02000-1 [81.0 kB] Get:125 http://ftpmaster.internal/ubuntu focal/main i386 liblist-moreutils-perl i386 0.416-1build5 [56.7 kB] Get:126 http://ftpmaster.internal/ubuntu focal/main i386 libnet-http-perl all 6.19-1 [22.8 kB] Get:127 http://ftpmaster.internal/ubuntu focal/main i386 libtry-tiny-perl all 0.30-1 [20.5 kB] Get:128 http://ftpmaster.internal/ubuntu focal/main i386 libwww-robotrules-perl all 6.02-1 [12.6 kB] Get:129 http://ftpmaster.internal/ubuntu focal/main i386 libwww-perl all 6.39-1 [139 kB] Get:130 http://ftpmaster.internal/ubuntu focal/main i386 liblwp-protocol-https-perl all 6.07-2ubuntu2 [8560 B] Get:131 http://ftpmaster.internal/ubuntu focal/universe i386 libmodule-build-perl all 0.422900-1 [200 kB] Get:132 http://ftpmaster.internal/ubuntu focal/universe i386 libstatistics-descriptive-perl all 3.0702-1 [60.1 kB] Get:133 http://ftpmaster.internal/ubuntu focal/universe i386 libstring-approx-perl i386 3.28-1build2 [37.1 kB] Get:134 http://ftpmaster.internal/ubuntu focal/main i386 libterm-readkey-perl i386 2.38-1build1 [25.1 kB] Get:135 http://ftpmaster.internal/ubuntu focal/main i386 libxml-namespacesupport-perl all 1.12-1 [13.2 kB] Get:136 http://ftpmaster.internal/ubuntu focal/main i386 libxml-sax-base-perl all 1.09-1 [18.8 kB] Get:137 http://ftpmaster.internal/ubuntu focal/main i386 libxml-sax-perl all 1.02+dfsg-1 [56.2 kB] Get:138 http://ftpmaster.internal/ubuntu focal/main i386 libxml-libxml-perl i386 2.0134+dfsg-1build1 [340 kB] Get:139 http://ftpmaster.internal/ubuntu focal/main i386 libxml-simple-perl all 2.25-1 [64.9 kB] Get:140 http://ftpmaster.internal/ubuntu focal/universe i386 libvm-ec2-perl all 1.28-2build1 [757 kB] Get:141 http://ftpmaster.internal/ubuntu focal/universe i386 rename all 1.10-1 [16.1 kB] Get:142 http://ftpmaster.internal/ubuntu focal-proposed/main i386 sqlite3 i386 3.30.1-1 [944 kB] Get:143 http://ftpmaster.internal/ubuntu focal/main i386 dh-exec i386 0.23.2 [25.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 35.7 MB in 3s (13.4 MB/s) Selecting previously unselected package libbsd0:i386. (Reading database ... 14652 files and directories currently installed.) Preparing to unpack .../000-libbsd0_0.10.0-1_i386.deb ... Unpacking libbsd0:i386 (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../001-bsdmainutils_11.1.2ubuntu2_i386.deb ... Unpacking bsdmainutils (11.1.2ubuntu2) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../002-libuchardet0_0.0.6-3_i386.deb ... Unpacking libuchardet0:i386 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../003-groff-base_1.22.4-3_i386.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../004-libpipeline1_1.5.1-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../005-man-db_2.9.0-1_i386.deb ... Unpacking man-db (2.9.0-1) ... Selecting previously unselected package libmagic-mgc. 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Unpacking apache2-dev (2.4.41-1ubuntu1) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../064-libio-string-perl_1.08-3_all.deb ... Unpacking libio-string-perl (1.08-3) ... Selecting previously unselected package libdata-stag-perl. Preparing to unpack .../065-libdata-stag-perl_0.14-2_all.deb ... Unpacking libdata-stag-perl (0.14-2) ... Selecting previously unselected package libbio-perl-perl. Preparing to unpack .../066-libbio-perl-perl_1.7.2-3_all.deb ... Unpacking libbio-perl-perl (1.7.2-3) ... Selecting previously unselected package libclass-data-inheritable-perl. Preparing to unpack .../067-libclass-data-inheritable-perl_0.08-3_all.deb ... Unpacking libclass-data-inheritable-perl (0.08-3) ... Selecting previously unselected package libdevel-stacktrace-perl. Preparing to unpack .../068-libdevel-stacktrace-perl_2.0400-1_all.deb ... Unpacking libdevel-stacktrace-perl (2.0400-1) ... Selecting previously unselected package libexception-class-perl. 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Selecting previously unselected package libhttp-daemon-perl. Preparing to unpack .../115-libhttp-daemon-perl_6.06-1_all.deb ... Unpacking libhttp-daemon-perl (6.06-1) ... Selecting previously unselected package libhttp-negotiate-perl. Preparing to unpack .../116-libhttp-negotiate-perl_6.01-1_all.deb ... Unpacking libhttp-negotiate-perl (6.01-1) ... Selecting previously unselected package perl-openssl-defaults:i386. Preparing to unpack .../117-perl-openssl-defaults_3build1_i386.deb ... Unpacking perl-openssl-defaults:i386 (3build1) ... Selecting previously unselected package libnet-ssleay-perl. Preparing to unpack .../118-libnet-ssleay-perl_1.88-0ubuntu2_i386.deb ... Unpacking libnet-ssleay-perl (1.88-0ubuntu2) ... Selecting previously unselected package libio-socket-ssl-perl. Preparing to unpack .../119-libio-socket-ssl-perl_2.066-0ubuntu4_all.deb ... Unpacking libio-socket-ssl-perl (2.066-0ubuntu4) ... Selecting previously unselected package libjs-prototype. 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Selecting previously unselected package libwww-robotrules-perl. Preparing to unpack .../126-libwww-robotrules-perl_6.02-1_all.deb ... Unpacking libwww-robotrules-perl (6.02-1) ... Selecting previously unselected package libwww-perl. Preparing to unpack .../127-libwww-perl_6.39-1_all.deb ... Unpacking libwww-perl (6.39-1) ... Selecting previously unselected package liblwp-protocol-https-perl. Preparing to unpack .../128-liblwp-protocol-https-perl_6.07-2ubuntu2_all.deb ... Unpacking liblwp-protocol-https-perl (6.07-2ubuntu2) ... Selecting previously unselected package libmodule-build-perl. Preparing to unpack .../129-libmodule-build-perl_0.422900-1_all.deb ... Adding 'diversion of /usr/bin/config_data to /usr/bin/config_data.diverted by libmodule-build-perl' Adding 'diversion of /usr/share/man/man1/config_data.1.gz to /usr/share/man/man1/config_data.diverted.1.gz by libmodule-build-perl' Unpacking libmodule-build-perl (0.422900-1) ... Selecting previously unselected package libstatistics-descriptive-perl. Preparing to unpack .../130-libstatistics-descriptive-perl_3.0702-1_all.deb ... Unpacking libstatistics-descriptive-perl (3.0702-1) ... Selecting previously unselected package libstring-approx-perl. Preparing to unpack .../131-libstring-approx-perl_3.28-1build2_i386.deb ... Unpacking libstring-approx-perl (3.28-1build2) ... Selecting previously unselected package libterm-readkey-perl. Preparing to unpack .../132-libterm-readkey-perl_2.38-1build1_i386.deb ... Unpacking libterm-readkey-perl (2.38-1build1) ... Selecting previously unselected package libxml-namespacesupport-perl. Preparing to unpack .../133-libxml-namespacesupport-perl_1.12-1_all.deb ... Unpacking libxml-namespacesupport-perl (1.12-1) ... Selecting previously unselected package libxml-sax-base-perl. Preparing to unpack .../134-libxml-sax-base-perl_1.09-1_all.deb ... Unpacking libxml-sax-base-perl (1.09-1) ... 