gbrowse →
2.56+dfsg-3 →
armhf → 2017-09-25 22:46:05
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| gbrowse 2.56+dfsg-3 (armhf) Mon, 25 Sep 2017 22:39:35 +0000 |
+==============================================================================+
Package: gbrowse
Version: 2.56+dfsg-3
Source Version: 2.56+dfsg-3
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-ae1d6e0c-62e0-4571-8147-7fe17e80b387' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.2 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.1 MB]
Fetched 22.3 MB in 7s (2907 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'gbrowse' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/gbrowse.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/gbrowse.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 4383 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main gbrowse 2.56+dfsg-3 (dsc) [2676 B]
Get:2 http://172.17.0.1/private buster-staging/main gbrowse 2.56+dfsg-3 (tar) [4356 kB]
Get:3 http://172.17.0.1/private buster-staging/main gbrowse 2.56+dfsg-3 (diff) [23.9 kB]
Fetched 4383 kB in 0s (8166 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/gbrowse-VqR8EV/gbrowse-2.56+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/gbrowse-VqR8EV' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-UVd1eb/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-UVd1eb/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-UVd1eb/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-UVd1eb/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-UVd1eb/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-UVd1eb/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-UVd1eb/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-UVd1eb/apt_archive ./ Packages [431 B]
Fetched 2107 B in 0s (8466 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
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:
ca-certificates libsasl2-modules libssl1.1 openssl
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 72 not upgraded.
Need to get 772 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-UVd1eb/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [772 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 772 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15017 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: bioperl, debhelper (>= 10), 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 (>= 10), dh-apache2, dh-exec, apache2-dev, libbio-graphics-perl (>= 2.31), libbio-coordinate-perl, libcapture-tiny-perl, libcgi-session-perl, libgd-gd2-perl, libio-string-perl, libjson-perl, libstatistics-descriptive-perl, libwww-perl, libhttp-daemon-perl, perl, sqlite3, libdbd-sqlite3-perl, libterm-readkey-perl, libjs-prototype, libjs-scriptaculous, libvm-ec2-perl, libmodule-build-perl, libcgi-pm-perl, rename
dpkg-deb: building package 'sbuild-build-depends-gbrowse-dummy' in '/<<BUILDDIR>>/resolver-UVd1eb/apt_archive/sbuild-build-depends-gbrowse-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-gbrowse-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-UVd1eb/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-UVd1eb/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-UVd1eb/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-UVd1eb/apt_archive ./ Sources [697 B]
Get:5 copy:/<<BUILDDIR>>/resolver-UVd1eb/apt_archive ./ Packages [754 B]
Fetched 2784 B in 0s (10.9 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install gbrowse build dependencies (apt-based resolver)
-------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
libsasl2-modules
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
apache2-dev autoconf automake autopoint autotools-dev bioperl bsdmainutils
debhelper dh-autoreconf dh-exec dh-strip-nondeterminism 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 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 libdevel-stacktrace-perl 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 libhtml-parser-perl
libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl
libhttp-daemon-perl libhttp-date-perl libhttp-message-perl
libhttp-negotiate-perl libicu57 libio-html-perl libio-socket-ssl-perl
libio-string-perl libjbig0 libjpeg62-turbo libjs-prototype
libjs-scriptaculous libjson-perl libldap2-dev liblist-moreutils-perl
liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1
libmodule-build-perl libnet-http-perl libnet-ssleay-perl libperl5.26
libpipeline1 libsctp-dev libsctp1 libsigsegv2 libsqlite3-0
libstatistics-descriptive-perl libstring-approx-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 liburi-perl libuuid1 libvm-ec2-perl
libwebp6 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 perl-base perl-modules-5.26 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 less www-browser perl-doc
libterm-readline-gnu-perl | libterm-readline-perl-perl libmail-box-perl
sqlite3-doc
Recommended packages:
bioperl-run perl-doc libcache-cache-perl libbio-perl-run-perl
libapache-dbi-perl libyaml-perl libace-perl libxml-twig-perl
libset-scalar-perl curl | wget | lynx-cur 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 libltdl-dev uuid-runtime
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 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 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 libdevel-stacktrace-perl 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 libhtml-parser-perl
libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl
libhttp-daemon-perl libhttp-date-perl libhttp-message-perl
libhttp-negotiate-perl libicu57 libio-html-perl libio-socket-ssl-perl
libio-string-perl libjbig0 libjpeg62-turbo libjs-prototype
libjs-scriptaculous libjson-perl 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
libsctp-dev libsctp1 libsigsegv2 libstatistics-descriptive-perl
libstring-approx-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 liburi-perl libvm-ec2-perl libwebp6 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
The following packages will be upgraded:
libperl5.26 libsqlite3-0 libuuid1 perl perl-base perl-modules-5.26
6 upgraded, 123 newly installed, 0 to remove and 66 not upgraded.
Need to get 45.1 MB of archives.
After this operation, 128 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-UVd1eb/apt_archive ./ sbuild-build-depends-gbrowse-dummy 0.invalid.0 [962 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libperl5.26 armhf 5.26.0-8 [2885 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf perl armhf 5.26.0-8 [201 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf perl-base armhf 5.26.0-8 [1239 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf perl-modules-5.26 all 5.26.0-8 [2822 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.6-2 [95.8 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 9.0.12+nmu1 [178 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.4.2-1 [24.2 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libuuid1 armhf 2.29.2-5 [69.7 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libsqlite3-0 armhf 3.20.1-1 [500 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf netbase all 5.4 [19.1 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.32-1 [225 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.32-1 [105 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.32-1 [63.7 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-4 [117 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-6 [7427 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-4 [609 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf ucf all 3.0036 [70.2 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libapr1 armhf 1.6.2-1 [82.3 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf uuid-dev armhf 2.29.2-5 [83.7 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libsctp1 armhf 1.0.17+dfsg-1 [27.3 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libsctp-dev armhf 1.0.17+dfsg-1 [82.6 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libapr1-dev armhf 1.6.2-1 [687 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libexpat1 armhf 2.2.3-1 [67.1 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libaprutil1 armhf 1.6.0-2 [82.0 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libldap2-dev armhf 2.4.45+dfsg-1 [297 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libexpat1-dev armhf 2.2.3-1 [120 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libaprutil1-dev armhf 1.6.0-2 [396 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.11-1 [29.3 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3 [736 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-4 [434 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 14 [15.9 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.038-1 [17.6 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.038-1 [11.1 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.54.0-1 [2650 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-1 [132 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-4 [1218 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf debhelper all 10.8 [973 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf apache2-dev armhf 2.4.27-5 [318 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libio-string-perl all 1.08-3 [12.3 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libdata-stag-perl all 0.14-2 [448 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libbio-perl-perl all 1.7.1-3 [4591 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libclass-data-inheritable-perl all 0.08-2 [9296 B]
