gbrowse →
2.56+dfsg-4 →
armhf → 2018-10-08 07:14:00
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testwandboard
+==============================================================================+
| gbrowse 2.56+dfsg-4 (armhf) Mon, 08 Oct 2018 06:54:53 +0000 |
+==============================================================================+
Package: gbrowse
Version: 2.56+dfsg-4
Source Version: 2.56+dfsg-4
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-56d3a6b8-f0f5-4c1b-8b1e-15937a5ffa6b' 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 [11.1 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.8 MB]
Fetched 23.9 MB in 31s (765 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://salsa.debian.org/med-team/gbrowse.git
Please use:
git clone https://salsa.debian.org/med-team/gbrowse.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 4382 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main gbrowse 2.56+dfsg-4 (dsc) [2660 B]
Get:2 http://172.17.0.1/private buster-staging/main gbrowse 2.56+dfsg-4 (tar) [4356 kB]
Get:3 http://172.17.0.1/private buster-staging/main gbrowse 2.56+dfsg-4 (diff) [23.6 kB]
Fetched 4382 kB in 2s (2731 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/gbrowse-4AqvDB/gbrowse-2.56+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/gbrowse-4AqvDB' 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-kd5ZV2/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-kd5ZV2/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-kd5ZV2/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: 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 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: 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-kd5ZV2/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-kd5ZV2/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-kd5ZV2/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-kd5ZV2/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-kd5ZV2/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (3140 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 dbus dbus-user-session e2fsprogs-l10n libexpat1
libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
systemd-sysv
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 79 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-kd5ZV2/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (35.8 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15733 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 (>= 11~), dh-apache2, dh-exec, apache2-dev, libbio-graphics-perl (>= 2.31), libbio-coordinate-perl, libcapture-tiny-perl, libcgi-session-perl, libgd-gd2-perl | libgd-gd2-noxpm-perl, libio-string-perl, libjson-perl, libstatistics-descriptive-perl, libwww-perl, libhttp-daemon-perl, perl, sqlite3, libdbd-sqlite3-perl, libterm-readkey-perl, libjs-prototype, libjs-scriptaculous, libvm-ec2-perl, libmodule-build-perl, libcgi-pm-perl | perl (<< 5.19), rename
Filtered Build-Depends: bioperl, debhelper (>= 11~), dh-apache2, dh-exec, apache2-dev, libbio-graphics-perl (>= 2.31), libbio-coordinate-perl, libcapture-tiny-perl, libcgi-session-perl, libgd-gd2-perl, 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-kd5ZV2/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-kd5ZV2/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-kd5ZV2/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-kd5ZV2/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-kd5ZV2/apt_archive ./ Sources [704 B]
Get:5 copy:/<<BUILDDIR>>/resolver-kd5ZV2/apt_archive ./ Packages [759 B]
Fetched 2796 B in 1s (4130 B/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 packages were automatically installed and are no longer required:
dbus dbus-user-session e2fsprogs-l10n libnss-systemd libpam-systemd
libsasl2-modules systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
apache2-dev autoconf automake autopoint autotools-dev bioperl bsdmainutils
debhelper dh-autoreconf dh-exec dh-strip-nondeterminism dwz file
fontconfig-config fonts-dejavu-core gettext gettext-base groff-base
intltool-debian libalgorithm-diff-perl libanyevent-cachedns-perl
libanyevent-http-perl libanyevent-perl libapr1 libapr1-dev libaprutil1
libaprutil1-dev libarchive-zip-perl 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 libelf1 libencode-locale-perl
libexception-class-perl libexpat1 libexpat1-dev libexporter-tiny-perl
libfile-listing-perl libfile-stripnondeterminism-perl libfontconfig1
libfreetype6 libgd-perl libgd3 libglib2.0-0 libgraphite2-3 libharfbuzz0b
libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl
libhttp-cookies-perl libhttp-daemon-perl libhttp-date-perl
libhttp-message-perl libhttp-negotiate-perl libicu-le-hb0 libicu60
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 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 libtry-tiny-perl 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 perl-openssl-defaults po-debconf rename sqlite3 ucf uuid-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libev-perl libevent-perl libio-async-perl libpoe-perl libtask-weaken-perl
python libxml-sax-expatxs-perl libclone-perl libmldbm-perl
libnet-daemon-perl libsql-statement-perl libgd-tools libdata-dump-perl
libcrypt-ssleay-perl lksctp-tools libtool-doc gfortran | fortran95-compiler
gcj-jdk libauthen-ntlm-perl m4-doc apparmor less www-browser
libmail-box-perl sqlite3-doc
Recommended packages:
bioperl-run perl-doc libcache-cache-perl libbio-perl-run-perl
libapache-dbi-perl libyaml-perl libace-perl libxml-twig-perl
libset-scalar-perl curl | wget | lynx libalgorithm-diff-xs-perl
libasync-interrupt-perl libev-perl | libevent-perl libguard-perl
libbio-scf-perl libberkeleydb-perl libgd-svg-perl bioperl-run
| libbio-perl-run-perl libalgorithm-munkres-perl libarray-compare-perl
libbio-asn1-entrezgene-perl libclone-perl libconvert-binary-c-perl
libdbd-mysql-perl libdbd-pg-perl libgraph-perl libgraphviz-perl
libhtml-tableextract-perl libpostscript-perl libsoap-lite-perl
libsort-naturally-perl libspreadsheet-parseexcel-perl
libspreadsheet-writeexcel-perl libsvg-perl libsvg-graph-perl
libxml-dom-xpath-perl libxml-parser-perl libxml-sax-writer-perl
libxml-writer-perl libcgi-fast-perl libfreezethaw-perl perl-tk
libxml-libxslt-perl libmldbm-perl libxml-perl libarchive-cpio-perl
libglib2.0-data shared-mime-info xdg-user-dirs libhtml-format-perl
javascript-common libjson-xs-perl libmodule-signature-perl
libpod-readme-perl libsoftware-license-perl libltdl-dev libdata-dump-perl
libhtml-form-perl libmailtools-perl libxml-sax-expat-perl
libmail-sendmail-perl
The following NEW packages will be installed:
apache2-dev autoconf automake autopoint autotools-dev bioperl bsdmainutils
debhelper dh-autoreconf dh-exec dh-strip-nondeterminism dwz file
fontconfig-config fonts-dejavu-core gettext gettext-base groff-base
intltool-debian libalgorithm-diff-perl libanyevent-cachedns-perl
libanyevent-http-perl libanyevent-perl libapr1 libapr1-dev libaprutil1
libaprutil1-dev libarchive-zip-perl 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 libelf1 libencode-locale-perl
libexception-class-perl libexpat1-dev libexporter-tiny-perl
libfile-listing-perl libfile-stripnondeterminism-perl libfontconfig1
libfreetype6 libgd-perl libgd3 libglib2.0-0 libgraphite2-3 libharfbuzz0b
libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl
libhttp-cookies-perl libhttp-daemon-perl libhttp-date-perl
libhttp-message-perl libhttp-negotiate-perl libicu-le-hb0 libicu60
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
libtry-tiny-perl 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
perl-openssl-defaults po-debconf rename sbuild-build-depends-gbrowse-dummy
sqlite3 ucf uuid-dev
The following packages will be upgraded:
libexpat1 libsqlite3-0
2 upgraded, 127 newly installed, 0 to remove and 77 not upgraded.