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Selecting previously unselected package dh-exec. Preparing to unpack .../141-dh-exec_0.23.2_i386.deb ... Unpacking dh-exec (0.23.2) ... Selecting previously unselected package sbuild-build-depends-gbrowse-dummy. Preparing to unpack .../142-sbuild-build-depends-gbrowse-dummy_0.invalid.0_i386.deb ... Unpacking sbuild-build-depends-gbrowse-dummy (0.invalid.0) ... Setting up libexpat1:i386 (2.2.9-1) ... Setting up libanyevent-perl (7.160-1build1) ... Setting up libpipeline1:i386 (1.5.1-2) ... Setting up libstring-approx-perl (3.28-1build2) ... Setting up libxau6:i386 (1:1.0.9-0ubuntu1) ... Setting up libtest-deep-perl (1.128-1) ... Setting up libmagic-mgc (1:5.37-6) ... Setting up libalgorithm-diff-perl (1.19.03-2) ... Setting up libarchive-zip-perl (1.67-1) ... Setting up libglib2.0-0:i386 (2.62.2-1) ... No schema files found: doing nothing. Setting up libhtml-tagset-perl (3.20-3) ... Setting up libdebhelper-perl (12.7.1ubuntu1) ... Setting up liblwp-mediatypes-perl (6.04-1) ... Setting up libtry-tiny-perl (0.30-1) ... Setting up libmagic1:i386 (1:5.37-6) ... Setting up libapr1:i386 (1.6.5-1) ... Setting up perl-openssl-defaults:i386 (3build1) ... Setting up libcommon-sense-perl (3.74-2build6) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up libanyevent-http-perl (2.24-1) ... Setting up libencode-locale-perl (1.05-1) ... Setting up rename (1.10-1) ... update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode Setting up file (1:5.37-6) ... Setting up libldap-common (2.4.48+dfsg-1ubuntu2) ... Setting up libjbig0:i386 (2.1-3.1build1) ... Setting up libicu63:i386 (63.2-2) ... Setting up libmodule-build-perl (0.422900-1) ... Setting up libsasl2-modules-db:i386 (2.1.27+dfsg-1build3) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up libio-string-perl (1.08-3) ... Setting up autotools-dev (20180224.1) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libexpat1-dev:i386 (2.2.9-1) ... Setting up libfreetype6:i386 (2.10.1-2) ... Setting up libx11-data (2:1.6.8-1) ... Setting up libtext-diff-perl (1.45-1) ... Setting up uuid-dev:i386 (2.34-0.1ubuntu2) ... Setting up libsigsegv2:i386 (2.12-2) ... Setting up libanyevent-cachedns-perl (0.08-2) ... Setting up libio-html-perl (1.001-1) ... Setting up autopoint (0.19.8.1-9) ... Setting up libwebp6:i386 (0.6.1-2) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up ucf (3.0038+nmu1) ... Setting up libjpeg-turbo8:i386 (2.0.3-0ubuntu1) ... Setting up libjs-prototype (1.7.1-3) ... Setting up libsasl2-2:i386 (2.1.27+dfsg-1build3) ... Setting up libroken18-heimdal:i386 (7.5.0+dfsg-3build1) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsctp1:i386 (1.0.18+dfsg-1) ... Setting up libdata-stag-perl (0.14-2) ... Setting up libuchardet0:i386 (0.0.6-3) ... Setting up libjson-perl (4.02000-1) ... Setting up libsub-uplevel-perl (0.2800-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up netbase (5.6) ... Setting up libdevel-stacktrace-perl (2.0400-1) ... Setting up libbio-perl-perl (1.7.2-3) ... Setting up libexporter-tiny-perl (1.002001-1) ... Setting up libterm-readkey-perl (2.38-1build1) ... Setting up libbsd0:i386 (0.10.0-1) ... Setting up libelf1:i386 (0.176-1.1) ... Setting up libxml2:i386 (2.9.4+dfsg1-7ubuntu5) ... Setting up liburi-perl (1.76-1) ... Setting up sqlite3 (3.30.1-1) ... Setting up libdbi-perl:i386 (1.642-1build1) ... Setting up libheimbase1-heimdal:i386 (7.5.0+dfsg-3build1) ... Setting up libaprutil1:i386 (1.6.1-4build1) ... Setting up libnet-ssleay-perl (1.88-0ubuntu2) ... Setting up libjpeg8:i386 (8c-2ubuntu8) ... Setting up libfile-stripnondeterminism-perl (1.6.1-1) ... Setting up libhttp-date-perl (6.02-1) ... Setting up libxdmcp6:i386 (1:1.1.3-0ubuntu1) ... Setting up libxcb1:i386 (1.13.1-2) ... Setting up libfile-listing-perl (6.04-1) ... Setting up libtool (2.4.6-11) ... Setting up fontconfig-config (2.13.1-2ubuntu2) ... Setting up libjs-scriptaculous (1.9.0-2) ... Setting up liblist-moreutils-perl (0.416-1build5) ... Setting up libtest-warn-perl (0.36-1) ... Setting up libasn1-8-heimdal:i386 (7.5.0+dfsg-3build1) ... Setting up libtest-differences-perl (0.67-1) ... Setting up libnet-http-perl (6.19-1) ... Setting up m4 (1.4.18-2) ... Setting up libexception-class-perl (1.44-1) ... Setting up libxml-sax-perl (1.02+dfsg-1) ... 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 libhcrypto4-heimdal:i386 (7.5.0+dfsg-3build1) ... Setting up libwind0-heimdal:i386 (7.5.0+dfsg-3build1) ... Setting up libtest-exception-perl (0.43-1) ... Setting up bsdmainutils (11.1.2ubuntu2) ... 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 libcroco3:i386 (0.6.13-1) ... Setting up libsctp-dev:i386 (1.0.18+dfsg-1) ... Setting up autoconf (2.69-11ubuntu1) ... Setting up libxml-libxml-perl (2.0134+dfsg-1build1) ... 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 libwww-robotrules-perl (6.02-1) ... Setting up dwz (0.13-1) ... Setting up groff-base (1.22.4-3) ... Setting up libhtml-parser-perl (3.72-3build3) ... Setting up libx11-6:i386 (2:1.6.8-1) ... Setting up libdbd-sqlite3-perl:i386 (1.64-1build1) ... Setting up libtiff5:i386 (4.0.10+git191003-1) ... Setting up libfontconfig1:i386 (2.13.1-2ubuntu2) ... Setting up libio-socket-ssl-perl (2.066-0ubuntu4) ... Setting up libhttp-message-perl (6.18-1) ... Setting up automake (1:1.16.1-4ubuntu3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libhttp-negotiate-perl (6.01-1) ... Setting up gettext (0.19.8.1-9) ... Setting up libstatistics-descriptive-perl (3.0702-1) ... Setting up libxpm4:i386 (1:3.5.12-1) ... Setting up libhttp-cookies-perl (6.04-2) ... Setting up libtest-most-perl (0.35-1) ... Setting up libhx509-5-heimdal:i386 (7.5.0+dfsg-3build1) ... Setting up libhtml-tree-perl (5.07-2) ... Setting up libcgi-pm-perl (4.44-1) ... Setting up man-db (2.9.0-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libcgi-session-perl (4.48-3) ... Setting up libapr1-dev (1.6.5-1) ... Setting up libgd3:i386 (2.2.5-5.2) ... Setting up libxml-simple-perl (2.25-1) ... Setting up libhttp-daemon-perl (6.06-1) ... Setting up libkrb5-26-heimdal:i386 (7.5.0+dfsg-3build1) ... Setting up bioperl (1.7.2-3) ... Setting up po-debconf (1.0.21) ... Setting up libheimntlm0-heimdal:i386 (7.5.0+dfsg-3build1) ... Setting up libbio-coordinate-perl (1.7.1-3) ... Setting up libgd-perl (2.71-2build1) ... Setting up libgssapi3-heimdal:i386 (7.5.0+dfsg-3build1) ... Setting up libbio-graphics-perl (2.40-3) ... Setting up libldap-2.4-2:i386 (2.4.48+dfsg-1ubuntu2) ... Setting up libldap2-dev:i386 (2.4.48+dfsg-1ubuntu2) ... Setting up libaprutil1-dev (1.6.1-4build1) ... Setting up libwww-perl (6.39-1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.6.1-1) ... Setting up liblwp-protocol-https-perl (6.07-2ubuntu2) ... Setting up libvm-ec2-perl (1.28-2build1) ... Setting up debhelper (12.7.1ubuntu1) ... Setting up dh-exec (0.23.2) ... Setting up apache2-dev (2.4.41-1ubuntu1) ... Setting up sbuild-build-depends-gbrowse-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.30-0ubuntu2) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-166-generic amd64 (i686) Toolchain package versions: binutils_2.33.1-1ubuntu1 dpkg-dev_1.19.7ubuntu2 g++-9_9.2.1-14ubuntu1 gcc-9_9.2.1-14ubuntu1 libc6-dev_2.30-0ubuntu2 libstdc++-9-dev_9.2.1-14ubuntu1 libstdc++6_9.2.1-14ubuntu1 linux-libc-dev_5.3.0-18.19 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1 apache2-dev_2.4.41-1ubuntu1 apt_1.9.4 autoconf_2.69-11ubuntu1 automake_1:1.16.1-4ubuntu3 