Get:54 http://172.17.0.1/private buster-staging/main armhf libdevel-stacktrace-perl all 2.0200-1 [27.3 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libexception-class-perl all 1.42-1 [31.5 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libtest-deep-perl all 1.127-1 [48.5 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libcapture-tiny-perl all 0.46-1 [25.7 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf libalgorithm-diff-perl all 1.19.03-1 [48.7 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libtext-diff-perl all 1.44-1 [27.4 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libtest-differences-perl all 0.64-1 [18.0 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libsub-uplevel-perl all 0.2800-1 [16.3 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf libtest-exception-perl all 0.43-1 [18.7 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libtest-warn-perl all 0.32-1 [15.1 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libtest-most-perl all 0.35-1 [24.5 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf bioperl all 1.7.1-3 [421 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf fonts-dejavu-core all 2.37-1 [1068 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf fontconfig-config all 2.12.3-0.2 [304 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libanyevent-perl armhf 7.130-2+b1 [391 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libanyevent-cachedns-perl all 0.08-2 [7150 B]
Get:70 http://172.17.0.1/private buster-staging/main armhf libcommon-sense-perl armhf 3.74-2+b1 [23.9 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libanyevent-http-perl all 2.23-1 [34.6 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libbio-coordinate-perl all 1.7.1-2 [55.9 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libfreetype6 armhf 2.8-0.2 [393 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libfontconfig1 armhf 2.12.3-0.2 [349 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libjpeg62-turbo armhf 1:1.5.2-2 [110 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libjbig0 armhf 2.1-3.1+b2 [27.6 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libtiff5 armhf 4.0.8-5 [218 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf libwebp6 armhf 0.6.0-3 [217 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf libxcb1 armhf 1.12-1 [129 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf libx11-data all 2:1.6.4-3 [290 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf libx11-6 armhf 2:1.6.4-3 [683 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf libxpm4 armhf 1:3.5.12-1 [43.6 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf libgd3 armhf 2.2.5-3 [115 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf libgd-perl armhf 2.66-1+b1 [173 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf libbio-graphics-perl all 2.40-2 [610 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf libhtml-tagset-perl all 3.20-3 [12.7 kB]
Get:89 http://172.17.0.1/private buster-staging/main armhf liburi-perl all 1.72-1 [88.7 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf libhtml-parser-perl armhf 3.72-3+b1 [101 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf libcgi-pm-perl all 4.36-1 [222 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf libcgi-session-perl all 4.48-3 [119 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf libdbi-perl armhf 1.637-1 [760 kB]
Get:94 http://172.17.0.1/private buster-staging/main armhf libdbd-sqlite3-perl armhf 1.54-2 [157 kB]
Get:95 http://172.17.0.1/private buster-staging/main armhf libencode-locale-perl all 1.05-1 [13.7 kB]
Get:96 http://172.17.0.1/private buster-staging/main armhf libexporter-tiny-perl all 0.042-1 [32.4 kB]
Get:97 http://172.17.0.1/private buster-staging/main armhf libhttp-date-perl all 6.02-1 [10.7 kB]
Get:98 http://172.17.0.1/private buster-staging/main armhf libfile-listing-perl all 6.04-1 [10.3 kB]
Get:99 http://172.17.0.1/private buster-staging/main armhf libhtml-tree-perl all 5.03-2 [210 kB]
Get:100 http://172.17.0.1/private buster-staging/main armhf libio-html-perl all 1.001-1 [17.6 kB]
Get:101 http://172.17.0.1/private buster-staging/main armhf liblwp-mediatypes-perl all 6.02-1 [22.1 kB]
Get:102 http://172.17.0.1/private buster-staging/main armhf libhttp-message-perl all 6.13-1 [71.6 kB]
Get:103 http://172.17.0.1/private buster-staging/main armhf libhttp-cookies-perl all 6.01-1 [17.4 kB]
Get:104 http://172.17.0.1/private buster-staging/main armhf libhttp-daemon-perl all 6.01-1 [17.3 kB]
Get:105 http://172.17.0.1/private buster-staging/main armhf libhttp-negotiate-perl all 6.00-2 [13.6 kB]
Get:106 http://172.17.0.1/private buster-staging/main armhf perl-openssl-defaults armhf 3 [6782 B]
Get:107 http://172.17.0.1/private buster-staging/main armhf libnet-ssleay-perl armhf 1.80-1+b1 [270 kB]
Get:108 http://172.17.0.1/private buster-staging/main armhf libio-socket-ssl-perl all 2.051-1 [201 kB]
Get:109 http://172.17.0.1/private buster-staging/main armhf libjs-prototype all 1.7.1-3 [44.3 kB]
Get:110 http://172.17.0.1/private buster-staging/main armhf libjs-scriptaculous all 1.9.0-2 [129 kB]
Get:111 http://172.17.0.1/private buster-staging/main armhf libjson-perl all 2.94-1 [80.2 kB]
Get:112 http://172.17.0.1/private buster-staging/main armhf liblist-moreutils-perl armhf 0.416-1+b2 [59.2 kB]
Get:113 http://172.17.0.1/private buster-staging/main armhf libnet-http-perl all 6.16-1 [24.2 kB]
Get:114 http://172.17.0.1/private buster-staging/main armhf libwww-robotrules-perl all 6.01-1 [14.3 kB]
Get:115 http://172.17.0.1/private buster-staging/main armhf libwww-perl all 6.15-2 [184 kB]
Get:116 http://172.17.0.1/private buster-staging/main armhf liblwp-protocol-https-perl all 6.07-2 [9242 B]
Get:117 http://172.17.0.1/private buster-staging/main armhf libmodule-build-perl all 0.422400-1 [259 kB]
Get:118 http://172.17.0.1/private buster-staging/main armhf libstatistics-descriptive-perl all 3.0612-1 [41.9 kB]
Get:119 http://172.17.0.1/private buster-staging/main armhf libstring-approx-perl armhf 3.27-1+b5 [38.2 kB]
Get:120 http://172.17.0.1/private buster-staging/main armhf libterm-readkey-perl armhf 2.37-1+b1 [26.6 kB]
Get:121 http://172.17.0.1/private buster-staging/main armhf libxml-namespacesupport-perl all 1.11-1 [14.8 kB]
Get:122 http://172.17.0.1/private buster-staging/main armhf libxml-sax-base-perl all 1.09-1 [20.4 kB]
Get:123 http://172.17.0.1/private buster-staging/main armhf libxml-sax-perl all 0.99+dfsg-2 [68.3 kB]
Get:124 http://172.17.0.1/private buster-staging/main armhf libxml-libxml-perl armhf 2.0128+dfsg-3 [319 kB]
Get:125 http://172.17.0.1/private buster-staging/main armhf libxml-simple-perl all 2.24-1 [70.7 kB]
Get:126 http://172.17.0.1/private buster-staging/main armhf libvm-ec2-perl all 1.28-2 [768 kB]
Get:127 http://172.17.0.1/private buster-staging/main armhf rename all 0.20-6 [12.8 kB]
Get:128 http://172.17.0.1/private buster-staging/main armhf sqlite3 armhf 3.20.1-1 [736 kB]
Get:129 http://172.17.0.1/private buster-staging/main armhf dh-exec armhf 0.23 [24.9 kB]
debconf: delaying package configuration, since apt-utils is not installed
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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'
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Setting up libldap2-dev:armhf (2.4.45+dfsg-1) ...
Setting up libapr1:armhf (1.6.2-1) ...
Setting up libexpat1:armhf (2.2.3-1) ...
Setting up libjpeg62-turbo:armhf (1:1.5.2-2) ...
Setting up libsctp1:armhf (1.0.17+dfsg-1) ...
Setting up libjbig0:armhf (2.1-3.1+b2) ...
Setting up libsigsegv2:armhf (2.11-1) ...
Setting up fonts-dejavu-core (2.37-1) ...
Setting up perl-openssl-defaults:armhf (3) ...
Setting up groff-base (1.22.3-9) ...
Setting up libglib2.0-0:armhf (2.54.0-1) ...
No schema files found: doing nothing.
Setting up uuid-dev:armhf (2.29.2-5) ...
Setting up libtiff5:armhf (4.0.8-5) ...
Setting up gettext-base (0.19.8.1-4) ...
Setting up libpipeline1:armhf (1.4.2-1) ...
Setting up perl-modules-5.26 (5.26.0-8) ...
Setting up m4 (1.4.18-1) ...
Setting up libicu57:armhf (57.1-6) ...
Setting up libbsd0:armhf (0.8.6-2) ...
Setting up ucf (3.0036) ...
Setting up libxml2:armhf (2.9.4+dfsg1-4) ...
Setting up sqlite3 (3.20.1-1) ...
Setting up libfreetype6:armhf (2.8-0.2) ...
Setting up libmagic-mgc (1:5.32-1) ...
Setting up libmagic1:armhf (1:5.32-1) ...
Setting up libcroco3:armhf (0.6.12-1) ...
Processing triggers for libc-bin (2.24-14) ...
Setting up libperl5.26:armhf (5.26.0-8) ...
Setting up autotools-dev (20161112.1) ...
Setting up libaprutil1:armhf (1.6.0-2) ...
Setting up libexpat1-dev:armhf (2.2.3-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up bsdmainutils (9.0.12+nmu1) ...
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
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Setting up autopoint (0.19.8.1-4) ...
Setting up netbase (5.4) ...
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Setting up libsctp-dev (1.0.17+dfsg-1) ...
Setting up fontconfig-config (2.12.3-0.2) ...
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Setting up gettext (0.19.8.1-4) ...
Setting up libaprutil1-dev (1.6.0-2) ...
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Setting up file (1:5.32-1) ...
Setting up perl (5.26.0-8) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
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Setting up liblwp-mediatypes-perl (6.02-1) ...