Need to get 36.0 MB/38.2 MB of archives.
After this operation, 131 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-kd5ZV2/apt_archive ./ sbuild-build-depends-gbrowse-dummy 0.invalid.0 [1040 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.4-2 [1161 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libsqlite3-0 armhf 3.25.2-1 [544 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.34-2 [107 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.34-2 [65.0 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-7 [117 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-1.1 [771 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-7 [434 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-4 [547 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.043-1 [20.2 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.043-1 [12.1 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.5 [160 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.1-2 [1051 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libgraphite2-3 armhf 1.3.12-1 [69.1 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.9.0-1+rpi1 [877 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb0 armhf 1.0.3+git161113-5 [12.8 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libicu60 armhf 60.2-6 [7789 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7 [602 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-7 [1218 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.4.1 [989 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libapr1 armhf 1.6.3-3 [83.2 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf uuid-dev armhf 2.32.1-0.1 [91.9 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libsctp1 armhf 1.0.18+dfsg-1 [27.6 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libsctp-dev armhf 1.0.18+dfsg-1 [81.1 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libapr1-dev armhf 1.6.3-3 [687 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libexpat1 armhf 2.2.6-1 [76.8 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libaprutil1 armhf 1.6.1-3 [82.3 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libldap2-dev armhf 2.4.46+dfsg-5+rpi1 [298 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libexpat1-dev armhf 2.2.6-1 [127 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libaprutil1-dev armhf 1.6.1-3 [395 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf apache2-dev armhf 2.4.34-1 [326 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libio-string-perl all 1.08-3 [12.3 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libdata-stag-perl all 0.14-2 [448 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libbio-perl-perl all 1.7.2-2 [4560 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libclass-data-inheritable-perl all 0.08-3 [8588 B]
Get:50 http://172.17.0.1/private buster-staging/main armhf libdevel-stacktrace-perl all 2.0300-1 [28.0 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libexception-class-perl all 1.44-1 [32.3 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libtest-deep-perl all 1.128-1 [48.8 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libcapture-tiny-perl all 0.48-1 [26.0 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libalgorithm-diff-perl all 1.19.03-2 [47.9 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libtext-diff-perl all 1.45-1 [27.7 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libtest-differences-perl all 0.64-2 [18.3 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libsub-uplevel-perl all 0.2800-1 [16.3 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf libtest-exception-perl all 0.43-1 [18.7 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libtest-warn-perl all 0.36-1 [16.2 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libtest-most-perl all 0.35-1 [24.5 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf bioperl all 1.7.2-2 [418 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf fontconfig-config all 2.13.1-1 [280 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libanyevent-perl armhf 7.140-2 [392 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libanyevent-cachedns-perl all 0.08-2 [7150 B]
Get:65 http://172.17.0.1/private buster-staging/main armhf libcommon-sense-perl armhf 3.74-2+b12 [24.0 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf libanyevent-http-perl all 2.24-1 [35.5 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libbio-coordinate-perl all 1.7.1-3 [56.0 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libfontconfig1 armhf 2.13.1-1 [326 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libtiff5 armhf 4.0.9-6 [225 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libxcb1 armhf 1.13-3 [132 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libx11-data all 2:1.6.6-1 [298 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libx11-6 armhf 2:1.6.6-1 [688 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libgd-perl armhf 2.66-1+b1 [173 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libbio-graphics-perl all 2.40-3 [610 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libhtml-tagset-perl all 3.20-3 [12.7 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf liburi-perl all 1.74-1 [89.4 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libhtml-parser-perl armhf 3.72-3+b1 [101 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf libcgi-pm-perl all 4.40-1 [222 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libcgi-session-perl all 4.48-3 [119 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libdbi-perl armhf 1.641-1 [765 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf libdbd-sqlite3-perl armhf 1.58-1 [159 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf libencode-locale-perl all 1.05-1 [13.7 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf libexporter-tiny-perl all 1.002001-1 [36.9 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf libhttp-date-perl all 6.02-1 [10.7 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf libfile-listing-perl all 6.04-1 [10.3 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf libhtml-tree-perl all 5.07-1 [213 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf libio-html-perl all 1.001-1 [17.6 kB]