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_11ubuntu1 base-passwd_3.5.46 bash_5.0-4ubuntu1 binutils_2.33.1-1ubuntu1 binutils-common_2.33.1-1ubuntu1 binutils-i686-linux-gnu_2.33.1-1ubuntu1 bioperl_1.7.2-3 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.34-0.1ubuntu2 build-essential_12.8ubuntu1 bzip2_1.0.8-2 ca-certificates_20190110 coreutils_8.30-3ubuntu2 cpp_4:9.2.1-3.1ubuntu1 cpp-9_9.2.1-14ubuntu1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.1ubuntu1 debianutils_4.9 dh-autoreconf_19 dh-exec_0.23.2 dh-strip-nondeterminism_1.6.1-1 diffutils_1:3.7-3 dpkg_1.19.7ubuntu2 dpkg-dev_1.19.7ubuntu2 dwz_0.13-1 e2fsprogs_1.45.3-4ubuntu2 fakeroot_1.24-1 fdisk_2.34-0.1ubuntu2 file_1:5.37-6 findutils_4.6.0+git+20190209-2ubuntu1 fontconfig-config_2.13.1-2ubuntu2 fonts-dejavu-core_2.37-1 g++_4:9.2.1-3.1ubuntu1 g++-9_9.2.1-14ubuntu1 gcc_4:9.2.1-3.1ubuntu1 gcc-9_9.2.1-14ubuntu1 gcc-9-base_9.2.1-14ubuntu1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpg_2.2.12-1ubuntu3 gpg-agent_2.2.12-1ubuntu3 gpgconf_2.2.12-1ubuntu3 gpgv_2.2.12-1ubuntu3 grep_3.3-1build1 groff-base_1.22.4-3 gzip_1.10-0ubuntu3 hostname_3.22 init_1.57 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-5 libalgorithm-diff-perl_1.19.03-2 libanyevent-cachedns-perl_0.08-2 libanyevent-http-perl_2.24-1 libanyevent-perl_7.160-1build1 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liblwp-protocol-https-perl_6.07-2ubuntu2 liblz4-1_1.9.1-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-6 libmagic1_1:5.37-6 libmodule-build-perl_0.422900-1 libmount1_2.34-0.1ubuntu2 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses6_6.1+20191019-1ubuntu1 libncursesw6_6.1+20191019-1ubuntu1 libnet-http-perl_6.19-1 libnet-ssleay-perl_1.88-0ubuntu2 libnettle6_3.4.1-1 libnpth0_1.6-1 libp11-kit0_0.23.18.1-2 libpam-modules_1.3.1-5ubuntu1 libpam-modules-bin_1.3.1-5ubuntu1 libpam-runtime_1.3.1-5ubuntu1 libpam0g_1.3.1-5ubuntu1 libpcre2-8-0_10.32-5 libpcre3_2:8.39-12 libperl5.28_5.28.1-6build1 libperl5.30_5.30.0-8 libpipeline1_1.5.1-2 libpng16-16_1.6.37-1 libprocps7_2:3.3.15-2ubuntu3 libquadmath0_9.2.1-14ubuntu1 libreadline8_8.0-3 libroken18-heimdal_7.5.0+dfsg-3build1 libsasl2-2_2.1.27+dfsg-1build3 libsasl2-modules-db_2.1.27+dfsg-1build3 libsctp-dev_1.0.18+dfsg-1 libsctp1_1.0.18+dfsg-1 libseccomp2_2.4.1-0ubuntu0.19.10.3 libselinux1_2.9-2build1 libsemanage-common_2.9-3build1 libsemanage1_2.9-3build1 libsepol1_2.9-2 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1ubuntu2 libsqlite3-0_3.30.1-1 libss2_1.45.3-4ubuntu2 libssl1.1_1.1.1c-1ubuntu4 libstatistics-descriptive-perl_3.0702-1 libstdc++-9-dev_9.2.1-14ubuntu1 libstdc++6_9.2.1-14ubuntu1 libstring-approx-perl_3.28-1build2 libsub-override-perl_0.09-2 libsub-uplevel-perl_0.2800-1 libsystemd0_243-2ubuntu1 libtasn1-6_4.14-3 libterm-readkey-perl_2.38-1build1 libtest-deep-perl_1.128-1 libtest-differences-perl_0.67-1 libtest-exception-perl_0.43-1 libtest-most-perl_0.35-1 libtest-warn-perl_0.36-1 libtext-diff-perl_1.45-1 libtiff5_4.0.10+git191003-1 libtimedate-perl_2.3000-2 libtinfo6_6.1+20191019-1ubuntu1 libtool_2.4.6-11 libtry-tiny-perl_0.30-1 libubsan1_9.2.1-14ubuntu1 libuchardet0_0.0.6-3 libudev1_243-2ubuntu1 libunistring2_0.9.10-2 liburi-perl_1.76-1 libuuid1_2.34-0.1ubuntu2 libvm-ec2-perl_1.28-2build1 libwebp6_0.6.1-2 libwind0-heimdal_7.5.0+dfsg-3build1 libwww-perl_6.39-1 libwww-robotrules-perl_6.02-1 libx11-6_2:1.6.8-1 libx11-data_2:1.6.8-1 libxau6_1:1.0.9-0ubuntu1 libxcb1_1.13.1-2 libxdmcp6_1:1.1.3-0ubuntu1 libxml-libxml-perl_2.0134+dfsg-1build1 libxml-namespacesupport-perl_1.12-1 libxml-sax-base-perl_1.09-1 libxml-sax-perl_1.02+dfsg-1 libxml-simple-perl_2.25-1 libxml2_2.9.4+dfsg1-7ubuntu5 libxpm4_1:3.5.12-1 libzstd1_1.4.3+dfsg-1 linux-libc-dev_5.3.0-18.19 lockfile-progs_0.1.18 login_1:4.5-1.1ubuntu4 logsave_1.45.3-4ubuntu2 lsb-base_11.1.0ubuntu1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.9.0-1 mawk_1.3.3-17ubuntu3 mount_2.34-0.1ubuntu2 ncurses-base_6.1+20191019-1ubuntu1 ncurses-bin_6.1+20191019-1ubuntu1 netbase_5.6 openssl_1.1.1c-1ubuntu4 optipng_0.7.7-1 passwd_1:4.5-1.1ubuntu4 patch_2.7.6-6 perl_5.30.0-8 perl-base_5.30.0-8 perl-modules-5.28_5.28.1-6build1 perl-modules-5.30_5.30.0-8 perl-openssl-defaults_3build1 pinentry-curses_1.1.0-3 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu3 readline-common_8.0-3 rename_1.10-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gbrowse-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sqlite3_3.30.1-1 systemd_243-2ubuntu1 systemd-sysv_243-2ubuntu1 sysvinit-utils_2.96~beta-3ubuntu2 tar_1.30+dfsg-6 tzdata_2019c-3 ubuntu-keyring_2018.09.18.1 ucf_3.0038+nmu1 util-linux_2.34-0.1ubuntu2 uuid-dev_2.34-0.1ubuntu2 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1ubuntu3 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Sat Oct 19 10:39:11 2019 UTC gpgv: using RSA key D56571B88A8BBAF140BF63D6BD7EAA60778FA6F5 gpgv: issuer "doko@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./gbrowse_2.56+dfsg-4build1.dsc dpkg-source: info: extracting gbrowse in gbrowse-2.56+dfsg dpkg-source: info: unpacking gbrowse_2.56+dfsg.orig.tar.gz dpkg-source: info: unpacking gbrowse_2.56+dfsg-4build1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying debian-packaging-patch dpkg-source: info: applying gbrowse-slave-fix_defaults_path dpkg-source: info: applying manpages.patch dpkg-source: info: applying fix_pop_url dpkg-source: info: applying skip_check_installed_test.patch dpkg-source: info: applying source_init_functions dpkg-source: info: applying init_script_dependency.patch dpkg-source: info: applying fix_runlevel.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying fix_whatis_entry.patch dpkg-source: info: applying remove_copy_of_LoadHelper.pm.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-17934572 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-17934572 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-17934572 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package gbrowse dpkg-buildpackage: info: source version 2.56+dfsg-4build1 dpkg-buildpackage: info: source distribution focal dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean --with apache2 dh_clean debian/rules build-arch dh build-arch --with apache2 dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/<>/gbrowse-2.56+dfsg' dh_auto_configure -- --conf=/etc/gbrowse --htdocs=/usr/share/gbrowse/htdocs --tmp=/var/cache/gbrowse --databases=/var/lib/gbrowse/databases --cgibin=/usr/lib/cgi-bin/gbrowse --www-user=www-data --registration_done=1 --persistent=/var/lib/gbrowse perl Build.PL --installdirs vendor --config "optimize=-g -O2 -fdebug-prefix-map=/<>/gbrowse-2.56+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" --config "ld=i686-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/gbrowse-2.56+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now" --conf=/etc/gbrowse --htdocs=/usr/share/gbrowse/htdocs --tmp=/var/cache/gbrowse --databases=/var/lib/gbrowse/databases --cgibin=/usr/lib/cgi-bin/gbrowse --www-user=www-data --registration_done=1 --persistent=/var/lib/gbrowse WARNING: the following files are missing in your kit: contrib/ace2gff.pl contrib/AxtPairwise_convert/axt2phy.pl contrib/blast2gff.pl