Setting up liburi-perl (1.72-1) ...
Setting up libio-string-perl (1.08-3) ...
Setting up libalgorithm-diff-perl (1.19.03-1) ...
Setting up man-db (2.7.6.1-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libnet-http-perl (6.16-1) ...
Setting up libmodule-build-perl (0.422400-1) ...
Setting up libstring-approx-perl (3.27-1+b5) ...
Setting up libjson-perl (2.94-1) ...
Setting up libsub-uplevel-perl (0.2800-1) ...
Setting up libwww-robotrules-perl (6.01-1) ...
Setting up libxcb1:armhf (1.12-1) ...
Setting up libdbi-perl (1.637-1) ...
Setting up libdata-stag-perl (0.14-2) ...
Setting up libtest-warn-perl (0.32-1) ...
Setting up libhtml-tagset-perl (3.20-3) ...
Setting up libtool (2.4.6-2) ...
Setting up libfontconfig1:armhf (2.12.3-0.2) ...
Setting up libtest-deep-perl (1.127-1) ...
Setting up libcommon-sense-perl (3.74-2+b1) ...
Setting up libclass-data-inheritable-perl (0.08-2) ...
Setting up libarchive-zip-perl (1.59-1) ...
Setting up libdbd-sqlite3-perl (1.54-2) ...
Setting up libbio-perl-perl (1.7.1-3) ...
Setting up po-debconf (1.0.20) ...
Setting up libxml-namespacesupport-perl (1.11-1) ...
Setting up libanyevent-perl (7.130-2+b1) ...
Setting up libencode-locale-perl (1.05-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up rename (0.20-6) ...
update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode
Setting up libnet-ssleay-perl (1.80-1+b1) ...
Setting up libdevel-stacktrace-perl (2.0200-1) ...
Setting up libtext-diff-perl (1.44-1) ...
Setting up libtest-exception-perl (0.43-1) ...
Setting up libcapture-tiny-perl (0.46-1) ...
Setting up libio-html-perl (1.001-1) ...
Setting up libexporter-tiny-perl (0.042-1) ...
Setting up libx11-6:armhf (2:1.6.4-3) ...
Setting up autoconf (2.69-11) ...
Setting up libio-socket-ssl-perl (2.051-1) ...
Setting up libterm-readkey-perl (2.37-1+b1) ...
Setting up libanyevent-http-perl (2.23-1) ...
Setting up libhtml-parser-perl (3.72-3+b1) ...
Setting up automake (1:1.15.1-3) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up libcgi-pm-perl (4.36-1) ...
Setting up libxpm4:armhf (1:3.5.12-1) ...
Setting up libanyevent-cachedns-perl (0.08-2) ...
Setting up libfile-stripnondeterminism-perl (0.038-1) ...
Setting up libxml-sax-perl (0.99+dfsg-2) ...
update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...
Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version
Setting up liblist-moreutils-perl (0.416-1+b2) ...
Setting up libstatistics-descriptive-perl (3.0612-1) ...
Setting up libhttp-date-perl (6.02-1) ...
Setting up libcgi-session-perl (4.48-3) ...
Setting up libtest-differences-perl (0.64-1) ...
Setting up libexception-class-perl (1.42-1) ...
Setting up libgd3:armhf (2.2.5-3) ...
Setting up libgd-perl (2.66-1+b1) ...
Setting up libhtml-tree-perl (5.03-2) ...
Setting up libfile-listing-perl (6.04-1) ...
Setting up libhttp-message-perl (6.13-1) ...
Setting up libxml-libxml-perl (2.0128+dfsg-3) ...
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 libhttp-negotiate-perl (6.00-2) ...
Setting up libtest-most-perl (0.35-1) ...
Setting up libhttp-cookies-perl (6.01-1) ...
Setting up libhttp-daemon-perl (6.01-1) ...
Setting up libxml-simple-perl (2.24-1) ...
Setting up bioperl (1.7.1-3) ...
Setting up libbio-graphics-perl (2.40-2) ...
Setting up libbio-coordinate-perl (1.7.1-2) ...
Setting up dh-autoreconf (14) ...
Setting up liblwp-protocol-https-perl (6.07-2) ...
Setting up dh-strip-nondeterminism (0.038-1) ...
Setting up libwww-perl (6.15-2) ...
Setting up debhelper (10.8) ...
Setting up libvm-ec2-perl (1.28-2) ...
Setting up dh-exec (0.23) ...
Setting up apache2-dev (2.4.27-5) ...
Setting up sbuild-build-depends-gbrowse-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-14) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-79-generic armhf (armv8l)
Toolchain package versions: binutils_2.29-4+rpi1 dpkg-dev_1.18.24 g++-7_7.2.0-1 gcc-7_7.2.0-1 libc6-dev_2.24-14 libstdc++-7-dev_7.2.0-1 libstdc++6_7.2.0-1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.116 apache2-dev_2.4.27-5 apt_1.5~rc1 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20161112.1 base-files_10+rpi1 base-passwd_3.5.43 bash_4.4-5 binutils_2.29-4+rpi1 bioperl_1.7.1-3 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-2+rpi1 build-essential_12.3 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.26-3 cpio_2.11+dfsg-6 cpp_4:7.1.0-2 cpp-7_7.2.0-1 dash_0.5.8-2.5 debconf_1.5.63 debhelper_10.8 debianutils_4.8.2 dh-autoreconf_14 dh-exec_0.23 dh-strip-nondeterminism_0.038-1 diffutils_1:3.6-1 dirmngr_2.1.23-2 dmsetup_2:1.02.142-1 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.6-1 e2fsprogs_1.43.6-1 fakeroot_1.22-1 file_1:5.32-1 findutils_4.6.0+git+20170729-2 fontconfig-config_2.12.3-0.2 fonts-dejavu-core_2.37-1 g++_4:7.1.0-2 g++-7_7.2.0-1 gcc_4:7.1.0-2 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-5-base_5.4.1-4 gcc-7_7.2.0-1 gcc-7-base_7.2.0-1 gettext_0.19.8.1-4 gettext-base_0.19.8.1-4 gnupg_2.1.23-2 gnupg-agent_2.1.23-2 gnupg-l10n_2.1.23-2 gnupg-utils_2.1.23-2 gpg_2.1.23-2 gpg-agent_2.1.23-2 gpg-wks-client_2.1.23-2 gpg-wks-server_2.1.23-2 gpgconf_2.1.23-2 gpgsm_2.1.23-2 gpgv_2.1.23-2 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5 hostname_3.18 init-system-helpers_1.49 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_24-1 libacl1_2.2.52-3 libalgorithm-diff-perl_1.19.03-1 libanyevent-cachedns-perl_0.08-2 libanyevent-http-perl_2.23-1 libanyevent-perl_7.130-2+b1 libapparmor1_2.11.0-10 libapr1_1.6.2-1 libapr1-dev_1.6.2-1 libaprutil1_1.6.0-2 libaprutil1-dev_1.6.0-2 libapt-pkg5.0_1.5~rc1 libarchive-zip-perl_1.59-1 libasan4_7.2.0-1 libassuan0_2.4.3-3 libatomic1_7.2.0-1 libattr1_1:2.4.47-2 libaudit-common_1:2.7.7-1 libaudit1_1:2.7.7-1+b1 libbio-coordinate-perl_1.7.1-2 libbio-graphics-perl_2.40-2 libbio-perl-perl_1.7.1-3 libblkid1_2.29.2-2+rpi1 libbsd0_0.8.6-2 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-14 libc-dev-bin_2.24-14 libc6_2.24-14 libc6-dev_2.24-14 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcapture-tiny-perl_0.46-1 libcc1-0_7.2.0-1 libcgi-pm-perl_4.36-1 libcgi-session-perl_4.48-3 libcilkrts5_7.2.0-1 libclass-data-inheritable-perl_0.08-2 libcomerr2_1.43.6-1 libcommon-sense-perl_3.74-2+b1 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.3-4 libdata-stag-perl_0.14-2 libdb5.3_5.3.28-13+rpi1 libdbd-sqlite3-perl_1.54-2 libdbi-perl_1.637-1 libdbus-1-3_1.11.16+really1.10.22-1 libdebconfclient0_0.229 libdevel-stacktrace-perl_2.0200-1 libdevmapper1.02.1_2:1.02.142-1 libdpkg-perl_1.18.24 libdrm-common_2.4.82-1+rpi1 libdrm2_2.4.82-1+rpi1 libencode-locale-perl_1.05-1 libexception-class-perl_1.42-1 libexpat1_2.2.3-1 libexpat1-dev_2.2.3-1 libexporter-tiny-perl_0.042-1 libfakeroot_1.22-1 libfdisk1_2.29.2-2+rpi1 libffi6_3.2.1-6 libfile-listing-perl_6.04-1 libfile-stripnondeterminism-perl_0.038-1 libfontconfig1_2.12.3-0.2 libfreetype6_2.8-0.2 libgcc-7-dev_7.2.0-1 libgcc1_1:7.2.0-1 libgcrypt20_1.7.9-1 libgd-perl_2.66-1+b1 libgd3_2.2.5-3 libgdbm3_1.8.3-14 libglib2.0-0_2.54.0-1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.15-2 libgomp1_7.2.0-1 libgpg-error0_1.27-3 libhogweed4_3.3-1 libhtml-parser-perl_3.72-3+b1 libhtml-tagset-perl_3.20-3 libhtml-tree-perl_5.03-2 libhttp-cookies-perl_6.01-1 