Get:89 http://172.17.0.1/private buster-staging/main armhf liblwp-mediatypes-perl all 6.02-1 [22.1 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf libhttp-message-perl all 6.18-1 [77.8 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf libhttp-cookies-perl all 6.04-1 [17.8 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf libhttp-daemon-perl all 6.01-1 [17.3 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf libhttp-negotiate-perl all 6.01-1 [12.8 kB]
Get:94 http://172.17.0.1/private buster-staging/main armhf perl-openssl-defaults armhf 3 [6782 B]
Get:95 http://172.17.0.1/private buster-staging/main armhf libnet-ssleay-perl armhf 1.85-1 [284 kB]
Get:96 http://172.17.0.1/private buster-staging/main armhf libio-socket-ssl-perl all 2.059-1 [206 kB]
Get:97 http://172.17.0.1/private buster-staging/main armhf libjs-prototype all 1.7.1-3 [44.3 kB]
Get:98 http://172.17.0.1/private buster-staging/main armhf libjs-scriptaculous all 1.9.0-2 [129 kB]
Get:99 http://172.17.0.1/private buster-staging/main armhf libjson-perl all 2.97001-1 [80.6 kB]
Get:100 http://172.17.0.1/private buster-staging/main armhf liblist-moreutils-perl armhf 0.416-1+b2 [59.2 kB]
Get:101 http://172.17.0.1/private buster-staging/main armhf libnet-http-perl all 6.18-1 [24.5 kB]
Get:102 http://172.17.0.1/private buster-staging/main armhf libtry-tiny-perl all 0.30-1 [23.3 kB]
Get:103 http://172.17.0.1/private buster-staging/main armhf libwww-robotrules-perl all 6.02-1 [12.9 kB]
Get:104 http://172.17.0.1/private buster-staging/main armhf libwww-perl all 6.35-2 [187 kB]
Get:105 http://172.17.0.1/private buster-staging/main armhf liblwp-protocol-https-perl all 6.07-2 [9242 B]
Get:106 http://172.17.0.1/private buster-staging/main armhf libmodule-build-perl all 0.422400-1 [259 kB]
Get:107 http://172.17.0.1/private buster-staging/main armhf libstatistics-descriptive-perl all 3.0701-1 [66.7 kB]
Get:108 http://172.17.0.1/private buster-staging/main armhf libstring-approx-perl armhf 3.28-1 [38.2 kB]
Get:109 http://172.17.0.1/private buster-staging/main armhf libterm-readkey-perl armhf 2.37-1+b1 [26.6 kB]
Get:110 http://172.17.0.1/private buster-staging/main armhf libxml-namespacesupport-perl all 1.12-1 [14.8 kB]
Get:111 http://172.17.0.1/private buster-staging/main armhf libxml-sax-base-perl all 1.09-1 [20.4 kB]
Get:112 http://172.17.0.1/private buster-staging/main armhf libxml-sax-perl all 1.00+dfsg-1 [58.6 kB]
Get:113 http://172.17.0.1/private buster-staging/main armhf libxml-libxml-perl armhf 2.0132+dfsg-2 [321 kB]
Get:114 http://172.17.0.1/private buster-staging/main armhf libxml-simple-perl all 2.25-1 [72.0 kB]
Get:115 http://172.17.0.1/private buster-staging/main armhf libvm-ec2-perl all 1.28-2 [768 kB]
Get:116 http://172.17.0.1/private buster-staging/main armhf rename all 1.10-1 [17.2 kB]
Get:117 http://172.17.0.1/private buster-staging/main armhf sqlite3 armhf 3.25.2-1 [818 kB]
Get:118 http://172.17.0.1/private buster-staging/main armhf dh-exec armhf 0.23+b5 [25.3 kB]
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Adding 'diversion of /usr/bin/config_data to /usr/bin/config_data.diverted by libmodule-build-perl'
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Setting up libtest-deep-perl (1.128-1) ...
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Setting up libtimedate-perl (2.3000-2) ...
Setting up libjbig0:armhf (2.1-3.1+b2) ...
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Setting up rename (1.10-1) ...
update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode
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No schema files found: removed existing output file.
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update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
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Setting up libfile-stripnondeterminism-perl (0.043-1) ...
Setting up libxml-sax-perl (1.00+dfsg-1) ...
update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...
Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version
Setting up liblist-moreutils-perl (0.416-1+b2) ...
Setting up libsctp-dev:armhf (1.0.18+dfsg-1) ...
Setting up libstatistics-descriptive-perl (3.0701-1) ...
Setting up fontconfig-config (2.13.1-1) ...
Installing new version of config file /etc/fonts/fonts.conf ...
Setting up libhttp-date-perl (6.02-1) ...
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Setting up libapr1-dev (1.6.3-3) ...
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Setting up autoconf (2.69-11) ...
Setting up libjs-scriptaculous (1.9.0-2) ...
Setting up file (1:5.34-2) ...
Setting up libio-socket-ssl-perl (2.059-1) ...
Setting up libhtml-tree-perl (5.07-1) ...
Setting up automake (1:1.16.1-1.1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-listing-perl (6.04-1) ...
Setting up man-db (2.8.4-2) ...
Not building database; man-db/auto-update is not 'true'.
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Setting up bioperl (1.7.2-2) ...
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Setting up dh-autoreconf (19) ...
Setting up libicu-le-hb0:armhf (1.0.3+git161113-5) ...
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Setting up dh-strip-nondeterminism (0.043-1) ...
Setting up libwww-perl (6.35-2) ...
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Setting up libxml2:armhf (2.9.4+dfsg1-7) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up libxml-libxml-perl (2.0132+dfsg-2) ...
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 gettext (0.19.8.1-7) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libxml-simple-perl (2.25-1) ...
Setting up po-debconf (1.0.20) ...
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Setting up debhelper (11.4.1) ...
Setting up dh-exec (0.23+b5) ...
Setting up apache2-dev (2.4.34-1) ...