contrib/conf_files/01.yeast.conf contrib/conf_files/02.wormbase.conf contrib/conf_files/03.fly.conf contrib/conf_files/04.human.conf contrib/conf_files/05.embl_proxy.conf contrib/conf_files/06.biosql.conf contrib/conf_files/07.chado.conf contrib/conf_files/08.genbank.conf contrib/conf_files/09.human_karyotype.conf contrib/conf_files/index.html contrib/conf_files/wormbase.syn contrib/Coverage/INSTALL contrib/Coverage/plugin/Coverage.pm contrib/Coverage/README contrib/gdump.pl contrib/GeneFinder/genefinder/gfcode.c contrib/GeneFinder/genefinder/README contrib/GeneFinder/genefinder/readseq.c contrib/GeneFinder/genefinder/readseq.h contrib/GeneFinder/nematode_gftables/cds.hex contrib/GeneFinder/nematode_gftables/gftables contrib/GeneFinder/nematode_gftables/newnem.atg contrib/GeneFinder/nematode_gftables/newnem.codon contrib/GeneFinder/nematode_gftables/newnem.gene contrib/GeneFinder/nematode_gftables/newnem.intron3 contrib/GeneFinder/nematode_gftables/newnem.intron5 contrib/GeneFinder/nematode_gftables/ref.hist contrib/GeneFinder/nematode_gftables/zk637.atg contrib/GeneFinder/nematode_gftables/zk637.intron3 contrib/GeneFinder/nematode_gftables/zk637.intron5 contrib/GeneFinder/nematode_gftables/zk637.trinuc contrib/import_ncbi_mv_hs.pl contrib/install_macosx/BuildConfig.pm contrib/install_macosx/README.html contrib/install_macosx/README.pod contrib/install_macosx/scripts/build-gbrowse.pl contrib/install_macosx/scripts/build-libraries.pl contrib/README contrib/SynView/cgi-lib/DAS/GUS.pm contrib/SynView/cgi-lib/DAS/GUS/Segment.pm contrib/SynView/cgi-lib/DAS/GUS/Segment/Feature.pm contrib/SynView/cgi-lib/DAS/Util/SqlParser.pm contrib/SynView/gbrowse.conf/plasmodb.conf contrib/SynView/gbrowse.conf/plasmodb.xml contrib/SynView/MAL11/MAL11.conf contrib/SynView/MAL11/MAL11.fa contrib/SynView/MAL11/MAL11.gff3 contrib/SynView/README contrib/TextDumper/README contrib/TextDumper/TextDumper.pm lib/Bio/DB/SeqFeature/Store/LoadHelper.pm Please inform the author. Checking prerequisites... recommends: * Bio::DB::BigFile is not installed * Bio::DB::Sam is not installed * Bio::Das is not installed * Crypt::SSLeay is not installed * DBD::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 '2.56' make[1]: Leaving directory '/<>/gbrowse-2.56+dfsg' dh_auto_build -a perl Build NOTE: Run ./Build reconfig to change existing configuration. Building GBrowse i686-linux-gnu-gcc -I/<>/gbrowse-2.56+dfsg/libalign -I/usr/lib/i386-linux-gnu/perl/5.30/CORE -DVERSION="2.56" -DXS_VERSION="2.56" -fPIC -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<>/gbrowse-2.56+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>/gbrowse-2.56+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o lib/Bio/Graphics/Browser2/CAlign.o lib/Bio/Graphics/Browser2/CAlign.c ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/Graphics/Browser2/CAlign/CAlign.bs') i686-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/gbrowse-2.56+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -L/usr/local/lib -fstack-protector-strong -o blib/arch/auto/Bio/Graphics/Browser2/CAlign/CAlign.so lib/Bio/Graphics/Browser2/CAlign.o Performing variable substitutions in blib/conf/aws_balancer.conf Performing variable substitutions in blib/conf/detail_select_menu.conf Performing variable substitutions in blib/conf/enzymes.txt Performing variable substitutions in blib/conf/GBrowse.conf Performing variable substitutions in blib/conf/log4perl.conf Performing variable substitutions in blib/conf/MobyServices/moby.conf Performing variable substitutions in blib/conf/pop_demo.conf Performing variable substitutions in blib/conf/renderfarm.conf Performing variable substitutions in blib/conf/slave_preload.conf Performing variable substitutions in blib/conf/submitter_plugin.conf Performing variable substitutions in blib/conf/synteny/oryza.synconf.disabled.conf Performing variable substitutions in blib/conf/synteny/rice_synteny.conf Performing variable substitutions in blib/conf/synteny/wild_rice_synteny.conf Performing variable substitutions in blib/conf/themes/solid_gray_colors Performing variable substitutions in blib/conf/themes/transparent_colors Performing variable substitutions in blib/conf/themes/warm_colors Performing variable substitutions in blib/conf/volvox.conf Performing variable substitutions in blib/conf/yeast_chr1+2.conf Performing variable substitutions in blib/conf/yeast_renderfarm.conf Performing variable substitutions in blib/conf/yeast_simple.conf Performing variable substitutions in blib/htdocs/annotation_help.html Performing variable substitutions in blib/htdocs/cloud_index.html Performing variable substitutions in blib/htdocs/example_scripts/index.html Performing variable substitutions in blib/htdocs/example_scripts/README Performing variable substitutions in blib/htdocs/gbrowse_karyotype_help.html Performing variable substitutions in blib/htdocs/gbrowse_syn_help.html Performing variable substitutions in blib/htdocs/general_help.html Performing variable substitutions in blib/htdocs/index.html Performing variable substitutions in blib/htdocs/tutorial/conf_files/elegans_core.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/elegans_extra.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/HEADER.html Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_final.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_final_withPhylo.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_halfway.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_Phylo.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_quarter.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_refactored.conf Performing variable substitutions in blib/htdocs/tutorial/data_files/HEADER.html Performing variable substitutions in blib/htdocs/tutorial/tutorial.html Performing variable substitutions in blib/htdocs/tutorial/tutorial.phyTreeEdit.html Performing variable substitutions in blib/htdocs/vbox_index.html Use of uninitialized value in pattern match (m//) at /<>/gbrowse-2.56+dfsg/install_util/GBrowseInstall.pm line 778. debian/rules override_dh_auto_test make[1]: Entering directory '/<>/gbrowse-2.56+dfsg' dh_auto_test -- TEST_FILES="t/02.rearchitecture.t t/05.deferredrendering.t t/00.compile.t t/01.yeast.t t/07.balancer.t t/08.calign.t" perl Build test --verbose 1 "TEST_FILES=t/02.rearchitecture.t t/05.deferredrendering.t t/00.compile.t t/01.yeast.t t/07.balancer.t t/08.calign.t" NOTE: Run ./Build reconfig to change existing configuration. Use of uninitialized value in pattern match (m//) at /<>/gbrowse-2.56+dfsg/install_util/GBrowseInstall.pm line 778. t/00.compile.t ............ ok 1 - cgi-bin/das compiled ok ok 2 - cgi-bin/das stderr said "syntax OK" ok 3 - cgi-bin/das nothing on stdout ok 4 - cgi-bin/gbgff compiled ok ok 5 - cgi-bin/gbgff stderr said "syntax OK" ok 6 - cgi-bin/gbgff nothing on stdout ok 7 - cgi-bin/gbrowse compiled ok ok 8 - cgi-bin/gbrowse stderr said "syntax OK" ok 9 - cgi-bin/gbrowse nothing on stdout ok 10 - cgi-bin/gbrowse_details compiled ok ok 11 - cgi-bin/gbrowse_details stderr said "syntax OK" ok 12 - cgi-bin/gbrowse_details nothing on stdout ok 13 # skip explicitly skipping cgi-bin/gbrowse_gmap ok 14 - cgi-bin/gbrowse_img compiled ok ok 15 - cgi-bin/gbrowse_img stderr said "syntax OK" ok 16 - cgi-bin/gbrowse_img nothing on stdout ok 17 - cgi-bin/gbrowse_key_img compiled ok ok 18 - cgi-bin/gbrowse_key_img stderr said "syntax OK" ok 19 - cgi-bin/gbrowse_key_img nothing on stdout ok 20 - cgi-bin/gbrowse_login compiled ok ok 21 - cgi-bin/gbrowse_login stderr said "syntax OK" ok 22 - cgi-bin/gbrowse_login nothing on stdout ok 23 - cgi-bin/gbrowse_syn compiled ok ok 24 - cgi-bin/gbrowse_syn stderr said "syntax OK" ok 25 - cgi-bin/gbrowse_syn nothing on stdout ok 26 - bin/auto_install_databases.pl compiled ok ok 27 - bin/auto_install_databases.pl stderr said "syntax OK" ok 28 - bin/auto_install_databases.pl nothing on stdout ok 29 - bin/bed2gff3.pl compiled ok ok 30 - bin/bed2gff3.pl stderr said "syntax OK" ok 31 - bin/bed2gff3.pl nothing on stdout ok 32 - bin/bp_load_gff.pl compiled ok ok 33 - bin/bp_load_gff.pl stderr said "syntax OK" ok 34 - bin/bp_load_gff.pl nothing on stdout ok 35 # skip explicitly skipping bin/gbrowse_aws_balancer.pl ok 36 - bin/gbrowse_change_passwd.pl compiled ok ok 37 - bin/gbrowse_change_passwd.pl stderr said "syntax OK" ok 38 - bin/gbrowse_change_passwd.pl nothing on stdout ok 39 - bin/gbrowse_clean.pl compiled ok ok 40 - bin/gbrowse_clean.pl stderr said "syntax OK" ok 41 - bin/gbrowse_clean.pl nothing on stdout ok 42 - bin/gbrowse_configure_slaves.pl compiled ok ok 43 - bin/gbrowse_configure_slaves.pl stderr said "syntax OK" ok 44 - bin/gbrowse_configure_slaves.pl nothing on stdout ok 45 - bin/gbrowse_create_account.pl compiled ok ok 46 - bin/gbrowse_create_account.pl stderr said "syntax OK" ok 47 - bin/gbrowse_create_account.pl nothing on stdout ok 48 # skip explicitly skipping bin/gbrowse_grow_cloud_vol.pl ok 49 - bin/gbrowse_import_ucsc_db.pl compiled ok ok 50 - bin/gbrowse_import_ucsc_db.pl stderr said "syntax OK" ok 51 - bin/gbrowse_import_ucsc_db.pl nothing on stdout ok 52 - bin/gbrowse_metadb_config.pl compiled ok ok 53 - bin/gbrowse_metadb_config.pl stderr said "syntax OK" ok 54 - bin/gbrowse_metadb_config.pl nothing on stdout ok 55 # skip explicitly skipping bin/gbrowse_netinstall.pl ok 56 # skip explicitly skipping bin/gbrowse_netinstall2.pl ok 57 - bin/gbrowse_set_admin_passwd.pl compiled ok ok 58 - bin/gbrowse_set_admin_passwd.pl stderr said "syntax OK" ok 59 - bin/gbrowse_set_admin_passwd.pl nothing on stdout ok 60 - bin/gbrowse_slave compiled ok ok 61 - bin/gbrowse_slave stderr said "syntax OK" ok 62 - bin/gbrowse_slave nothing on stdout ok 63 # skip explicitly skipping bin/gbrowse_slave_start_aws.sh ok 64 - bin/gbrowse_syn_load_alignment_database.pl compiled ok ok 65 - bin/gbrowse_syn_load_alignment_database.pl stderr said "syntax OK" ok 66 - bin/gbrowse_syn_load_alignment_database.pl nothing on stdout ok 67 - bin/gbrowse_syn_load_alignments_msa.pl compiled ok ok 68 - bin/gbrowse_syn_load_alignments_msa.pl stderr said "syntax OK" ok 69 - bin/gbrowse_syn_load_alignments_msa.pl nothing on stdout ok 70 # skip explicitly skipping bin/gbrowse_sync_aws_slave.pl ok 71 - bin/gtf2gff3.pl compiled ok ok 72 - bin/gtf2gff3.pl stderr said "syntax OK" ok 73 - bin/gtf2gff3.pl nothing on stdout ok 74 - bin/load_genbank.pl compiled ok ok 75 - bin/load_genbank.pl stderr said "syntax OK" ok 76 - bin/load_genbank.pl nothing on stdout ok 77 # skip explicitly skipping bin/make_das_conf.pl ok 78 - bin/process_bamfiles.pl compiled ok ok 79 - bin/process_bamfiles.pl stderr said "syntax OK" ok 80 - bin/process_bamfiles.pl nothing on stdout ok 81 - bin/process_gadfly.pl compiled ok ok 82 - bin/process_gadfly.pl stderr said "syntax OK" ok 83 - bin/process_gadfly.pl nothing on stdout ok 84 - bin/process_ncbi_human.pl compiled ok ok 85 - bin/process_ncbi_human.pl stderr said "syntax OK" ok 86 - bin/process_ncbi_human.pl nothing on stdout ok 87 - bin/process_sgd.pl compiled ok ok 88 - bin/process_sgd.pl stderr said "syntax OK" ok 89 - bin/process_sgd.pl nothing on stdout ok 90 - bin/report_missing_language_tags.pl compiled ok ok 91 - bin/report_missing_language_tags.pl stderr said "syntax OK" ok 92 - bin/report_missing_language_tags.pl nothing on stdout ok 93 - bin/scan_gbrowse.pl compiled ok ok 94 - bin/scan_gbrowse.pl stderr said "syntax OK" ok 95 - bin/scan_gbrowse.pl nothing on stdout ok 96 - bin/split_wig.pl compiled ok ok 97 - bin/split_wig.pl stderr said "syntax OK" ok 98 - bin/split_wig.pl nothing on stdout ok 99 - bin/ucsc_genes2gff.pl compiled ok ok 100 - bin/ucsc_genes2gff.pl stderr said "syntax OK" ok 101 - bin/ucsc_genes2gff.pl nothing on stdout ok 102 - bin/wiggle2gff3.pl compiled ok ok 103 - bin/wiggle2gff3.pl stderr said "syntax OK" ok 104 - bin/wiggle2gff3.pl nothing on stdout 1..104 ok Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. t/01.yeast.t .............. 1..7 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok t/02.rearchitecture.t ..... 1..90 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Use of uninitialized value $_[5] in pack at /usr/share/perl5/Bio/DB/IndexedBase.pm line 1044, line 2. Use of uninitialized value $_[5] in pack at /usr/share/perl5/Bio/DB/IndexedBase.pm line 1044, line 2. t/03.render.t ............. 1..150 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok Sometimes this test gets 'stuck'. If this happens, kill the test and Build test again. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. t/04.remoteserver.t ....... 1..43 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. 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 Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, <> line 132. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. t/06.featuresearch.t ...... 1..26 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok t/07.balancer.t ........... skipped: Optional module Parse::Apache::ServerStatus not installed t/07.karyotype.t .......... 1..3 ok 1 ok 2 ok 3 ok t/08.calign.t ............. 1..6 # Running under perl version 5.030000 for linux # Current time local: Sat Oct 26 17:12:51 2019 # Current time GMT: Sat Oct 26 17:12:51 2019 # Using Test.pm version 1.31 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok All tests successful. Files=10, Tests=448, 19 wallclock secs ( 0.08 usr 0.00 sys + 13.24 cusr 1.56 csys = 14.88 CPU) Result: PASS make[1]: Leaving directory '/<>/gbrowse-2.56+dfsg' create-stamp debian/debhelper-build-stamp 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 '/<>/gbrowse-2.56+dfsg' # svn(-buildpackage) seems to ignore the x bit chmod +x debian/gbrowse-calign.dirs dh_installdirs make[1]: Leaving directory '/<>/gbrowse-2.56+dfsg' debian/rules override_dh_auto_install make[1]: Entering directory '/<>/gbrowse-2.56+dfsg' ./Build --install_base=debian/gbrowse debianinstall NOTE: Run ./Build reconfig to change existing configuration. Use of uninitialized value in pattern match (m//) at /<>/gbrowse-2.56+dfsg/install_util/GBrowseInstall.pm line 778. Building GBrowse Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/auto/Bio/Graphics/Browser2/CAlign/CAlign.bs Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/auto/Bio/Graphics/Browser2/CAlign/CAlign.so Installing debian/gbrowse/man/man1/gbrowse_aws_balancer.pl.1p Installing debian/gbrowse/man/man1/gbrowse_clean.pl.1p Installing debian/gbrowse/man/man1/gbrowse_sync_aws_slave.pl.1p Installing debian/gbrowse/man/man1/make_das_conf.pl.1p Installing debian/gbrowse/man/man1/wiggle2gff3.pl.1p Installing debian/gbrowse/man/man1/bed2gff3.pl.1p Installing debian/gbrowse/man/man1/gbrowse_grow_cloud_vol.pl.1p Installing debian/gbrowse/man/man1/ucsc_genes2gff.pl.1p Installing debian/gbrowse/man/man1/load_genbank.pl.1p Installing debian/gbrowse/man/man1/gtf2gff3.pl.1p Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse Installing 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debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/Region.