On 12/16/2013 11:25 AM, Andreas Tille wrote:
> Package: soapdenovo
> Severity: normal
>
> Hi Olivier,
>
> I stumbled upon soapdenovo since on one hand there seems to be a watch
> file that for whatever reason reports a new version if you look at
>
>http://blends.debian.org/med/tasks/bio#soapde
On 12/16/2013 01:47 PM, Martin Weiser wrote:
> Andreas Tille píše v Po 16. 12. 2013 v 13:33 +0100:
>> Hi Martin,
>>
>> On Mon, Dec 16, 2013 at 12:55:33PM +0100, Martin Weiser wrote:
>>> Dear friends,
>>>
>>> maybe there is something else involved (should I open another bug?), as
>>> Olivier's work
On 11/10/2013 03:03 AM, Andreas Beckmann wrote:
> I can reproduce this problem in pbuilder using the sid tarball as created by
> piuparts and the following commands:
>
> sudo pbuilder login --basetgz /srv/piuparts/slave/basetgz/sid_amd64.tar.gz
>
> export DEBIAN_FRONTEND=noninteractive
> sed -i /
Those sources files are not really "source files" , they are
added/generated by GWT, used to build the war file.
Those files are not used to build the package, and are
regenerated/copied by the build process from GWT.
As biomaj-watcher is in contrib, this should not be an issue.
I will, however,
file is included in source but not used in application.
I gonna remove it from upstream code.
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with a
Package: wnpp
Severity: wishlist
Owner: Olivier Sallou
* Package name: cassiopee
Version : 1.0.0
Upstream Author : Olivier Sallou
* URL : https://github.com/osallou/cassiopee-c
* License : MIT
Programming Lang: C++
Description : index and search tool i
Upstream is responsible of modifying the load.conf file. I gonna try to
remove it from package to see if file is necessary or what should be
done to avoid this.
Regarding password in conf file:
- this file is needed by library to access the database (read and
write). I gonna change read access to
Password set in "clear" in postinst is only a template with default
values set at first-time install.
User/Admin must update values to a correct db user to access the database.
This is needed because application setup needs a password information.
Password echoed at this step is not a security fl
Le 6/23/12 8:31 PM, Christian PERRIER a écrit :
> Hello,
>
> This package is in my radar as it is one of those that have
> incomplete translations for debconf templates, for at least one of the
> seven languages targeting 100% in wheezy (fr, de, cs, sv, pt, ru, es)
>
> Do you actually plan to upl
Package: libbio-graphics-perl
Severity: wishlist
GBrowse package needs version 2.26 of Bio::Graphics. Package needs to be
updated.
Olivier
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Le 7/2/12 10:01 PM, Aaron M. Ucko a écrit :
> Source: logol
> Version: 1.5.0-2
> Severity: serious
> Justification: fails to build from source
>
> For some reason, logol's test suite has been failing on ia64 and
> sparc. The ia64 log
> (https://buildd.debian.org/status/fetch.php?pkg=logol&arch=i
After investigation on ia64, repdocuding the error on anyspacer.logol
test, there is a segmentation fault in prolog executable.
It occurs in the middle of the treatment.
WIth logs we see the seg fault occuring at:
write(LogolVAR_Before_2),nl,sleep(1),*SEGFAULT HERE*
isexact_pos(LogolVAR_Before_2['
Le 9/6/12 9:53 PM, Andreas Tille a écrit :
> Hi Sebastian,
>
> On Mon, Aug 27, 2012 at 08:20:14PM +0200, Sebastian Hilbert wrote:
>>> after reading the bug report twice I noticed that the problem is
>>> actually not comparable to the issue discussed currently on
>>> debian-devel@l.d.o, because the
Package: wnpp
Severity: wishlist
Owner: Olivier Sallou
X-Debbugs-Cc: debian-...@lists.debian.org
* Package name: libvm-ec2-perl
Version : 1.17
Upstream Author : Lincoln D. Stein
* URL : http://search.cpan.org/~lds/VM-EC2-1.02/
* License : Artistic 1 and GPL-1
Package: wnpp
Severity:wishlist
* Package name: soapdenovo2
Version : 2.2.3
Upstream Author : BGI-Shenzhen
* URL : http://soap.genomics.org.cn/soapdenovo.html
* License : GPL3+
Programming Lang: C
Description : short-read assembly method that can build
Package: wnpp
Owner: olivier sallou
Severity: wishlist
X-Debbugs-CC:
debian-de...@lists.alioth.debian.org,debian-perl-packag...@lists.alioth.debian.org,debian-med-packag...@lists.alioth.debian.org
* Package name: libgetopt-complete-perl