Setting up sbuild-build-depends-gbrowse-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-5+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.8.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.31.1-2+rpi1 dpkg-dev_1.19.0.5 g++-8_8.1.0-12+rpi1 gcc-8_8.1.0-12+rpi1 libc6-dev_2.27-5+rpi1 libstdc++-8-dev_8.1.0-12+rpi1 libstdc++6_8.1.0-12+rpi1 linux-libc-dev_4.16.16-2+rpi1
Package versions: adduser_3.117 apache2-dev_2.4.34-1 apt_1.6.3 autoconf_2.69-11 automake_1:1.16.1-1.1 autopoint_0.19.8.1-7 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-2+rpi1 binutils-arm-linux-gnueabihf_2.31.1-2+rpi1 binutils-common_2.31.1-2+rpi1 bioperl_1.7.2-2 bsdmainutils_11.1.2 bsdutils_1:2.32.1-0.1 build-essential_12.5 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:8.1.0-1+rpi1 cpp-8_8.1.0-12+rpi1 dash_0.5.8-2.10 dbus_1.12.10-1 dbus-user-session_1.12.10-1 debconf_1.5.69 debhelper_11.4.1 debianutils_4.8.6 dh-autoreconf_19 dh-exec_0.23+b5 dh-strip-nondeterminism_0.043-1 diffutils_1:3.6-1 dirmngr_2.2.9-1+rpi1 dmsetup_2:1.02.145-4.1+b4 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.3-1 e2fsprogs_1.44.3-1 e2fsprogs-l10n_1.44.3-1 fakeroot_1.23-1 fdisk_2.32.1-0.1 file_1:5.34-2 findutils_4.6.0+git+20171230-2 fontconfig-config_2.13.1-1 fonts-dejavu-core_2.37-1 g++_4:8.1.0-1+rpi1 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libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.1.0-12+rpi1 libassuan0_2.5.1-2 libatomic1_8.1.0-12+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.3-1 libaudit1_1:2.8.3-1 libbinutils_2.31.1-2+rpi1 libbio-coordinate-perl_1.7.1-3 libbio-graphics-perl_2.40-3 libbio-perl-perl_1.7.2-2 libblkid1_2.32.1-0.1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-5+rpi1 libc-dev-bin_2.27-5+rpi1 libc6_2.27-5+rpi1 libc6-dev_2.27-5+rpi1 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcapture-tiny-perl_0.48-1 libcc1-0_8.1.0-12+rpi1 libcgi-pm-perl_4.40-1 libcgi-session-perl_4.48-3 libclass-data-inheritable-perl_0.08-3 libcom-err2_1.44.3-1 libcommon-sense-perl_3.74-2+b12 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.4-2 libcryptsetup4_2:1.7.5-1 libdata-stag-perl_0.14-2 libdb5.3_5.3.28-13.1 libdbd-sqlite3-perl_1.58-1 libdbi-perl_1.641-1 libdbus-1-3_1.12.10-1 libdebconfclient0_0.244 libdevel-stacktrace-perl_2.0300-1 libdevmapper1.02.1_2:1.02.145-4.1+b4 libdpkg-perl_1.19.0.5 libdrm-common_2.4.92-1+rpi1 libdrm2_2.4.92-1+rpi1 libelf1_0.170-0.5 libencode-locale-perl_1.05-1 libexception-class-perl_1.44-1 libexpat1_2.2.6-1 libexpat1-dev_2.2.6-1 libexporter-tiny-perl_1.002001-1 libext2fs2_1.44.3-1 libfakeroot_1.23-1 libfdisk1_2.32.1-0.1 libffi6_3.2.1-8 libfile-listing-perl_6.04-1 libfile-stripnondeterminism-perl_0.043-1 libfontconfig1_2.13.1-1 libfreetype6_2.8.1-2 libgcc-8-dev_8.1.0-12+rpi1 libgcc1_1:8.1.0-12+rpi1 libgcrypt20_1.8.3-1 libgd-perl_2.66-1+b1 libgd3_2.2.5-4 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libglib2.0-0_2.58.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.19-1 libgomp1_8.1.0-12+rpi1 libgpg-error0_1.32-1 libgraphite2-3_1.3.12-1 libharfbuzz0b_1.9.0-1+rpi1 libhogweed4_3.4-1 libhtml-parser-perl_3.72-3+b1 libhtml-tagset-perl_3.20-3 libhtml-tree-perl_5.07-1 libhttp-cookies-perl_6.04-1 libhttp-daemon-perl_6.01-1 libhttp-date-perl_6.02-1 libhttp-message-perl_6.18-1 libhttp-negotiate-perl_6.01-1 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.4-2.2 libio-html-perl_1.001-1 libio-socket-ssl-perl_2.059-1 libio-string-perl_1.08-3 libip4tc0_1.6.2-1.1 libisl19_0.20-1 libjbig0_2.1-3.1+b2 libjpeg62-turbo_1:1.5.2-2+b1 libjs-prototype_1.7.1-3 libjs-scriptaculous_1.9.0-2 libjson-c3_0.12.1-1.3 libjson-perl_2.97001-1 libklibc_2.0.4-14+rpi1 libkmod2_25-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.46+dfsg-5+rpi1 libldap-common_2.4.46+dfsg-5+rpi1 libldap2-dev_2.4.46+dfsg-5+rpi1 liblist-moreutils-perl_0.416-1+b2 liblocale-gettext-perl_1.07-3+b2 liblwp-mediatypes-perl_6.02-1 liblwp-protocol-https-perl_6.07-2 liblz4-1_1.8.2-1+rpi1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmodule-build-perl_0.422400-1 libmount1_2.32.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1+20180714-1 libncurses6_6.1+20180714-1 libncursesw5_6.1+20180714-1 libncursesw6_6.1+20180714-1 libnet-http-perl_6.18-1 libnet-ssleay-perl_1.85-1 libnettle6_3.4-1 libnpth0_1.6-1 libnss-systemd_239-7 libp11-kit0_0.23.12-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_239-7 libpam0g_1.1.8-3.7 libpcre3_2:8.39-10 libperl5.24_5.24.1-4 libperl5.26_5.26.2-7 libpipeline1_1.5.0-1 libplymouth4_0.9.3-3 libpng16-16_1.6.34-2+rpi1 libprocps7_2:3.3.15-2 libreadline7_7.0-5 libsasl2-2_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libsctp-dev_1.0.18+dfsg-1 libsctp1_1.0.18+dfsg-1 libseccomp2_2.3.3-3 libselinux1_2.8-1 libsemanage-common_2.8-1 libsemanage1_2.8-1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.32.1-0.1 libsqlite3-0_3.25.2-1 libss2_1.44.3-1 libssl1.1_1.1.0h-4 libstatistics-descriptive-perl_3.0701-1 libstdc++-8-dev_8.1.0-12+rpi1 libstdc++6_8.1.0-12+rpi1 libstring-approx-perl_3.28-1 libsub-uplevel-perl_0.2800-1 libsystemd0_239-7 libtasn1-6_4.13-3 libterm-readkey-perl_2.37-1+b1 libtest-deep-perl_1.128-1 libtest-differences-perl_0.64-2 libtest-exception-perl_0.43-1 libtest-most-perl_0.35-1 libtest-warn-perl_0.36-1 libtext-charwidth-perl_0.04-7.1 libtext-diff-perl_1.45-1 libtext-iconv-perl_1.7-5+b9 libtext-wrapi18n-perl_0.06-7.1 libtiff5_4.0.9-6 libtimedate-perl_2.3000-2 libtinfo5_6.1+20180714-1 libtinfo6_6.1+20180714-1 libtool_2.4.6-4 libtry-tiny-perl_0.30-1 libubsan1_8.1.0-12+rpi1 libudev1_239-7 libunistring2_0.9.10-1 liburi-perl_1.74-1 libustr-1.0-1_1.0.4-6 libuuid1_2.32.1-0.1 libvm-ec2-perl_1.28-2 libwebp6_0.6.1-2 libwww-perl_6.35-2 libwww-robotrules-perl_6.02-1 libx11-6_2:1.6.6-1 libx11-data_2:1.6.6-1 libxau6_1:1.0.8-1+b2 libxcb1_1.13-3 libxdmcp6_1:1.1.2-3 libxml-libxml-perl_2.0132+dfsg-2 libxml-namespacesupport-perl_1.12-1 libxml-sax-base-perl_1.09-1 libxml-sax-perl_1.00+dfsg-1 libxml-simple-perl_2.25-1 libxml2_2.9.4+dfsg1-7 libxpm4_1:3.5.12-1 libzstd1_1.3.4+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.16.16-2+rpi1 login_1:4.5-1.1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.2.1-1.2 makedev_2.3.1-93 man-db_2.8.4-2 mawk_1.3.3-17 mount_2.32.1-0.1 multiarch-support_2.27-5+rpi1 nano_2.9.8-1 ncurses-base_6.1+20180714-1 ncurses-bin_6.1+20180714-1 netbase_5.4 openssl_1.1.0h-4 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.26.2-7 perl-base_5.26.2-7 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-7 perl-openssl-defaults_3 pinentry-curses_1.1.0-1 plymouth_0.9.3-3 po-debconf_1.0.20 procps_2:3.3.15-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 rename_1.10-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gbrowse-dummy_0.invalid.0 sed_4.5-1 sensible-utils_0.0.12 sqlite3_3.25.2-1 systemd_239-7 systemd-sysv_239-7 sysvinit-utils_2.88dsf-59.10 tar_1.30+dfsg-2 tzdata_2018e-1 ucf_3.0038 udev_239-7 util-linux_2.32.1-0.1 uuid-dev_2.32.1-0.1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed Oct 3 13:32:13 2018 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./gbrowse_2.56+dfsg-4.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-4.debian.tar.xz