libhttp-daemon-perl_6.01-1 libhttp-date-perl_6.02-1 libhttp-message-perl_6.13-1 libhttp-negotiate-perl_6.00-2 libicu57_57.1-6 libidn11_1.33-1 libidn2-0_2.0.2-3 libio-html-perl_1.001-1 libio-socket-ssl-perl_2.051-1 libio-string-perl_1.08-3 libip4tc0_1.6.1-2 libisl15_0.18-1 libjbig0_2.1-3.1+b2 libjpeg62-turbo_1:1.5.2-2 libjs-prototype_1.7.1-3 libjs-scriptaculous_1.9.0-2 libjson-perl_2.94-1 libklibc_2.0.4-9+rpi1 libkmod2_24-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 libldap2-dev_2.4.45+dfsg-1 liblist-moreutils-perl_0.416-1+b2 liblwp-mediatypes-perl_6.02-1 liblwp-protocol-https-perl_6.07-2 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-1 libmagic1_1:5.32-1 libmodule-build-perl_0.422400-1 libmount1_2.29.2-2+rpi1 libmpc3_1.0.3-1+b2 libmpfr4_3.1.6~rc1-1 libncurses5_6.0+20170715-2 libncursesw5_6.0+20170715-2 libnet-http-perl_6.16-1 libnet-ssleay-perl_1.80-1+b1 libnettle6_3.3-1 libnih-dbus1_1.0.3-8 libnih1_1.0.3-8 libnpth0_1.5-2 libp11-kit0_0.23.7-3 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre3_2:8.39-4 libperl5.24_5.24.1-7 libperl5.26_5.26.0-8 libpipeline1_1.4.2-1 libplymouth4_0.9.2-5 libpng16-16_1.6.32-1 libprocps6_2:3.3.12-3 libreadline5_5.2+dfsg-3 libreadline7_7.0-3 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libsctp-dev_1.0.17+dfsg-1 libsctp1_1.0.17+dfsg-1 libseccomp2_2.3.1-2.1 libselinux1_2.6-3 libsemanage-common_2.6-2 libsemanage1_2.6-2 libsepol1_2.6-2 libsigsegv2_2.11-1 libsmartcols1_2.29.2-2+rpi1 libsqlite3-0_3.20.1-1 libss2_1.43.6-1 libssl1.1_1.1.0f-5 libstatistics-descriptive-perl_3.0612-1 libstdc++-7-dev_7.2.0-1 libstdc++6_7.2.0-1 libstring-approx-perl_3.27-1+b5 libsub-uplevel-perl_0.2800-1 libsystemd0_234-2.3 libtasn1-6_4.12-2.1 libterm-readkey-perl_2.37-1+b1 libtest-deep-perl_1.127-1 libtest-differences-perl_0.64-1 libtest-exception-perl_0.43-1 libtest-most-perl_0.35-1 libtest-warn-perl_0.32-1 libtext-diff-perl_1.44-1 libtiff5_4.0.8-5 libtimedate-perl_2.3000-2 libtinfo5_6.0+20170715-2 libtool_2.4.6-2 libubsan0_7.2.0-1 libudev1_234-2.3 libunistring2_0.9.7-2 liburi-perl_1.72-1 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-5 libvm-ec2-perl_1.28-2 libwebp6_0.6.0-3 libwww-perl_6.15-2 libwww-robotrules-perl_6.01-1 libx11-6_2:1.6.4-3 libx11-data_2:1.6.4-3 libxau6_1:1.0.8-1+b2 libxcb1_1.12-1 libxdmcp6_1:1.1.2-3 libxml-libxml-perl_2.0128+dfsg-3 libxml-namespacesupport-perl_1.11-1 libxml-sax-base-perl_1.09-1 libxml-sax-perl_0.99+dfsg-2 libxml-simple-perl_2.24-1 libxml2_2.9.4+dfsg1-4 libxpm4_1:3.5.12-1 linux-base_4.5 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.4-4.1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 mawk_1.3.3-17 mount_2.29.2-2+rpi1 mountall_2.54 multiarch-support_2.24-14 ncurses-base_6.0+20170715-2 ncurses-bin_6.0+20170715-2 netbase_5.4 openssl_1.1.0f-5 passwd_1:4.4-4.1 patch_2.7.5-1 perl_5.26.0-8 perl-base_5.26.0-8 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.0-8 perl-openssl-defaults_3 pinentry-curses_1.0.0-2 plymouth_0.9.2-5 po-debconf_1.0.20 procps_2:3.3.12-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 rename_0.20-6 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gbrowse-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.10 sqlite3_3.20.1-1 systemd_234-2.3 sysvinit-utils_2.88dsf-59.9 tar_1.29b-2 tzdata_2017b-2 ucf_3.0036 udev_234-2.3 util-linux_2.29.2-2+rpi1 uuid-dev_2.29.2-5 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Fri Sep 15 21:47:22 2017 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tillea@rki.de"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./gbrowse_2.56+dfsg-3.dsc
dpkg-source: info: extracting gbrowse in /<<BUILDDIR>>/gbrowse-2.56+dfsg
dpkg-source: info: unpacking gbrowse_2.56+dfsg.orig.tar.gz
dpkg-source: info: unpacking gbrowse_2.56+dfsg-3.debian.tar.xz
dpkg-source: info: applying debian-packaging-patch
dpkg-source: info: applying gbrowse-slave-fix_defaults_path
dpkg-source: info: applying manpages.patch
dpkg-source: info: applying fix_pop_url
dpkg-source: info: applying 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 disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-ae1d6e0c-62e0-4571-8147-7fe17e80b387
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package gbrowse
dpkg-buildpackage: info: source version 2.56+dfsg-3
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build gbrowse-2.56+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --with apache2
dh_auto_clean
dh_autoreconf_clean
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 '/<<BUILDDIR>>/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 -I. Build.PL --installdirs vendor --config "optimize=-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/gbrowse-2.56+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" --config "ld=arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/gbrowse-2.56+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now" --conf=/etc/gbrowse --htdocs=/usr/share/gbrowse/htdocs --tmp=/var/cache/gbrowse --databases=/var/lib/gbrowse/databases --cgibin=/usr/lib/cgi-bin/gbrowse --www-user=www-data --registration_done=1 --persistent=/var/lib/gbrowse
WARNING: the following files are missing in your kit:
contrib/ace2gff.pl
contrib/AxtPairwise_convert/axt2phy.pl
contrib/blast2gff.pl
contrib/conf_files/01.yeast.conf
contrib/conf_files/02.wormbase.conf
contrib/conf_files/03.fly.conf
contrib/conf_files/04.human.conf
contrib/conf_files/05.embl_proxy.conf
contrib/conf_files/06.biosql.conf
contrib/conf_files/07.chado.conf
contrib/conf_files/08.genbank.conf
contrib/conf_files/09.human_karyotype.conf
contrib/conf_files/index.html
contrib/conf_files/wormbase.syn
contrib/Coverage/INSTALL
contrib/Coverage/plugin/Coverage.pm
contrib/Coverage/README
contrib/gdump.pl
contrib/GeneFinder/genefinder/gfcode.c
contrib/GeneFinder/genefinder/README
contrib/GeneFinder/genefinder/readseq.c
contrib/GeneFinder/genefinder/readseq.h
contrib/GeneFinder/nematode_gftables/cds.hex
contrib/GeneFinder/nematode_gftables/gftables
contrib/GeneFinder/nematode_gftables/newnem.atg
contrib/GeneFinder/nematode_gftables/newnem.codon
contrib/GeneFinder/nematode_gftables/newnem.gene
contrib/GeneFinder/nematode_gftables/newnem.intron3
contrib/GeneFinder/nematode_gftables/newnem.intron5
contrib/GeneFinder/nematode_gftables/ref.hist
contrib/GeneFinder/nematode_gftables/zk637.atg
contrib/GeneFinder/nematode_gftables/zk637.intron3
contrib/GeneFinder/nematode_gftables/zk637.intron5
contrib/GeneFinder/nematode_gftables/zk637.trinuc
contrib/import_ncbi_mv_hs.pl
contrib/install_macosx/BuildConfig.pm
contrib/install_macosx/README.html
contrib/install_macosx/README.pod
contrib/install_macosx/scripts/build-gbrowse.pl
contrib/install_macosx/scripts/build-libraries.pl
contrib/README
contrib/SynView/cgi-lib/DAS/GUS.pm
contrib/SynView/cgi-lib/DAS/GUS/Segment.pm
contrib/SynView/cgi-lib/DAS/GUS/Segment/Feature.pm
contrib/SynView/cgi-lib/DAS/Util/SqlParser.pm
contrib/SynView/gbrowse.conf/plasmodb.conf
contrib/SynView/gbrowse.conf/plasmodb.xml
contrib/SynView/MAL11/MAL11.conf
contrib/SynView/MAL11/MAL11.fa
contrib/SynView/MAL11/MAL11.gff3
contrib/SynView/README
contrib/TextDumper/README
contrib/TextDumper/TextDumper.pm
lib/Bio/DB/SeqFeature/Store/LoadHelper.pm
Please inform the author.