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/DataSource.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/Render/Login.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/Render/SnapshotManager.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/Render/HTML.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/Render/TrackConfig.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/Render/Slave.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/Render/HTML/TrackListing.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/Render/HTML/TrackListing/Categories.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/Render/Slave/AWS_Balancer.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/Render/Slave/Status.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/Plugin/AuthPlugin.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/TrackDumper/RichSeqMaker.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/bigbed.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/sam.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/useq.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/wig2bigwig.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/bigwig.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/generic.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/wiggle.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/archive.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/gff3.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/bed.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/gff.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/featurefile.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/bam.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/UserTracks/Filesystem.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Bio/Graphics/Browser2/UserTracks/Database.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Legacy/DB/SyntenyBlock.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Legacy/DB/SyntenyIO.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Legacy/Graphics/Browser.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Legacy/Graphics/Browser/I18n.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Legacy/Graphics/Browser/Synteny.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Legacy/Graphics/Browser/PageSettings.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/Legacy/Graphics/Browser/Util.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/GBrowse/ConfigData.pm Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/CGI/Toggle.pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render::Slave::Status.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::PluginSet.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataLoader::archive.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::GFFhelper.3pm Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RemoteSet.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Plugin::AuthPlugin.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::AuthorizedFeatureFile.3pm Installing debian/gbrowse/man/man3/CGI::Toggle.3pm Installing debian/gbrowse/man/man3/Bio::DB::SeqFeature::Store::Alias.3pm Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Plugin.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RenderPanels.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Markup.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Region.3pm Installing debian/gbrowse/man/man3/Legacy::Graphics::Browser.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataLoader::useq.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataSource.3pm Installing debian/gbrowse/man/man3/GBrowse::ConfigData.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::PadAlignment.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::Realign.3pm Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Util.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render::Slave::AWS_Balancer.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::OptionPick.3pm Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::match_gap.3pm Installing debian/gbrowse/man/man3/Bio::DB::Tagger::Tag.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataBase.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::CAlign.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RegionSearch.3pm Installing debian/gbrowse/bin/gbrowse_aws_balancer.pl Installing debian/gbrowse/bin/gbrowse_configure_slaves.pl Installing debian/gbrowse/bin/make_das_conf.pl Installing debian/gbrowse/bin/gbrowse_sync_aws_slave.pl Installing debian/gbrowse/bin/gtf2gff3.pl Installing debian/gbrowse/bin/gbrowse_set_admin_passwd.pl Installing debian/gbrowse/bin/bed2gff3.pl Installing debian/gbrowse/bin/gbrowse_clean.pl Installing debian/gbrowse/bin/ucsc_genes2gff.pl Installing debian/gbrowse/bin/scan_gbrowse.pl Installing debian/gbrowse/bin/gbrowse_create_account.pl Installing debian/gbrowse/bin/gbrowse_syn_load_alignments_msa.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_grow_cloud_vol.pl Installing debian/gbrowse/bin/gbrowse_metadb_config.pl Installing debian/gbrowse/bin/gbrowse_change_passwd.pl Installing debian/gbrowse/bin/gbrowse_slave Installing debian/gbrowse/bin/wiggle2gff3.pl Installing debian/gbrowse/bin/load_genbank.pl #./Build apache_conf > debian/gbrowse/etc/gbrowse/gbrowse_apache2.conf perl Build.PL --conf=/etc/gbrowse --htdocs=/usr/share/gbrowse/htdocs --tmp=/var/cache/gbrowse --databases=/var/lib/gbrowse/databases --cgibin=/usr/lib/cgi-bin/gbrowse --www-user=www-data --registration_done=1 --persistent=/var/lib/gbrowse --installetc=y WARNING: the following files are missing in your kit: contrib/ace2gff.pl contrib/AxtPairwise_convert/axt2phy.pl contrib/blast2gff.pl contrib/conf_files/01.yeast.conf contrib/conf_files/02.wormbase.conf contrib/conf_files/03.fly.conf contrib/conf_files/04.human.conf contrib/conf_files/05.embl_proxy.conf contrib/conf_files/06.biosql.conf contrib/conf_files/07.chado.conf contrib/conf_files/08.genbank.conf contrib/conf_files/09.human_karyotype.conf contrib/conf_files/index.html contrib/conf_files/wormbase.syn contrib/Coverage/INSTALL contrib/Coverage/plugin/Coverage.pm contrib/Coverage/README contrib/gdump.pl contrib/GeneFinder/genefinder/gfcode.c contrib/GeneFinder/genefinder/README contrib/GeneFinder/genefinder/readseq.c contrib/GeneFinder/genefinder/readseq.h contrib/GeneFinder/nematode_gftables/cds.hex contrib/GeneFinder/nematode_gftables/gftables