dpkg-source: info: applying debian-packaging-patch
dpkg-source: info: applying gbrowse-slave-fix_defaults_path
dpkg-source: info: applying manpages.patch
dpkg-source: info: applying fix_pop_url
dpkg-source: info: applying skip_check_installed_test.patch
dpkg-source: info: applying source_init_functions
dpkg-source: info: applying init_script_dependency.patch
dpkg-source: info: applying fix_runlevel.patch
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying fix_whatis_entry.patch
dpkg-source: info: applying remove_copy_of_LoadHelper.pm.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
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=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-56d3a6b8-f0f5-4c1b-8b1e-15937a5ffa6b
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package gbrowse
dpkg-buildpackage: info: source version 2.56+dfsg-4
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_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 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
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
t/01.yeast.t ..............
1..7
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok
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
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok
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.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, <STDIN> line 1.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, <STDIN> line 1.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
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.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, <STDIN> line 1.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, <STDIN> line 1.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
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.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, <STDIN> line 1.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, <STDIN> line 1.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
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.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, <STDIN> line 1.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, <STDIN> line 1.
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.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
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.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, <STDIN> line 1.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, <STDIN> line 1.
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.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
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.
Use of uninitialized value $_[5] in pack at /usr/share/perl5/Bio/DB/IndexedBase.pm line 1044, <GEN171> line 2.
Use of uninitialized value $_[5] in pack at /usr/share/perl5/Bio/DB/IndexedBase.pm line 1044, <GEN176> line 2.
t/03.render.t .............
1..150
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
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ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
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ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
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ok 109
ok 110
ok 111
ok 112
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ok 114
ok 115
ok 116
ok 117
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ok 137
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ok 139
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ok 141
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok
Sometimes this test gets 'stuck'. If this happens, kill the test and Build test again.
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.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, <STDIN> line 1.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, <STDIN> line 1.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
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.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, <STDIN> line 1.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, <STDIN> line 1.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
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
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok
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.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, <STDIN> line 1.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, <STDIN> line 1.
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.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
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.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, <STDIN> line 1.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, <STDIN> line 1.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
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/05.deferredrendering.t ..
1..19
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok
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.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, <> line 132.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, <STDIN> line 1.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, <STDIN> line 1.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
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.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, <STDIN> line 1.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, <STDIN> line 1.
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.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
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.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, <STDIN> line 1.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, <STDIN> line 1.
Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817.
Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820.
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 ......
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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 ..........
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t/08.calign.t .............
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# Running under perl version 5.026002 for linux
# Current time local: Mon Oct 8 07:13:04 2018
# Current time GMT: Mon Oct 8 07:13:04 2018
# Using Test.pm version 1.30
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All tests successful.