Version : 0.26
Upstream Author : Washingto
Package: wnpp
Owner: olivier sallou
Severity: wishlist
X-Debbugs-CC:
debian-de...@lists.alioth.debian.org,debian-perl-packag...@lists.alioth.debian.org,debian-med-packag...@lists.alioth.debian.org
* Package name: libclass-autoloadcan-perl
Version : 0.03
Upstream Author : Ben Till
Package: wnpp
Owner: olivier sallou
Severity: wishlist
X-Debbugs-CC:
debian-de...@lists.alioth.debian.org,debian-perl-packag...@lists.alioth.debian.org,debian-med-packag...@lists.alioth.debian.org
* Package name: libtest-fork-perl
Version : 0.02
Upstream Author : Michael G Schwe
Package: wnpp
Owner: olivier sallou
Severity: wishlist
X-Debbugs-CC:
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* Package name: libur-perl
Version : 0.392
Upstream Author : Anthony Brummett ,Sc
Package: wnpp
Owner: olivier sallou
Severity: wishlist
X-Debbugs-CC:
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* Package name: libgenome-perl
Version : 0.06
Upstream Author : 2007-2011 Washingt
Package: wnpp
Owner: olivier sallou
Severity: wishlist
X-Debbugs-CC:
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* Package name: libgenome-model-tools-music-perl
Version : 0.4
Upstream Author : Th
This should have been fixed in 1.4-1 with classpath related to
sa-jdi.jar in debian/patches/fix_classpath_in_build_xml.patch
This jar has been added to build path.
Build has been tested with pbuilder from sid.
This could be related to JAVA_HOME not being set in environment
Olivier
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Package: wnpp
Severity: wishlist
Owner: Olivier Sallou
* Package name: opennebula-context
Version : 4.2.0
Upstream Author : OpenNebula
* URL : http://opennebula.org/
* License : Apache 2.0
Programming Lang: bash
Description : Contextualization package f
I see a test failing in t/Ontology/IO/obo.t line 47 at is
(scalar(@terms), 5), used to work in a previous perl release:
Code of test:
my $parser = Bio::OntologyIO->new(
-format=> "obo",
^I^I -file => test_input_file('so.obo'));
my $ont = $parser->next_ontology
Running several times *perl t/Ontology/IO/obo.t* leads to different results
We sometimes have 1 or 6 or 7 failing tests
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It appears that: (in obo ontology test)
my @terms = $ont->get_child_terms($roots[0]);
@terms array order is not always the same.
As following tests take first element of array, it explains why
sometimes it succeed, sometimes it fails
Now I don't know why order is different
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On 08/26/2013 08:54 PM, gregor herrmann wrote:
> On Mon, 26 Aug 2013 12:56:16 +0200, olivier.sal...@codeless.fr wrote:
>
>> As following tests take first element of array, it explains why
>> sometimes it succeed, sometimes it
Package: wnpp
Severity: wishlist
Owner: Olivier Sallou
X-Debbugs-Cc: debian-...@lists.debian.org
* Package name: mmtk
Version : 2.6.1
Upstream Author : Konrad Hinsen
* URL : https://sourcesup.cru.fr/projects/mmtk/
* License : CeCILL C
Programming Lang: C, P
On 08/16/2015 11:28 AM, Chris West (Faux) wrote:
> Source: biojava4-live
> Version: 4.1.0+dfsg-1
> Severity: serious
> Justification: fails to build from source
> Tags: sid stretch
> User: reproducible-bui...@lists.alioth.debian.org
> Usertags: ftbfs
> X-Debbugs-CC: reproducible-bui...@lists.alio
On 08/17/2015 01:57 PM, Chris Lamb wrote:
> Source: biojava4-live
> Version: 4.1.0+dfsg-1
> Severity: serious
> Justification: fails to build from source
> User: reproducible-bui...@lists.alioth.debian.org
> Usertags: ftbfs
> X-Debbugs-Cc: reproducible-bui...@lists.alioth.debian.org
>
> Dear Main
On 08/31/2015 09:27 AM, Andreas Tille wrote:
> Hi,
>
> I commited a fix for the library transition to SVN. (Besides this
> I also tried to fix some lintian issues but failed with the
> wrong-whatis-entry-in-manpage one.)
>
> Olivier, could you please check and either upload or ping me for
> team
On 12/14/2014 03:19 PM, Emilien Klein wrote:
> TLDR: Please check if the "/var/lib/tomcat8/shared" folder is still used
> with Tomcat 8.
>
>
> I have applied the previously attached patch, the package builds fine,
> but when installing the .deb the following error occurs:
>
> Setting up biomaj-wat
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