contrib/GeneFinder/nematode_gftables/newnem.atg contrib/GeneFinder/nematode_gftables/newnem.codon contrib/GeneFinder/nematode_gftables/newnem.gene contrib/GeneFinder/nematode_gftables/newnem.intron3 contrib/GeneFinder/nematode_gftables/newnem.intron5 contrib/GeneFinder/nematode_gftables/ref.hist contrib/GeneFinder/nematode_gftables/zk637.atg contrib/GeneFinder/nematode_gftables/zk637.intron3 contrib/GeneFinder/nematode_gftables/zk637.intron5 contrib/GeneFinder/nematode_gftables/zk637.trinuc contrib/import_ncbi_mv_hs.pl contrib/install_macosx/BuildConfig.pm contrib/install_macosx/README.html contrib/install_macosx/README.pod contrib/install_macosx/scripts/build-gbrowse.pl contrib/install_macosx/scripts/build-libraries.pl contrib/README contrib/SynView/cgi-lib/DAS/GUS.pm contrib/SynView/cgi-lib/DAS/GUS/Segment.pm contrib/SynView/cgi-lib/DAS/GUS/Segment/Feature.pm contrib/SynView/cgi-lib/DAS/Util/SqlParser.pm contrib/SynView/gbrowse.conf/plasmodb.conf contrib/SynView/gbrowse.conf/plasmodb.xml contrib/SynView/MAL11/MAL11.conf contrib/SynView/MAL11/MAL11.fa contrib/SynView/MAL11/MAL11.gff3 contrib/SynView/README contrib/TextDumper/README contrib/TextDumper/TextDumper.pm lib/Bio/DB/SeqFeature/Store/LoadHelper.pm Please inform the author. Checking prerequisites... recommends: * Bio::DB::BigFile is not installed * Bio::DB::Sam is not installed * Bio::Das is not installed * Crypt::SSLeay is not installed * DBD::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 '2.56' ./Build --install_base=debian/gbrowse install_slave NOTE: Run ./Build reconfig to change existing configuration. Performing variable substitutions in blib/conf/aws_balancer.conf Performing variable substitutions in blib/conf/detail_select_menu.conf Performing variable substitutions in blib/conf/enzymes.txt Performing variable substitutions in blib/conf/GBrowse.conf Performing variable substitutions in blib/conf/log4perl.conf Performing variable substitutions in blib/conf/MobyServices/moby.conf Performing variable substitutions in blib/conf/pop_demo.conf Performing variable substitutions in blib/conf/renderfarm.conf Performing variable substitutions in blib/conf/slave_preload.conf Performing variable substitutions in blib/conf/submitter_plugin.conf Performing variable substitutions in blib/conf/synteny/oryza.synconf.disabled.conf Performing variable substitutions in blib/conf/synteny/rice_synteny.conf Performing variable substitutions in blib/conf/synteny/wild_rice_synteny.conf Performing variable substitutions in blib/conf/themes/solid_gray_colors Performing variable substitutions in blib/conf/themes/transparent_colors Performing variable substitutions in blib/conf/themes/warm_colors Performing variable substitutions in blib/conf/volvox.conf Performing variable substitutions in blib/conf/yeast_chr1+2.conf Performing variable substitutions in blib/conf/yeast_renderfarm.conf Performing variable substitutions in blib/conf/yeast_simple.conf Performing variable substitutions in blib/htdocs/annotation_help.html Performing variable substitutions in blib/htdocs/cloud_index.html Performing variable substitutions in blib/htdocs/example_scripts/index.html Performing variable substitutions in blib/htdocs/example_scripts/README Performing variable substitutions in blib/htdocs/gbrowse_karyotype_help.html Performing variable substitutions in blib/htdocs/gbrowse_syn_help.html Performing variable substitutions in blib/htdocs/general_help.html Performing variable substitutions in blib/htdocs/index.html Performing variable substitutions in blib/htdocs/tutorial/conf_files/elegans_core.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/elegans_extra.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/HEADER.html Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_final.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_final_withPhylo.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_halfway.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_Phylo.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_quarter.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_refactored.conf Performing variable substitutions in blib/htdocs/tutorial/data_files/HEADER.html Performing variable substitutions in blib/htdocs/tutorial/tutorial.html Performing variable substitutions in blib/htdocs/tutorial/tutorial.phyTreeEdit.html Performing variable substitutions in blib/htdocs/vbox_index.html Performing variable substitutions in blib/etc/default/gbrowse-aws-balancer Use of uninitialized value $wwwuser in substitution (s///) at /<>/gbrowse-2.56+dfsg/install_util/GBrowseInstall.pm line 871, line 10. Performing variable substitutions in blib/etc/default/gbrowse-slave Performing variable substitutions in blib/etc/init.d/gbrowse-aws-balancer Performing variable substitutions in blib/etc/init.d/gbrowse-slave Use of uninitialized value $wwwuser in substitution (s///) at /<>/gbrowse-2.56+dfsg/install_util/GBrowseInstall.pm line 871, line 20. Building GBrowse Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing debian/gbrowse/etc/init.d/gbrowse-aws-balancer Installing debian/gbrowse/etc/init.d/gbrowse-slave Installing debian/gbrowse/etc/default/gbrowse-aws-balancer Installing debian/gbrowse/etc/default/gbrowse-slave Installing debian/gbrowse/lib/perl5/i686-linux-gnu-thread-multi-64int/GBrowse/ConfigData.pm mv debian/gbrowse/lib/perl5/* debian/gbrowse/usr/share/perl5 # Remove arch dependant data mkdir -p debian/gbrowse-calign/usr/lib/i386-linux-gnu/perl5/5.30/auto/Bio/Graphics/Browser2/CAlign/ mkdir -p debian/gbrowse-calign/usr/lib/i386-linux-gnu/perl5/5.30/Bio/Graphics/Browser2/ mv debian/gbrowse/usr/share/perl5/auto/Bio/Graphics/Browser2/CAlign/* debian/gbrowse-calign/usr/lib/i386-linux-gnu/perl5/5.30/auto/Bio/Graphics/Browser2/CAlign/ mv debian/gbrowse/usr/share/perl5/Bio/Graphics/Browser2/CAlign.pm debian/gbrowse-calign/usr/lib/i386-linux-gnu/perl5/5.30/Bio/Graphics/Browser2/CAlign.pm rm -rf debian/gbrowse/lib rm -f debian/gbrowse/usr/share/doc/gbrowse/INSTALL rm -f debian/gbrowse/usr/share/perl5/auto/GBrowse/.packlist rm -f debian/gbrowse/usr/share/gbrowse/htdocs/js/prototype.js rm -f debian/gbrowse/usr/share/gbrowse/htdocs/js/scriptaculous.js chmod 644 debian/gbrowse/etc/gbrowse/MobyServices/text_xml_renderer.pm chmod 644 debian/gbrowse/etc/gbrowse/synteny/oryza.synconf.disabled.conf #Remove database (kept as separate package) rm -rf debian/gbrowse/var/lib/gbrowse/databases/* #Rename pl scripts in bin file-rename 's/\.pl//' debian/gbrowse/bin/*.pl mv debian/gbrowse/bin debian/gbrowse/usr/bin # Activate configuration files. find /<>/gbrowse-2.56+dfsg/debian/gbrowse/etc -name '*.new' | xargs file-rename 's/.new//' rm -rf /<>/gbrowse-2.56+dfsg/debian/gbrowse/usr/share/perl5/auto # Update conf files sed -i 's/gbrowse2/gbrowse/g' /<>/gbrowse-2.56+dfsg/debian/gbrowse/etc/gbrowse/yeast*.conf sed -i 's/gbrowse2/gbrowse/g' /<>/gbrowse-2.56+dfsg/debian/gbrowse/etc/gbrowse/slave*.conf # move OpenID constumer secret to /etc/gbrowse to make it system admin configurable mv /<>/gbrowse-2.56+dfsg/debian/gbrowse/usr/share/perl5/GBrowse/ConfigData.pm /<>/gbrowse-2.56+dfsg/debian/gbrowse/etc/gbrowse/ConfigData.pm make[1]: Leaving