Files=10, Tests=448, 150 wallclock secs ( 0.51 usr 0.12 sys + 110.59 cusr 18.12 csys = 129.34 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.bs
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/auto/Bio/Graphics/Browser2/CAlign/CAlign.so
Installing debian/gbrowse/man/man1/bed2gff3.pl.1p
Installing debian/gbrowse/man/man1/gbrowse_aws_balancer.pl.1p
Installing debian/gbrowse/man/man1/gbrowse_clean.pl.1p
Installing debian/gbrowse/man/man1/gbrowse_grow_cloud_vol.pl.1p
Installing debian/gbrowse/man/man1/gbrowse_sync_aws_slave.pl.1p
Installing debian/gbrowse/man/man1/gtf2gff3.pl.1p
Installing debian/gbrowse/man/man1/load_genbank.pl.1p
Installing debian/gbrowse/man/man1/make_das_conf.pl.1p
Installing debian/gbrowse/man/man1/ucsc_genes2gff.pl.1p
Installing debian/gbrowse/man/man1/wiggle2gff3.pl.1p
Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/das
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Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_details
Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_gmap
Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_img
Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_key_img
Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_login
Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_syn
Installing debian/gbrowse/etc/gbrowse/aws_balancer.conf
Installing debian/gbrowse/etc/gbrowse/detail_select_menu.conf
Installing debian/gbrowse/etc/gbrowse/enzymes.txt
Installing debian/gbrowse/etc/gbrowse/GBrowse.conf
Installing debian/gbrowse/etc/gbrowse/log4perl.conf
Installing debian/gbrowse/etc/gbrowse/pop_demo.conf
Installing debian/gbrowse/etc/gbrowse/renderfarm.conf
Installing debian/gbrowse/etc/gbrowse/slave_preload.conf
Installing debian/gbrowse/etc/gbrowse/submitter_plugin.conf
Installing debian/gbrowse/etc/gbrowse/volvox.conf
Installing debian/gbrowse/etc/gbrowse/yeast_chr1+2.conf
Installing debian/gbrowse/etc/gbrowse/yeast_renderfarm.conf
Installing debian/gbrowse/etc/gbrowse/yeast_simple.conf
Installing debian/gbrowse/etc/gbrowse/languages/de.pm
Installing debian/gbrowse/etc/gbrowse/languages/en.pm
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Installing debian/gbrowse/etc/gbrowse/languages/fr.pm
Installing debian/gbrowse/etc/gbrowse/languages/is.pm
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Installing debian/gbrowse/etc/gbrowse/languages/pl.pm
Installing debian/gbrowse/etc/gbrowse/languages/POSIX.pm
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Installing debian/gbrowse/etc/gbrowse/languages/zh_cn.pm
Installing debian/gbrowse/etc/gbrowse/MobyServices/b64_encoded_gif_renderer.pm
Installing debian/gbrowse/etc/gbrowse/MobyServices/b64_encoded_jpeg_renderer.pm
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Installing debian/gbrowse/etc/gbrowse/MobyServices/GbrowseServices.PMS
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Installing debian/gbrowse/etc/gbrowse/MobyServices/text_xml_renderer.pm
Installing debian/gbrowse/etc/gbrowse/plugins/Aligner.pm
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Installing debian/gbrowse/etc/gbrowse/plugins/FilterTest.pm
Installing debian/gbrowse/etc/gbrowse/plugins/GeneFinder.pm
Installing debian/gbrowse/etc/gbrowse/plugins/LDAPAuthenticate.pm
Installing debian/gbrowse/etc/gbrowse/plugins/OligoFinder.pm
Installing debian/gbrowse/etc/gbrowse/plugins/PamAuthenticate.pm
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Installing debian/gbrowse/etc/gbrowse/plugins/RandomGene.pm
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Installing debian/gbrowse/etc/gbrowse/plugins/SinWave.pm
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Installing debian/gbrowse/etc/gbrowse/plugins/Submitter.pm
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Installing debian/gbrowse/etc/gbrowse/themes/solid_gray_colors
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Installing debian/gbrowse/etc/gbrowse/themes/warm_colors
Installing debian/gbrowse/var/lib/gbrowse/databases/admin_uploads/README
Installing debian/gbrowse/var/lib/gbrowse/databases/gbrowse_syn/alignments/rice.aln.gz
Installing debian/gbrowse/var/lib/gbrowse/databases/gbrowse_syn/rice/rice.gff3
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Installing debian/gbrowse/var/lib/gbrowse/databases/ideograms/human_cytobands.gff
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Installing debian/gbrowse/var/lib/gbrowse/databases/pop_demo/pop_demo.gff3
Installing debian/gbrowse/var/lib/gbrowse/databases/yeast_chr1+2/dummy.fa
Installing debian/gbrowse/var/lib/gbrowse/databases/yeast_chr1+2/yeast_chr1+2.gff3
Installing debian/gbrowse/var/lib/gbrowse/databases/yeast_scaffolds/chr1.fa
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Installing debian/gbrowse/var/lib/gbrowse/databases/yeast_scaffolds/chromosomes.gff3
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Installing debian/gbrowse/usr/share/gbrowse/htdocs/cloud_index.html
Installing debian/gbrowse/usr/share/gbrowse/htdocs/gbrowse_karyotype_help.html
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Installing debian/gbrowse/usr/share/gbrowse/htdocs/general_help.html.zh
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Installing debian/gbrowse/usr/share/gbrowse/htdocs/vbox_index.html
Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/gbrowse.css
Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/gbrowse_autocomplete.css
Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/gbrowse_elements.css
Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/gbrowse_solid.css
Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/gbrowse_transparent.css
Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/gbrowse_warm.css
Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/karyotype.css
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Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/snapshots.css
Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/subtracktable.css
Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/titlebar-default.css
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Installing debian/gbrowse/usr/share/gbrowse/htdocs/css/tracks.css
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Installing debian/gbrowse/usr/share/gbrowse/htdocs/example_scripts/gbrowse_get_sessionid.pl
Installing debian/gbrowse/usr/share/gbrowse/htdocs/example_scripts/gbrowse_new_sessionid.pl
Installing debian/gbrowse/usr/share/gbrowse/htdocs/example_scripts/gbrowse_upload_data.pl
Installing debian/gbrowse/usr/share/gbrowse/htdocs/example_scripts/gbrowse_upload_file.pl
Installing debian/gbrowse/usr/share/gbrowse/htdocs/example_scripts/index.html
Installing debian/gbrowse/usr/share/gbrowse/htdocs/example_scripts/README
Installing debian/gbrowse/usr/share/gbrowse/htdocs/example_scripts/test_file.bed
Installing debian/gbrowse/usr/share/gbrowse/htdocs/images/backgrounds/cloud.jpg
Installing debian/gbrowse/usr/share/gbrowse/htdocs/images/backgrounds/lrock005.jpg