Checking prerequisites...
recommends:
* Bio::DB::BigFile is not installed
* Bio::DB::Sam is not installed
* Bio::Das is not installed
* Crypt::SSLeay is not installed
* DBD::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 '/<<BUILDDIR>>/gbrowse-2.56+dfsg'
dh_auto_build -a
perl Build
NOTE: Run ./Build reconfig to change existing configuration.
Building GBrowse
arm-linux-gnueabihf-gcc -I/<<BUILDDIR>>/gbrowse-2.56+dfsg/libalign -I/usr/lib/arm-linux-gnueabihf/perl/5.26/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=/<<BUILDDIR>>/gbrowse-2.56+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/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')
arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/gbrowse-2.56+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -shared -L/usr/local/lib -fstack-protector-strong -o blib/arch/auto/Bio/Graphics/Browser2/CAlign/CAlign.so lib/Bio/Graphics/Browser2/CAlign.o
Performing variable substitutions in blib/conf/aws_balancer.conf
Performing variable substitutions in blib/conf/detail_select_menu.conf
Performing variable substitutions in blib/conf/enzymes.txt
Performing variable substitutions in blib/conf/GBrowse.conf
Performing variable substitutions in blib/conf/log4perl.conf
Performing variable substitutions in blib/conf/MobyServices/moby.conf
Performing variable substitutions in blib/conf/pop_demo.conf
Performing variable substitutions in blib/conf/renderfarm.conf
Performing variable substitutions in blib/conf/slave_preload.conf
Performing variable substitutions in blib/conf/submitter_plugin.conf
Performing variable substitutions in blib/conf/synteny/oryza.synconf.disabled.conf
Performing variable substitutions in blib/conf/synteny/rice_synteny.conf
Performing variable substitutions in blib/conf/synteny/wild_rice_synteny.conf
Performing variable substitutions in blib/conf/themes/solid_gray_colors
Performing variable substitutions in blib/conf/themes/transparent_colors
Performing variable substitutions in blib/conf/themes/warm_colors
Performing variable substitutions in blib/conf/volvox.conf
Performing variable substitutions in blib/conf/yeast_chr1+2.conf
Performing variable substitutions in blib/conf/yeast_renderfarm.conf
Performing variable substitutions in blib/conf/yeast_simple.conf
Performing variable substitutions in blib/htdocs/annotation_help.html
Performing variable substitutions in blib/htdocs/cloud_index.html
Performing variable substitutions in blib/htdocs/example_scripts/index.html
Performing variable substitutions in blib/htdocs/example_scripts/README
Performing variable substitutions in blib/htdocs/gbrowse_karyotype_help.html
Performing variable substitutions in blib/htdocs/gbrowse_syn_help.html
Performing variable substitutions in blib/htdocs/general_help.html
Performing variable substitutions in blib/htdocs/index.html
Performing variable substitutions in blib/htdocs/tutorial/conf_files/elegans_core.conf
Performing variable substitutions in blib/htdocs/tutorial/conf_files/elegans_extra.conf
Performing variable substitutions in blib/htdocs/tutorial/conf_files/HEADER.html
Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox.conf
Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_final.conf
Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_final_withPhylo.conf
Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_halfway.conf
Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_Phylo.conf
Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_quarter.conf
Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_refactored.conf
Performing variable substitutions in blib/htdocs/tutorial/data_files/HEADER.html
Performing variable substitutions in blib/htdocs/tutorial/tutorial.html
Performing variable substitutions in blib/htdocs/tutorial/tutorial.phyTreeEdit.html
Performing variable substitutions in blib/htdocs/vbox_index.html
Use of uninitialized value in pattern match (m//) at /<<BUILDDIR>>/gbrowse-2.56+dfsg/install_util/GBrowseInstall.pm line 778.
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/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 /<<BUILDDIR>>/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
t/01.yeast.t ..............
1..7
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/Graphics/FeatureFile.pm line 756.
t/02.rearchitecture.t .....
1..90
ok 1
ok 2
ok 3
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ok 5
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ok
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/Graphics/FeatureFile.pm line 756.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000.
t/03.render.t .............
1..150
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
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ok 10
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ok 12
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ok 150
ok
Sometimes this test gets 'stuck'. If this happens, kill the test and Build test again.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/Graphics/FeatureFile.pm line 756.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000.
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
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ok 19
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ok 24
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ok 26
ok 27
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ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
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ok 39
ok 40
ok 41
ok 42
ok 43
ok
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/Graphics/FeatureFile.pm line 756.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000.
cannot remove directory for /tmp/gbrowse_testing/e2Sz2a24Vf: No such file or directory at /usr/share/perl/5.26/File/Temp.pm line 778.
t/05.deferredrendering.t ..
1..19
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
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ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/Graphics/FeatureFile.pm line 756.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000.
t/06.featuresearch.t ......
1..26
ok 1
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ok 3
ok 4
ok 5
ok 6
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ok 10
ok 11
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ok 14
ok 15
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ok 24
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ok 26
ok
t/07.balancer.t ........... skipped: Optional module Parse::Apache::ServerStatus not installed
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/Graphics/FeatureFile.pm line 756.
t/07.karyotype.t ..........
1..3
ok 1
ok 2
ok 3
ok
t/08.calign.t .............
1..6
# Running under perl version 5.026000 for linux
# Current time local: Mon Sep 25 22:45:43 2017
# Current time GMT: Mon Sep 25 22:45:43 2017
# Using Test.pm version 1.30
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok
All tests successful.
