Your message dated Wed, 02 Dec 2015 11:48:56 +0000
with message-id <[email protected]>
and subject line Bug#806618: fixed in gbrowse 2.54+dfsg-6
has caused the Debian Bug report #806618,
regarding gbrowse: FTBFS when built with dpkg-buildpackage -A (mv: target is
not a directory)
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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misconfiguration somewhere. Please contact [email protected]
immediately.)
--
806618: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=806618
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:gbrowse
Version: 2.54+dfsg-5
User: [email protected]
Usertags: binary-indep
Severity: important
Dear maintainer:
I tried to build this package with "dpkg-buildpackage -A"
(i.e. only architecture-independent packages), and it failed:
--------------------------------------------------------------------------------
[...]
debian/rules build-indep
dh build-indep --with apache2
dh_testdir -i
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/gbrowse-2.54+dfsg'
dh_auto_configure -- --conf=/etc/gbrowse --htdocs=/usr/share/gbrowse/htdocs
--tmp=/var/cache/gbrowse --databases=/var/lib/gbrowse/databases
--cgibin=/usr/lib/cgi-bin/gbrowse --www-user=www-data --registration_done=1
--persistent=/var/lib/gbrowse
perl Build.PL --installdirs vendor --config "optimize=-g -O2
-fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2"
--config "ld=cc -g -O2 -fstack-protector-strong -Wformat
-Werror=format-security -Wl,-z,relro" --conf=/etc/gbrowse
--htdocs=/usr/share/gbrowse/htdocs --tmp=/var/cache/gbrowse
--databases=/var/lib/gbrowse/databases --cgibin=/usr/lib/cgi-bin/gbrowse
--www-user=www-data --registration_done=1 --persistent=/var/lib/gbrowse
Possible precedence issue with control flow operator at
/<<BUILDDIR>>/gbrowse-2.54+dfsg/install_util/GBrowseInstall.pm line 1032.
Checking prerequisites...
recommends:
* Bio::DB::BigFile is not installed
* Bio::DB::Sam is not installed
[... snipped ...]
Performing variable substitutions in blib/conf/yeast_simple.conf
Performing variable substitutions in blib/htdocs/annotation_help.html
Performing variable substitutions in blib/htdocs/cloud_index.html
Performing variable substitutions in blib/htdocs/example_scripts/index.html
Performing variable substitutions in blib/htdocs/example_scripts/README
Performing variable substitutions in blib/htdocs/gbrowse_karyotype_help.html
Performing variable substitutions in blib/htdocs/gbrowse_syn_help.html
Performing variable substitutions in blib/htdocs/general_help.html
Performing variable substitutions in blib/htdocs/index.html
Performing variable substitutions in
blib/htdocs/tutorial/conf_files/elegans_core.conf
Performing variable substitutions in
blib/htdocs/tutorial/conf_files/elegans_extra.conf
Performing variable substitutions in blib/htdocs/tutorial/conf_files/HEADER.html
Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox.conf
Performing variable substitutions in
blib/htdocs/tutorial/conf_files/volvox_final.conf
Performing variable substitutions in
blib/htdocs/tutorial/conf_files/volvox_final_withPhylo.conf
Performing variable substitutions in
blib/htdocs/tutorial/conf_files/volvox_halfway.conf
Performing variable substitutions in
blib/htdocs/tutorial/conf_files/volvox_Phylo.conf
Performing variable substitutions in
blib/htdocs/tutorial/conf_files/volvox_quarter.conf
Performing variable substitutions in
blib/htdocs/tutorial/conf_files/volvox_refactored.conf
Performing variable substitutions in blib/htdocs/tutorial/data_files/HEADER.html
Performing variable substitutions in blib/htdocs/tutorial/tutorial.html
Performing variable substitutions in
blib/htdocs/tutorial/tutorial.phyTreeEdit.html
Performing variable substitutions in blib/htdocs/vbox_index.html
Performing variable substitutions in blib/etc/default/gbrowse-slave
Performing variable substitutions in blib/etc/init.d/gbrowse-slave
Use of uninitialized value $wwwuser in substitution (s///) at
/<<BUILDDIR>>/gbrowse-2.54+dfsg/install_util/GBrowseInstall.pm line 821,
<GEN89> line 20.
Building GBrowse
Files found in blib/arch: installing files in blib/lib into architecture
dependent library tree
Installing debian/gbrowse/etc/init.d/gbrowse-slave
Installing debian/gbrowse/etc/default/gbrowse-slave
Installing
debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/GBrowse/ConfigData.pm
mv debian/gbrowse/lib/perl5/* debian/gbrowse/usr/share/perl5
# Remove arch dependant data
mv debian/gbrowse/usr/share/perl5/auto/Bio/Graphics/Browser2/CAlign/*
debian/gbrowse-calign/usr/lib/x86_64-linux-gnu/perl5/5.20/auto/Bio/Graphics/Browser2/CAlign/
mv: target
'debian/gbrowse-calign/usr/lib/x86_64-linux-gnu/perl5/5.20/auto/Bio/Graphics/Browser2/CAlign/'
is not a directory
debian/rules:18: recipe for target 'override_dh_auto_install' failed
make[1]: *** [override_dh_auto_install] Error 1
make[1]: Leaving directory '/<<BUILDDIR>>/gbrowse-2.54+dfsg'
debian/rules:7: recipe for target 'binary-indep' failed
make: *** [binary-indep] Error 2
dpkg-buildpackage: error: fakeroot debian/rules binary-indep gave error exit
status 2
--------------------------------------------------------------------------------
Sorry not to have a fix, as I am reporting many bugs similar to
this one. The common hints are:
* If the only architecture-independent packages are dummy transitional
ones and they were released with jessie, the easy fix is to drop them
now.
* When using "dh", it is allowed to use (independently)
optional targets override_dh_foo-arch and override_dh_foo-indep
(for several values of "foo").
Once that both "dpkg-buildpackage -A" and "dpkg-buildpackage -B" work
properly, the package would be suitable to be uploaded in source-only
form if you wish.
Thanks.
--- End Message ---
--- Begin Message ---
Source: gbrowse
Source-Version: 2.54+dfsg-6
We believe that the bug you reported is fixed in the latest version of
gbrowse, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated gbrowse package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Wed, 02 Dec 2015 10:16:15 +0100
Source: gbrowse
Binary: gbrowse gbrowse-data gbrowse-calign
Architecture: source amd64 all
Version: 2.54+dfsg-6
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
gbrowse - GMOD Generic Genome Browser
gbrowse-calign - CAlign helper
gbrowse-data - Sample data to use GBrowse
Closes: 806618
Changes:
gbrowse (2.54+dfsg-6) unstable; urgency=medium
.
* Team upload
.
[ Charles Plessy ]
* Use and build-depend on file-rename directly as /usr/bin/rename
will move out from the perl package.
.
[ Andreas Tille ]
* Echo hint to switch to Files-Excluded for next upstream version
* Enable arch independent build by ensuring that target directories
are existing
Closes: #806618
* Fix several lintian issues
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