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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/Session.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/SubtrackTable.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/UserDB.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/Util.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/bam.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/bigbed.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/featurefile.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/gff.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/sam.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/wig2bigwig.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/Plugin/AuthPlugin.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Render/HTML.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Render/Login.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Render/Slave.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/TrackConfig.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/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/TrackDumper/RichSeqMaker.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/UserTracks/Database.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/UserTracks/Filesystem.pm
Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/CGI/Toggle.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::DB::GFF::Aggregator::match_gap.3pm
Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Installing debian/gbrowse/man/man3/Bio::DB::SeqFeature::Store::Alias.3pm
Installing debian/gbrowse/man/man3/Bio::DB::Tagger.3pm
Installing debian/gbrowse/man/man3/Bio::DB::Tagger::Tag.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::AuthorizedFeatureFile.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::CAlign.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataBase.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataLoader::archive.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataLoader::useq.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataSource.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::GFFhelper.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Markup.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::OptionPick.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::PadAlignment.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Plugin.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Plugin::AuthPlugin.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::PluginSet.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Realign.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Region.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RegionSearch.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RemoteSet.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render::Slave::AWS_Balancer.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render::Slave::Status.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RenderPanels.3pm
Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Util.3pm
Installing debian/gbrowse/man/man3/CGI::Toggle.3pm
Installing debian/gbrowse/man/man3/GBrowse::ConfigData.3pm
Installing debian/gbrowse/man/man3/Legacy::Graphics::Browser.3pm
Installing debian/gbrowse/bin/bed2gff3.pl
Installing debian/gbrowse/bin/gbrowse_aws_balancer.pl
Installing debian/gbrowse/bin/gbrowse_change_passwd.pl
Installing debian/gbrowse/bin/gbrowse_clean.pl
Installing debian/gbrowse/bin/gbrowse_configure_slaves.pl
Installing debian/gbrowse/bin/gbrowse_create_account.pl
Installing debian/gbrowse/bin/gbrowse_grow_cloud_vol.pl
Installing debian/gbrowse/bin/gbrowse_import_ucsc_db.pl
Installing debian/gbrowse/bin/gbrowse_metadb_config.pl
Installing debian/gbrowse/bin/gbrowse_set_admin_passwd.pl
Installing debian/gbrowse/bin/gbrowse_slave
Installing debian/gbrowse/bin/gbrowse_syn_load_alignment_database.pl
Installing debian/gbrowse/bin/gbrowse_syn_load_alignments_msa.pl
Installing debian/gbrowse/bin/gbrowse_sync_aws_slave.pl
Installing debian/gbrowse/bin/gtf2gff3.pl
Installing debian/gbrowse/bin/load_genbank.pl
Installing debian/gbrowse/bin/make_das_conf.pl
Installing debian/gbrowse/bin/scan_gbrowse.pl
Installing debian/gbrowse/bin/ucsc_genes2gff.pl
Installing debian/gbrowse/bin/wiggle2gff3.pl
#./Build apache_conf > debian/gbrowse/etc/gbrowse/gbrowse_apache2.conf
perl Build.PL --conf=/etc/gbrowse --htdocs=/usr/share/gbrowse/htdocs --tmp=/var/cache/gbrowse --databases=/var/lib/gbrowse/databases --cgibin=/usr/lib/cgi-bin/gbrowse --www-user=www-data --registration_done=1 --persistent=/var/lib/gbrowse --installetc=y
WARNING: the following files are missing in your kit:
contrib/ace2gff.pl
contrib/AxtPairwise_convert/axt2phy.pl
contrib/blast2gff.pl
contrib/conf_files/01.yeast.conf
contrib/conf_files/02.wormbase.conf
contrib/conf_files/03.fly.conf
contrib/conf_files/04.human.conf
contrib/conf_files/05.embl_proxy.conf
contrib/conf_files/06.biosql.conf
contrib/conf_files/07.chado.conf
contrib/conf_files/08.genbank.conf
contrib/conf_files/09.human_karyotype.conf
contrib/conf_files/index.html
contrib/conf_files/wormbase.syn
contrib/Coverage/INSTALL
contrib/Coverage/plugin/Coverage.pm
contrib/Coverage/README
contrib/gdump.pl
contrib/GeneFinder/genefinder/gfcode.c
contrib/GeneFinder/genefinder/README
contrib/GeneFinder/genefinder/readseq.c
contrib/GeneFinder/genefinder/readseq.h
contrib/GeneFinder/nematode_gftables/cds.hex
contrib/GeneFinder/nematode_gftables/gftables
contrib/GeneFinder/nematode_gftables/newnem.atg
contrib/GeneFinder/nematode_gftables/newnem.codon
contrib/GeneFinder/nematode_gftables/newnem.gene
contrib/GeneFinder/nematode_gftables/newnem.intron3
contrib/GeneFinder/nematode_gftables/newnem.intron5
contrib/GeneFinder/nematode_gftables/ref.hist
contrib/GeneFinder/nematode_gftables/zk637.atg
contrib/GeneFinder/nematode_gftables/zk637.intron3
contrib/GeneFinder/nematode_gftables/zk637.intron5
contrib/GeneFinder/nematode_gftables/zk637.trinuc
contrib/import_ncbi_mv_hs.pl
contrib/install_macosx/BuildConfig.pm
contrib/install_macosx/README.html
contrib/install_macosx/README.pod
contrib/install_macosx/scripts/build-gbrowse.pl
contrib/install_macosx/scripts/build-libraries.pl
contrib/README
contrib/SynView/cgi-lib/DAS/GUS.pm
contrib/SynView/cgi-lib/DAS/GUS/Segment.pm
contrib/SynView/cgi-lib/DAS/GUS/Segment/Feature.pm
contrib/SynView/cgi-lib/DAS/Util/SqlParser.pm
contrib/SynView/gbrowse.conf/plasmodb.conf
contrib/SynView/gbrowse.conf/plasmodb.xml
contrib/SynView/MAL11/MAL11.conf
contrib/SynView/MAL11/MAL11.fa
contrib/SynView/MAL11/MAL11.gff3
contrib/SynView/README
contrib/TextDumper/README
contrib/TextDumper/TextDumper.pm
lib/Bio/DB/SeqFeature/Store/LoadHelper.pm
Please inform the author.
Checking prerequisites...
recommends:
* Bio::DB::BigFile is not installed
* Bio::DB::Sam is not installed
* Bio::Das is not installed
* Crypt::SSLeay is not installed
* DBD::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/default/gbrowse-aws-balancer
Installing debian/gbrowse/etc/default/gbrowse-slave
Installing debian/gbrowse/etc/init.d/gbrowse-aws-balancer
Installing debian/gbrowse/etc/init.d/gbrowse-slave
Installing debian/gbrowse/lib/perl5/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-dbgsym' in '../gbrowse-calign-dbgsym_2.56+dfsg-4_armhf.deb'.
dpkg-deb: building package 'gbrowse-calign' in '../gbrowse-calign_2.56+dfsg-4_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../gbrowse_2.56+dfsg-4_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 2018-10-08T07:13:50Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
gbrowse_2.56+dfsg-4_armhf.changes:
----------------------------------
Format: 1.8
Date: Wed, 03 Oct 2018 15:07:54 +0200
Source: gbrowse
Binary: gbrowse gbrowse-data gbrowse-calign
Architecture: armhf
Version: 2.56+dfsg-4
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <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
Changes:
gbrowse (2.56+dfsg-4) unstable; urgency=medium
.