Files=10, Tests=448, 61 wallclock secs ( 0.18 usr 0.04 sys + 32.08 cusr 16.66 csys = 48.96 CPU)
Result: PASS
make[1]: Leaving directory '/<<BUILDDIR>>/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 '/<<BUILDDIR>>/gbrowse-2.56+dfsg'
# svn(-buildpackage) seems to ignore the x bit
chmod +x debian/gbrowse-calign.dirs
dh_installdirs
make[1]: Leaving directory '/<<BUILDDIR>>/gbrowse-2.56+dfsg'
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/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 /<<BUILDDIR>>/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/arm-linux-gnueabihf-thread-multi-64int/auto/Bio/Graphics/Browser2/CAlign/CAlign.so
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/auto/Bio/Graphics/Browser2/CAlign/CAlign.bs
Installing debian/gbrowse/man/man1/bed2gff3.pl.1p
Installing debian/gbrowse/man/man1/load_genbank.pl.1p
Installing debian/gbrowse/man/man1/gbrowse_aws_balancer.pl.1p
Installing debian/gbrowse/man/man1/ucsc_genes2gff.pl.1p
Installing debian/gbrowse/man/man1/make_das_conf.pl.1p
Installing debian/gbrowse/man/man1/wiggle2gff3.pl.1p
Installing debian/gbrowse/man/man1/gbrowse_clean.pl.1p
Installing debian/gbrowse/man/man1/gbrowse_grow_cloud_vol.pl.1p
Installing debian/gbrowse/man/man1/gbrowse_sync_aws_slave.pl.1p
Installing debian/gbrowse/man/man1/gtf2gff3.pl.1p
Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse
Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_syn
Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_gmap
Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_key_img
Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/das
Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_img
Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_login
Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_details
Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbgff
Installing debian/gbrowse/etc/gbrowse/detail_select_menu.conf
Installing debian/gbrowse/etc/gbrowse/slave_preload.conf
Installing debian/gbrowse/etc/gbrowse/log4perl.conf
Installing debian/gbrowse/etc/gbrowse/enzymes.txt
Installing debian/gbrowse/etc/gbrowse/aws_balancer.conf
Installing debian/gbrowse/etc/gbrowse/renderfarm.conf
Installing debian/gbrowse/etc/gbrowse/yeast_chr1+2.conf
Installing debian/gbrowse/etc/gbrowse/GBrowse.conf
Installing debian/gbrowse/etc/gbrowse/submitter_plugin.conf
Installing debian/gbrowse/etc/gbrowse/yeast_renderfarm.conf
Installing debian/gbrowse/etc/gbrowse/pop_demo.conf
Installing debian/gbrowse/etc/gbrowse/volvox.conf
Installing debian/gbrowse/etc/gbrowse/yeast_simple.conf
Installing debian/gbrowse/etc/gbrowse/plugins/TrackDumper.pm
Installing debian/gbrowse/etc/gbrowse/plugins/PrimerDesigner.pm
Installing debian/gbrowse/etc/gbrowse/plugins/Blat.pm
Installing debian/gbrowse/etc/gbrowse/plugins/SourceTrackFinder.pm
Installing debian/gbrowse/etc/gbrowse/plugins/FilterTest.pm
Installing debian/gbrowse/etc/gbrowse/plugins/AlignTwoSequences.pm
Installing debian/gbrowse/etc/gbrowse/plugins/TestFinder.pm
Installing debian/gbrowse/etc/gbrowse/plugins/GeneFinder.pm
Installing debian/gbrowse/etc/gbrowse/plugins/FBTableDumper.pm
Installing debian/gbrowse/etc/gbrowse/plugins/ProteinDumper.pm
Installing debian/gbrowse/etc/gbrowse/plugins/CMapDumper.pm
Installing debian/gbrowse/etc/gbrowse/plugins/RestrictionAnnotator.pm
Installing debian/gbrowse/etc/gbrowse/plugins/PamAuthenticate.pm
Installing debian/gbrowse/etc/gbrowse/plugins/TestAuthenticator.pm
Installing debian/gbrowse/etc/gbrowse/plugins/SinWave.pm
Installing debian/gbrowse/etc/gbrowse/plugins/FastaDumper.pm
Installing debian/gbrowse/etc/gbrowse/plugins/CreateBlastDB.pm
Installing debian/gbrowse/etc/gbrowse/plugins/Submitter.pm
Installing debian/gbrowse/etc/gbrowse/plugins/SequenceDumper.pm
Installing debian/gbrowse/etc/gbrowse/plugins/TrackFinder.pm
Installing debian/gbrowse/etc/gbrowse/plugins/SimpleTrackFinder.pm
Installing debian/gbrowse/etc/gbrowse/plugins/OligoFinder.pm
Installing debian/gbrowse/etc/gbrowse/plugins/LDAPAuthenticate.pm
Installing debian/gbrowse/etc/gbrowse/plugins/test.pm
Installing debian/gbrowse/etc/gbrowse/plugins/Spectrogram.pm
Installing debian/gbrowse/etc/gbrowse/plugins/AttributeHiliter.pm
Installing debian/gbrowse/etc/gbrowse/plugins/Aligner.pm
Installing debian/gbrowse/etc/gbrowse/plugins/RandomGene.pm
Installing debian/gbrowse/etc/gbrowse/plugins/BatchDumper.pm
Installing debian/gbrowse/etc/gbrowse/MobyServices/GbrowseServices.pm
Installing debian/gbrowse/etc/gbrowse/MobyServices/b64_encoded_jpeg_renderer.pm
Installing debian/gbrowse/etc/gbrowse/MobyServices/b64_encoded_gif_renderer.pm
Installing debian/gbrowse/etc/gbrowse/MobyServices/text_xml_renderer.pm
Installing debian/gbrowse/etc/gbrowse/MobyServices/moby.conf
Installing debian/gbrowse/etc/gbrowse/MobyServices/GbrowseServices.PMS
Installing debian/gbrowse/etc/gbrowse/MobyServices/text_html_renderer.pm
Installing debian/gbrowse/etc/gbrowse/MobyServices/text_plain_renderer.pm
Installing debian/gbrowse/etc/gbrowse/MobyServices/text_formatted_renderer.pm
Installing debian/gbrowse/etc/gbrowse/languages/nl.pm
Installing debian/gbrowse/etc/gbrowse/languages/zh_cn.pm
Installing debian/gbrowse/etc/gbrowse/languages/de.pm
Installing debian/gbrowse/etc/gbrowse/languages/pl.pm
Installing debian/gbrowse/etc/gbrowse/languages/is.pm
Installing debian/gbrowse/etc/gbrowse/languages/zh.pm
Installing debian/gbrowse/etc/gbrowse/languages/ko.pm
Installing debian/gbrowse/etc/gbrowse/languages/it.pm
Installing debian/gbrowse/etc/gbrowse/languages/ru.pm
Installing debian/gbrowse/etc/gbrowse/languages/ja.pm
Installing debian/gbrowse/etc/gbrowse/languages/es.pm
Installing debian/gbrowse/etc/gbrowse/languages/fr.pm
Installing debian/gbrowse/etc/gbrowse/languages/POSIX.pm
Installing debian/gbrowse/etc/gbrowse/languages/en.pm
Installing debian/gbrowse/etc/gbrowse/themes/solid_gray_colors
Installing debian/gbrowse/etc/gbrowse/themes/warm_colors
Installing debian/gbrowse/etc/gbrowse/themes/transparent_colors
Installing debian/gbrowse/etc/gbrowse/synteny/oryza.synconf.disabled.conf
Installing debian/gbrowse/etc/gbrowse/synteny/wild_rice_synteny.conf
Installing debian/gbrowse/etc/gbrowse/synteny/rice_synteny.conf
Installing debian/gbrowse/var/lib/gbrowse/databases/yeast_chr1+2/yeast_chr1+2.gff3
Installing debian/gbrowse/var/lib/gbrowse/databases/yeast_chr1+2/dummy.fa
Installing debian/gbrowse/var/lib/gbrowse/databases/admin_uploads/README
Installing debian/gbrowse/var/lib/gbrowse/databases/gbrowse_syn/alignments/rice.aln.gz
Installing debian/gbrowse/var/lib/gbrowse/databases/gbrowse_syn/wild_rice/wild_rice.gff3
Installing debian/gbrowse/var/lib/gbrowse/databases/gbrowse_syn/rice/rice.gff3
Installing debian/gbrowse/var/lib/gbrowse/databases/ideograms/human_cytobands.gff
Installing debian/gbrowse/var/lib/gbrowse/databases/ideograms/mouse_cytobands.gff
Installing debian/gbrowse/var/lib/gbrowse/databases/ideograms/rat_cytobands.gff
Installing debian/gbrowse/var/lib/gbrowse/databases/yeast_scaffolds/chr2.fa
Installing debian/gbrowse/var/lib/gbrowse/databases/yeast_scaffolds/chromosomes.gff3
Installing debian/gbrowse/var/lib/gbrowse/databases/yeast_scaffolds/chr1.fa
Installing debian/gbrowse/var/lib/gbrowse/databases/pop_demo/pop_demo.gff3
Installing debian/gbrowse/usr/share/gbrowse/htdocs/index.html
Installing debian/gbrowse/usr/share/gbrowse/htdocs/gmod_cog.jpeg
Installing debian/gbrowse/usr/share/gbrowse/htdocs/gbrowse_karyotype_help.html
Installing debian/gbrowse/usr/share/gbrowse/htdocs/gbrowse_syn_help.html
Installing debian/gbrowse/usr/share/gbrowse/htdocs/vbox_index.html
Installing debian/gbrowse/usr/share/gbrowse/htdocs/general_help.html.zh
Installing debian/gbrowse/usr/share/gbrowse/htdocs/annotation_help.html
Installing debian/gbrowse/usr/share/gbrowse/htdocs/general_help.html
Installing debian/gbrowse/usr/share/gbrowse/htdocs/cloud_index.html
Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/tutorial.css
Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/tutorial.phyTreeEdit.html
Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/tutorial.html
Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/dbgff/data_files/volvox6.gff
Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/dbgff/data_files/elegans_core.gff
Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/dbgff/data_files/elegans_acceptor.gff
Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/dbgff/data_files/volvox4b.gff
Installing debian/gbrowse/usr/share/gbrowse/htdocs/tutorial/dbgff/data_files/volvox_all.gff