directory '/<>/gbrowse-2.56+dfsg' dh_install -a dh_apache2 -a dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installman make[1]: Entering directory '/<>/gbrowse-2.56+dfsg' #Rename due to perl extension seen as polish file-rename 's/\.pl\.1p/\.1p/' debian/gbrowse/man/man1/*.pl.1p mkdir -p debian/gbrowse-calign/man/man3/ mv debian/gbrowse/man/man3/Bio::Graphics::Browser2::CAlign.3pm debian/gbrowse-calign/man/man3/Bio::Graphics::Browser2::CAlign.3pm dh_installman rm -rf debian/gbrowse/man rm -rf debian/gbrowse-calign/man make[1]: Leaving directory '/<>/gbrowse-2.56+dfsg' dh_lintian -a dh_perl -a debian/rules override_dh_link make[1]: Entering directory '/<>/gbrowse-2.56+dfsg' dh_link # Fix broken link ... even if I habe no idea what a link to a not existing dir should serve for ln -sf /var/cache/gbrowse/images debian/gbrowse/usr/share/gbrowse/htdocs/i make[1]: Leaving directory '/<>/gbrowse-2.56+dfsg' dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 pkgstriptranslations: processing gbrowse-calign (in debian/gbrowse-calign); do_strip: , oemstrip: pkgstriptranslations: processing gbrowse-calign-dbgsym (in debian/.debhelper/gbrowse-calign/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/gbrowse-calign/DEBIAN/control, package gbrowse-calign, directory debian/gbrowse-calign pkgstripfiles: Truncating usr/share/doc/gbrowse-calign/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package gbrowse-calign ... pkgstripfiles: No PNG files. dpkg-deb: building package 'gbrowse-calign' in '../gbrowse-calign_2.56+dfsg-4build1_i386.deb'. pkgstripfiles: processing control file: debian/.debhelper/gbrowse-calign/dbgsym-root/DEBIAN/control, package gbrowse-calign-dbgsym, directory debian/.debhelper/gbrowse-calign/dbgsym-root dpkg-deb: building package 'gbrowse-calign-dbgsym' in 'debian/.debhelper/scratch-space/build-gbrowse-calign/gbrowse-calign-dbgsym_2.56+dfsg-4build1_i386.deb'. Renaming gbrowse-calign-dbgsym_2.56+dfsg-4build1_i386.deb to gbrowse-calign-dbgsym_2.56+dfsg-4build1_i386.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../gbrowse_2.56+dfsg-4build1_i386.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20191026-1712 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ gbrowse_2.56+dfsg-4build1_i386.changes: --------------------------------------- Format: 1.8 Date: Sat, 19 Oct 2019 10:37:25 +0000 Source: gbrowse Binary: gbrowse-calign Architecture: i386 Version: 2.56+dfsg-4build1 Distribution: focal-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Matthias Klose Description: gbrowse-calign - CAlign helper Changes: gbrowse (2.56+dfsg-4build1) focal; urgency=medium . * No-change rebuild for the perl update. Checksums-Sha1: 17abb5f1bd04a6e186591432c2e2667d6683579d 30124 gbrowse-calign-dbgsym_2.56+dfsg-4build1_i386.ddeb baa41d264643eeb0cd2f20455e91019c68207e5a 15956 gbrowse-calign_2.56+dfsg-4build1_i386.deb edc09168efdbe1da2a0f49f95533f283939bb3fc 9188 gbrowse_2.56+dfsg-4build1_i386.buildinfo Checksums-Sha256: d65748c1e20a947329f168ad6c96af587c348a0e19972b6e63ef83766fd7d5c7 30124 gbrowse-calign-dbgsym_2.56+dfsg-4build1_i386.ddeb 42f49ea7b50a8c1bcab2bc4889b85e44e2f65cb3070bffdf61e04216e7e6734b 15956 gbrowse-calign_2.56+dfsg-4build1_i386.deb 6e79414ce0528c4ba83defd73d208c7fb01d847d7db2b5e26280fe6ff42a2455 9188 gbrowse_2.56+dfsg-4build1_i386.buildinfo Files: 052c8887c8e30a67e7b92c23863399ff 30124 debug optional gbrowse-calign-dbgsym_2.56+dfsg-4build1_i386.ddeb f36d0e96b7612dfaa1065648288e84bc 15956 science optional gbrowse-calign_2.56+dfsg-4build1_i386.deb 4e771098d2006f52b4617d9b33d977af 9188 science optional gbrowse_2.56+dfsg-4build1_i386.buildinfo +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ gbrowse-calign_2.56+dfsg-4build1_i386.deb ----------------------------------------- new debian package, version 2.0. size 15956 bytes: control archive=956 bytes. 710 bytes, 18 lines control 572 bytes, 6 lines md5sums Package: gbrowse-calign Source: gbrowse Version: 2.56+dfsg-4build1 Architecture: i386 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 64 Depends: perl (>= 5.30.0-8), perlapi-5.30.0, libc6 (>= 2.4), gbrowse Section: science Priority: optional Homepage: http://www.gbrowse.org/ Description: CAlign helper Generic Genome Browser is a simple but highly configurable web-based genome browser. It is a component of the Generic Model Organism Systems Database project (GMOD). . This package provides the CAlign helper for use with Realign. It speeds up Smith-Waterman alignment. drwxr-xr-x root/root 0 2019-10-19 10:37 ./ drwxr-xr-x root/root 0 2019-10-19 10:37 ./usr/ drwxr-xr-x root/root 0 2019-10-19 10:37 ./usr/lib/ drwxr-xr-x root/root 0 2019-10-19 10:37 ./usr/lib/i386-linux-gnu/ drwxr-xr-x root/root 0 2019-10-19 10:37 ./usr/lib/i386-linux-gnu/perl5/ drwxr-xr-x root/root 0 2019-10-19 10:37 ./usr/lib/i386-linux-gnu/perl5/5.30/ drwxr-xr-x root/root 0 2019-10-19 10:37 ./usr/lib/i386-linux-gnu/perl5/5.30/Bio/ drwxr-xr-x root/root 0 2019-10-19 10:37 ./usr/lib/i386-linux-gnu/perl5/5.30/Bio/Graphics/ drwxr-xr-x root/root 0 2019-10-19 10:37 ./usr/lib/i386-linux-gnu/perl5/5.30/Bio/Graphics/Browser2/ -rw-r--r-- root/root 1129 2019-10-19 10:37 ./usr/lib/i386-linux-gnu/perl5/5.30/Bio/Graphics/Browser2/CAlign.pm drwxr-xr-x root/root 0 2019-10-19 10:37 ./usr/lib/i386-linux-gnu/perl5/5.30/auto/ drwxr-xr-x root/root 0 2019-10-19 10:37 ./usr/lib/i386-linux-gnu/perl5/5.30/auto/Bio/ drwxr-xr-x root/root 0 2019-10-19 10:37 ./usr/lib/i386-linux-gnu/perl5/5.30/auto/Bio/Graphics/ drwxr-xr-x root/root 0 2019-10-19 10:37 ./usr/lib/i386-linux-gnu/perl5/5.30/auto/Bio/Graphics/Browser2/ drwxr-xr-x root/root 0 2019-10-19 10:37 ./usr/lib/i386-linux-gnu/perl5/5.30/auto/Bio/Graphics/Browser2/CAlign/ -rw-r--r-- root/root 0 2019-10-19 10:37 ./usr/lib/i386-linux-gnu/perl5/5.30/auto/Bio/Graphics/Browser2/CAlign/CAlign.bs -rw-r--r-- root/root 17768 2019-10-19 10:37 ./usr/lib/i386-linux-gnu/perl5/5.30/auto/Bio/Graphics/Browser2/CAlign/CAlign.so drwxr-xr-x root/root 0 2019-10-19 10:37 ./usr/share/ drwxr-xr-x root/root 0 2019-10-19 10:37 ./usr/share/doc/ drwxr-xr-x root/root 0 2019-10-19 10:37 ./usr/share/doc/gbrowse-calign/ -rw-r--r-- root/root 1566 2019-10-19 10:37 ./usr/share/doc/gbrowse-calign/changelog.Debian.gz -rw-r--r-- root/root 18041 2018-10-03 13:07 ./usr/share/doc/gbrowse-calign/copyright drwxr-xr-x root/root 0 2019-10-19 10:37 ./usr/share/man/ drwxr-xr-x root/root 0 2019-10-19 10:37 ./usr/share/man/man3/ -rw-r--r-- root/root 2159 2019-10-19 10:37 ./usr/share/man/man3/Bio::Graphics::Browser2::CAlign.3pm.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: i386 Build-Space: 33644 Build-Time: 28 Distribution: focal-proposed Host Architecture: i386 Install-Time: 17 Job: gbrowse_2.56+dfsg-4build1.dsc Machine Architecture: amd64 Package: gbrowse Package-Time: 46 Source-Version: 2.56+dfsg-4build1 Space: 33644 Status: successful Version: 2.56+dfsg-4build1 -------------------------------------------------------------------------------- Finished at 20191026-1712 Build needed 00:00:46, 33644k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=focal --arch=i386 PACKAGEBUILD-17934572 Scanning for processes to kill in build PACKAGEBUILD-17934572