* Update URL in watch file
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.1
Checksums-Sha1:
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8a7119990bac63a4a755a6ea6db4020fa7825d35 8155 gbrowse_2.56+dfsg-4_armhf.buildinfo
Checksums-Sha256:
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Files:
b8603c40c14a0b2b1bbc9d9b6dd6494c 30352 debug optional gbrowse-calign-dbgsym_2.56+dfsg-4_armhf.deb
a26ac018081ee07f4e60f11141594ca7 35740 science optional gbrowse-calign_2.56+dfsg-4_armhf.deb
209f3f9eed727f884b0d2bf8fc5bee23 8155 science optional gbrowse_2.56+dfsg-4_armhf.buildinfo
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
gbrowse-calign-dbgsym_2.56+dfsg-4_armhf.deb
-------------------------------------------
new Debian package, version 2.0.
size 30352 bytes: control archive=544 bytes.
398 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: gbrowse-calign-dbgsym
Source: gbrowse
Version: 2.56+dfsg-4
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 42
Depends: gbrowse-calign (= 2.56+dfsg-4)
Section: debug
Priority: optional
Description: debug symbols for gbrowse-calign
Build-Ids: f7ea151c10e904980d008aacf7d29ba00461ae06
drwxr-xr-x root/root 0 2018-10-03 13:07 ./
drwxr-xr-x root/root 0 2018-10-03 13:07 ./usr/
drwxr-xr-x root/root 0 2018-10-03 13:07 ./usr/lib/
drwxr-xr-x root/root 0 2018-10-03 13:07 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-10-03 13:07 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-10-03 13:07 ./usr/lib/debug/.build-id/f7/
-rw-r--r-- root/root 32376 2018-10-03 13:07 ./usr/lib/debug/.build-id/f7/ea151c10e904980d008aacf7d29ba00461ae06.debug
drwxr-xr-x root/root 0 2018-10-03 13:07 ./usr/share/
drwxr-xr-x root/root 0 2018-10-03 13:07 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-10-03 13:07 ./usr/share/doc/gbrowse-calign-dbgsym -> gbrowse-calign
gbrowse-calign_2.56+dfsg-4_armhf.deb
------------------------------------
new Debian package, version 2.0.
size 35740 bytes: control archive=940 bytes.
626 bytes, 17 lines control
663 bytes, 7 lines md5sums
Package: gbrowse-calign
Source: gbrowse
Version: 2.56+dfsg-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 76
Depends: perl (>= 5.26.2-7), perlapi-5.26.2, 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 2018-10-03 13:07 ./
drwxr-xr-x root/root 0 2018-10-03 13:07 ./usr/
drwxr-xr-x root/root 0 2018-10-03 13:07 ./usr/lib/
drwxr-xr-x root/root 0 2018-10-03 13:07 ./usr/lib/arm-linux-gnueabihf/
drwxr-xr-x root/root 0 2018-10-03 13:07 ./usr/lib/arm-linux-gnueabihf/perl5/
drwxr-xr-x root/root 0 2018-10-03 13:07 ./usr/lib/arm-linux-gnueabihf/perl5/5.26/
drwxr-xr-x root/root 0 2018-10-03 13:07 ./usr/lib/arm-linux-gnueabihf/perl5/5.26/Bio/
drwxr-xr-x root/root 0 2018-10-03 13:07 ./usr/lib/arm-linux-gnueabihf/perl5/5.26/Bio/Graphics/
drwxr-xr-x root/root 0 2018-10-03 13:07 ./usr/lib/arm-linux-gnueabihf/perl5/5.26/Bio/Graphics/Browser2/
-rw-r--r-- root/root 1129 2018-10-03 13:07 ./usr/lib/arm-linux-gnueabihf/perl5/5.26/Bio/Graphics/Browser2/CAlign.pm
drwxr-xr-x root/root 0 2018-10-03 13:07 ./usr/lib/arm-linux-gnueabihf/perl5/5.26/auto/
drwxr-xr-x root/root 0 2018-10-03 13:07 ./usr/lib/arm-linux-gnueabihf/perl5/5.26/auto/Bio/
drwxr-xr-x root/root 0 2018-10-03 13:07 ./usr/lib/arm-linux-gnueabihf/perl5/5.26/auto/Bio/Graphics/
drwxr-xr-x root/root 0 2018-10-03 13:07 ./usr/lib/arm-linux-gnueabihf/perl5/5.26/auto/Bio/Graphics/Browser2/
drwxr-xr-x root/root 0 2018-10-03 13:07 ./usr/lib/arm-linux-gnueabihf/perl5/5.26/auto/Bio/Graphics/Browser2/CAlign/
-rw-r--r-- root/root 0 2018-10-03 13:07 ./usr/lib/arm-linux-gnueabihf/perl5/5.26/auto/Bio/Graphics/Browser2/CAlign/CAlign.bs
-rw-r--r-- root/root 9476 2018-10-03 13:07 ./usr/lib/arm-linux-gnueabihf/perl5/5.26/auto/Bio/Graphics/Browser2/CAlign/CAlign.so
drwxr-xr-x root/root 0 2018-10-03 13:07 ./usr/share/
drwxr-xr-x root/root 0 2018-10-03 13:07 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-10-03 13:07 ./usr/share/doc/gbrowse-calign/
-rw-r--r-- root/root 2192 2018-10-03 13:07 ./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 18041 2018-10-03 13:07 ./usr/share/doc/gbrowse-calign/copyright
drwxr-xr-x root/root 0 2018-10-03 13:07 ./usr/share/man/
drwxr-xr-x root/root 0 2018-10-03 13:07 ./usr/share/man/man3/
-rw-r--r-- root/root 2128 2018-10-03 13:07 ./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: 32348
Build-Time: 225
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 849
Job: gbrowse_2.56+dfsg-4
Machine Architecture: armhf
Package: gbrowse
Package-Time: 1137
Source-Version: 2.56+dfsg-4
Space: 32348
Status: successful
Version: 2.56+dfsg-4
--------------------------------------------------------------------------------
Finished at 2018-10-08T07:13:50Z
Build needed 00:18:57, 32348k disc space