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Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/CGI/Toggle.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/DB/Tagger.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/DB/GFF/Aggregator/waba_alignment.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/DB/GFF/Aggregator/reftranscript.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/DB/GFF/Aggregator/wormbase_gene.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/DB/GFF/Aggregator/match_gap.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/DB/SeqFeature/Store/Alias.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/DB/SeqFeature/Store/BedLoader.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/DB/Tagger/Tag.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/DB/Tagger/mysql.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/GBrowseFeature.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Karyotype.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/SendMail.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/RemoteSet.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/RegionSearch.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/TrackDumper.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/I18n.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/UserDB.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataSource.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Plugin.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/GFFhelper.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Realign.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Session.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Render.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/PadAlignment.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/ExternalData.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/UserTracks.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/OptionPick.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/PluginSet.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Region.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Action.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/CAlign.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/CachedTrack.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataBase.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataLoader.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Shellwords.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/RenderPanels.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Markup.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/SubtrackTable.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Util.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Render/HTML.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Render/TrackConfig.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Render/Login.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Render/Slave.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Render/SnapshotManager.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Render/Slave/AWS_Balancer.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Render/Slave/Status.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Render/HTML/TrackListing.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Render/HTML/TrackListing/Categories.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/UserTracks/Filesystem.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/UserTracks/Database.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/TrackDumper/RichSeqMaker.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/wiggle.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/sam.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/bed.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/gff.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/featurefile.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/useq.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/archive.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/generic.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/bam.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/bigwig.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/gff3.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/wig2bigwig.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/DataLoader/bigbed.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Plugin/AuthPlugin.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Legacy/DB/SyntenyBlock.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Legacy/DB/SyntenyIO.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Legacy/Graphics/Browser.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Legacy/Graphics/Browser/I18n.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Legacy/Graphics/Browser/PageSettings.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Legacy/Graphics/Browser/Synteny.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Legacy/Graphics/Browser/Util.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/GBrowse/ConfigData.pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::PadAlignment.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RenderPanels.3pm
Installing debian/gbrowse/man/man3/GBrowse::ConfigData.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Plugin.3pm
Installing debian/gbrowse/man/man3/Bio::DB::Tagger::Tag.3pm
Installing debian/gbrowse/man/man3/Bio::DB::SeqFeature::Store::Alias.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render::Slave::AWS_Balancer.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Markup.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::DB::Tagger.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Region.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Util.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::GFFhelper.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataSource.3pm
Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::OptionPick.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render::Slave::Status.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Plugin::AuthPlugin.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render.3pm
Installing debian/gbrowse/man/man3/Legacy::Graphics::Browser.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RegionSearch.3pm
Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Installing debian/gbrowse/man/man3/CGI::Toggle.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RemoteSet.3pm
Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataLoader::useq.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::CAlign.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Realign.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::AuthorizedFeatureFile.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataBase.3pm
Installing debian/gbrowse/bin/gbrowse_metadb_config.pl
Installing debian/gbrowse/bin/gbrowse_slave
Installing debian/gbrowse/bin/gbrowse_syn_load_alignment_database.pl
Installing debian/gbrowse/bin/bed2gff3.pl
Installing debian/gbrowse/bin/gbrowse_clean.pl
Installing debian/gbrowse/bin/load_genbank.pl
Installing debian/gbrowse/bin/gbrowse_import_ucsc_db.pl
Installing debian/gbrowse/bin/ucsc_genes2gff.pl
Installing debian/gbrowse/bin/gbrowse_syn_load_alignments_msa.pl
Installing debian/gbrowse/bin/gbrowse_configure_slaves.pl
Installing debian/gbrowse/bin/make_das_conf.pl
Installing debian/gbrowse/bin/wiggle2gff3.pl
Installing debian/gbrowse/bin/gtf2gff3.pl
Installing debian/gbrowse/bin/gbrowse_create_account.pl
Installing debian/gbrowse/bin/gbrowse_grow_cloud_vol.pl
Installing debian/gbrowse/bin/gbrowse_sync_aws_slave.pl
Installing debian/gbrowse/bin/gbrowse_change_passwd.pl
Installing debian/gbrowse/bin/gbrowse_aws_balancer.pl
Installing debian/gbrowse/bin/scan_gbrowse.pl
Installing debian/gbrowse/bin/gbrowse_set_admin_passwd.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 /<<BUILDDIR>>/gbrowse-2.56+dfsg/install_util/GBrowseInstall.pm line 871, <GEN91> 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 /<<BUILDDIR>>/gbrowse-2.56+dfsg/install_util/GBrowseInstall.pm line 871, <GEN97> line 20.
Building GBrowse
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing debian/gbrowse/etc/init.d/gbrowse-slave
Installing debian/gbrowse/etc/init.d/gbrowse-aws-balancer
Installing debian/gbrowse/etc/default/gbrowse-slave
Installing debian/gbrowse/etc/default/gbrowse-aws-balancer
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-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/arm-linux-gnueabihf/perl5/5.26/auto/Bio/Graphics/Browser2/CAlign/
mkdir -p debian/gbrowse-calign/usr/lib/arm-linux-gnueabihf/perl5/5.26/Bio/Graphics/Browser2/
mv debian/gbrowse/usr/share/perl5/auto/Bio/Graphics/Browser2/CAlign/* debian/gbrowse-calign/usr/lib/arm-linux-gnueabihf/perl5/5.26/auto/Bio/Graphics/Browser2/CAlign/
mv debian/gbrowse/usr/share/perl5/Bio/Graphics/Browser2/CAlign.pm debian/gbrowse-calign/usr/lib/arm-linux-gnueabihf/perl5/5.26/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 /<<BUILDDIR>>/gbrowse-2.56+dfsg/debian/gbrowse/etc -name '*.new' | xargs file-rename 's/.new//'
rm -rf /<<BUILDDIR>>/gbrowse-2.56+dfsg/debian/gbrowse/usr/share/perl5/auto
# Update conf files
sed -i 's/gbrowse2/gbrowse/g' /<<BUILDDIR>>/gbrowse-2.56+dfsg/debian/gbrowse/etc/gbrowse/yeast*.conf
sed -i 's/gbrowse2/gbrowse/g' /<<BUILDDIR>>/gbrowse-2.56+dfsg/debian/gbrowse/etc/gbrowse/slave*.conf
# move OpenID constumer secret to /etc/gbrowse to make it system admin configurable
mv /<<BUILDDIR>>/gbrowse-2.56+dfsg/debian/gbrowse/usr/share/perl5/GBrowse/ConfigData.pm /<<BUILDDIR>>/gbrowse-2.56+dfsg/debian/gbrowse/etc/gbrowse/ConfigData.pm
make[1]: Leaving directory '/<<BUILDDIR>>/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 '/<<BUILDDIR>>/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 '/<<BUILDDIR>>/gbrowse-2.56+dfsg'
dh_lintian -a
dh_perl -a
debian/rules override_dh_link
make[1]: Entering directory '/<<BUILDDIR>>/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 '/<<BUILDDIR>>/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
dpkg-deb: building package 'gbrowse-calign' in '../gbrowse-calign_2.56+dfsg-3_armhf.deb'.
dpkg-deb: building package 'gbrowse-calign-dbgsym' in '../gbrowse-calign-dbgsym_2.56+dfsg-3_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../gbrowse_2.56+dfsg-3_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build gbrowse-2.56+dfsg
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2017-09-25T22:45:58Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
gbrowse_2.56+dfsg-3_armhf.changes:
----------------------------------
Format: 1.8
Date: Fri, 15 Sep 2017 23:36:37 +0200
Source: gbrowse
Binary: gbrowse gbrowse-data gbrowse-calign
Architecture: armhf
Version: 2.56+dfsg-3
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
gbrowse - GMOD Generic Genome Browser
gbrowse-calign - CAlign helper
gbrowse-data - Sample data to use GBrowse
Closes: 857213
Changes:
gbrowse (2.56+dfsg-3) unstable; urgency=medium
.
* Fix broken link
Closes: #857213
* Standards-Version: 4.1.0 (no changes needed)
Checksums-Sha1:
fefda516f71a30700c76a39a67a5bdffe494df2a 28318 gbrowse-calign-dbgsym_2.56+dfsg-3_armhf.deb
bf31614fc26b596044ba99d0ddb57490ef44fd7b 35590 gbrowse-calign_2.56+dfsg-3_armhf.deb
e7f94a1b266b68ddc2e89ffd6d6350ef5a3ebbb4 7789 gbrowse_2.56+dfsg-3_armhf.buildinfo
Checksums-Sha256:
8988d5edb8876977e9e0bea0eb77a547ce9f8a6bfbd8b78897e01c1149abfcae 28318 gbrowse-calign-dbgsym_2.56+dfsg-3_armhf.deb
946434018873bf34f772ee608345b756657376960c689a06ede689cb546bc61a 35590 gbrowse-calign_2.56+dfsg-3_armhf.deb
f3e1d9bc44225630426e0fc1bb75b057cd1949cfc911227f0ebce29a9a2a23d0 7789 gbrowse_2.56+dfsg-3_armhf.buildinfo
Files:
52fa26c72652c3a508241d3d99334a9a 28318 debug optional gbrowse-calign-dbgsym_2.56+dfsg-3_armhf.deb
f0b57a8c6d7e3bc67bc3a32fdcfc293b 35590 science optional gbrowse-calign_2.56+dfsg-3_armhf.deb
167c335305490b4449f4822301b2ae13 7789 science optional gbrowse_2.56+dfsg-3_armhf.buildinfo
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
gbrowse-calign-dbgsym_2.56+dfsg-3_armhf.deb
-------------------------------------------
new debian package, version 2.0.
size 28318 bytes: control archive=462 bytes.
398 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: gbrowse-calign-dbgsym
Source: gbrowse
Version: 2.56+dfsg-3
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 40
Depends: gbrowse-calign (= 2.56+dfsg-3)
Section: debug
Priority: optional
Description: debug symbols for gbrowse-calign
Build-Ids: 9495c405f3e68345855429da17076e101f9149c8
drwxr-xr-x root/root 0 2017-09-15 21:36 ./
drwxr-xr-x root/root 0 2017-09-15 21:36 ./usr/
drwxr-xr-x root/root 0 2017-09-15 21:36 ./usr/lib/
drwxr-xr-x root/root 0 2017-09-15 21:36 ./usr/lib/debug/
drwxr-xr-x root/root 0 2017-09-15 21:36 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2017-09-15 21:36 ./usr/lib/debug/.build-id/94/
-rw-r--r-- root/root 30600 2017-09-15 21:36 ./usr/lib/debug/.build-id/94/95c405f3e68345855429da17076e101f9149c8.debug
drwxr-xr-x root/root 0 2017-09-15 21:36 ./usr/share/
drwxr-xr-x root/root 0 2017-09-15 21:36 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-09-15 21:36 ./usr/share/doc/gbrowse-calign-dbgsym -> gbrowse-calign
gbrowse-calign_2.56+dfsg-3_armhf.deb
------------------------------------
new debian package, version 2.0.
size 35590 bytes: control archive=854 bytes.
626 bytes, 17 lines control
663 bytes, 7 lines md5sums
Package: gbrowse-calign
Source: gbrowse
Version: 2.56+dfsg-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 76
Depends: perl (>= 5.26.0-8), perlapi-5.26.0, 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 2017-09-15 21:36 ./
drwxr-xr-x root/root 0 2017-09-15 21:36 ./usr/
drwxr-xr-x root/root 0 2017-09-15 21:36 ./usr/lib/
drwxr-xr-x root/root 0 2017-09-15 21:36 ./usr/lib/arm-linux-gnueabihf/
drwxr-xr-x root/root 0 2017-09-15 21:36 ./usr/lib/arm-linux-gnueabihf/perl5/
drwxr-xr-x root/root 0 2017-09-15 21:36 ./usr/lib/arm-linux-gnueabihf/perl5/5.26/
drwxr-xr-x root/root 0 2017-09-15 21:36 ./usr/lib/arm-linux-gnueabihf/perl5/5.26/Bio/
drwxr-xr-x root/root 0 2017-09-15 21:36 ./usr/lib/arm-linux-gnueabihf/perl5/5.26/Bio/Graphics/
drwxr-xr-x root/root 0 2017-09-15 21:36 ./usr/lib/arm-linux-gnueabihf/perl5/5.26/Bio/Graphics/Browser2/
-rw-r--r-- root/root 1129 2017-09-15 21:36 ./usr/lib/arm-linux-gnueabihf/perl5/5.26/Bio/Graphics/Browser2/CAlign.pm
drwxr-xr-x root/root 0 2017-09-15 21:36 ./usr/lib/arm-linux-gnueabihf/perl5/5.26/auto/
drwxr-xr-x root/root 0 2017-09-15 21:36 ./usr/lib/arm-linux-gnueabihf/perl5/5.26/auto/Bio/
drwxr-xr-x root/root 0 2017-09-15 21:36 ./usr/lib/arm-linux-gnueabihf/perl5/5.26/auto/Bio/Graphics/
drwxr-xr-x root/root 0 2017-09-15 21:36 ./usr/lib/arm-linux-gnueabihf/perl5/5.26/auto/Bio/Graphics/Browser2/
drwxr-xr-x root/root 0 2017-09-15 21:36 ./usr/lib/arm-linux-gnueabihf/perl5/5.26/auto/Bio/Graphics/Browser2/CAlign/
-rw-r--r-- root/root 0 2017-09-15 21:36 ./usr/lib/arm-linux-gnueabihf/perl5/5.26/auto/Bio/Graphics/Browser2/CAlign/CAlign.bs
-rw-r--r-- root/root 9476 2017-09-15 21:36 ./usr/lib/arm-linux-gnueabihf/perl5/5.26/auto/Bio/Graphics/Browser2/CAlign/CAlign.so
drwxr-xr-x root/root 0 2017-09-15 21:36 ./usr/share/
drwxr-xr-x root/root 0 2017-09-15 21:36 ./usr/share/doc/
drwxr-xr-x root/root 0 2017-09-15 21:36 ./usr/share/doc/gbrowse-calign/
-rw-r--r-- root/root 2129 2017-09-15 21:36 ./usr/share/doc/gbrowse-calign/changelog.Debian.gz
-rw-r--r-- root/root 19608 2017-01-15 21:26 ./usr/share/doc/gbrowse-calign/changelog.gz
-rw-r--r-- root/root 17978 2017-01-18 13:54 ./usr/share/doc/gbrowse-calign/copyright
drwxr-xr-x root/root 0 2017-09-15 21:36 ./usr/share/man/
drwxr-xr-x root/root 0 2017-09-15 21:36 ./usr/share/man/man3/
-rw-r--r-- root/root 2129 2017-09-15 21:36 ./usr/share/man/man3/Bio::Graphics::Browser2::CAlign.3pm.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 33644
Build-Time: 86
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 281
Job: gbrowse_2.56+dfsg-3
Machine Architecture: armhf
Package: gbrowse
Package-Time: 383
Source-Version: 2.56+dfsg-3
Space: 33644
Status: successful
Version: 2.56+dfsg-3
--------------------------------------------------------------------------------
Finished at 2017-09-25T22:45:58Z
Build needed 00:06:23, 33644k disk space