Bug#609038: ITP: biomaj -- a biological databank update and processing tool

2011-01-05 Thread Olivier Sallou
Package: biomaj Version: 1.1.0 Severity: wishlist I want to package the Biomaj tool (http://biomaj.genouest.org) for Debian. The tool is already on production on several servers worldwide. -- System Information: Debian Release: squeeze/sid APT prefers lucid-updates APT policy: (500,

Bug#609038: ITP: biomaj -- a biological databank update and processing tool

2011-01-06 Thread Olivier Sallou
for working on this package Andreas. On Wed, Jan 05, 2011 at 06:14:27PM +0100, Olivier Sallou wrote: Package: biomaj Version: 1.1.0 Severity: wishlist I want to package the Biomaj tool (http://biomaj.genouest.org) for Debian. The tool is already on production on several servers worldwide

Bug#609038: BioMAJ additional information

2011-01-06 Thread Olivier Sallou
Package name: biomaj Version : 1.1.0 Upstream Author : Olivier Sallou olivier.sal...@irisa.fr Programming Lang: Java License: CeCILL, french equivalent of GNU GPL Description: Biological banks updater BioMAJ downloads remote biological data banks, check their status

Bug#429610: GBrowse2 packaging

2011-02-23 Thread Olivier Sallou
Hi, I repackaged gbrowse2, I gonna update the svn of gbrowse on trunk I will let you know once ready to have a look ... Olivier Le 2/6/11 1:52 PM, Charles Plessy a écrit : Le Sun, Feb 06, 2011 at 10:49:42AM +0100, Olivier Sallou a écrit : I am looking at GBrowse2 packaging. If I succeed

Bug#429610: GBrowse2 packaging

2011-02-24 Thread Olivier Sallou
. Regards Olivier Le 2/23/11 2:36 PM, Olivier Sallou a écrit : Hi, I repackaged gbrowse2, I gonna update the svn of gbrowse on trunk I will let you know once ready to have a look ... Olivier Le 2/6/11 1:52 PM, Charles Plessy a écrit : Le Sun, Feb 06, 2011 at 10:49:42AM +0100, Olivier Sallou

Bug#429610: Gbrowse2 licensing issues, trigger upstream team at sourceforge

2011-03-10 Thread Olivier Sallou
I created a support request at upstream source to get more info on some licensing issues in files. I join mail exchange and reference Support Requests item #3201863, was opened at 2011-03-07 08:01 Message generated for change (Settings changed) made by scottcain You can respond by visiting:

Bug#429610: gbrowse2 licensing issue fixed

2011-04-01 Thread Olivier Sallou
I could have a look for dropdown css. License is GNU GPL. It comes from http://lwis.net/free-css-drop-down-menu/ For readseq.c, I decided to remove contrib directory from source, while other contribs are not clear from license point of view. Contribs are not required for software usage. --

Bug#622854: Please Add Olivier Sallou as Debian Maintainer

2011-04-15 Thread Olivier Sallou
/debian-newmaint/2011/04/msg00028.html Comment: Add olivier sallou olivier.sal...@irisa.fr as a Debian Maintainer Date: Fri, 15 Apr 2011 10:24:50 +0200 Action: import Data: -BEGIN PGP PUBLIC KEY BLOCK- Version: GnuPG v1.4.11 (GNU/Linux) mQINBE0

Bug#623242: context xml file not taken into account, only web.xml is used

2011-04-18 Thread Olivier Sallou
Package: tomcat6 Version: 6.0.32 Hi, when I put a context file in /etc/tomcat6/Catalina/localhost (such as myapp.xml), the context param values are not taken into account. This used to work on previous tests on an older update. To be sure, I took a Tomcat 6.0.24 version (not packaged), and

Bug#623242: possible related bug at apache

2011-04-18 Thread Olivier Sallou
Seems to be related to https://issues.apache.org/bugzilla/show_bug.cgi?id=50700 so should be fixed in 6.0.33 This bug is however blocking for applications Olivier -- gpg key id: 4096R/326D8438 (pgp.mit.edu) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To

Bug#429610: use debian javascript packages instead of included ones

2011-03-14 Thread Olivier Sallou
Package has been update to use javascript libraries packaged in Debian (prototype/scriptaculous) after maintainer has updated them on sid. -- gpg key id: 4096R/326D8438 (pgp.mit.edu) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to

Bug#618689: ITP: squizz bioinformatics sequence converter tool

2011-03-17 Thread Olivier Sallou
Package: wnpp Severity: wishlist X-Debbugs-CC: debian-...@lists.debian.org Maintainer: Olivier Sallou olivier.sal...@irisa.fr Language: C License: GNU v2 Upstream Author: Nicolas Joly nj...@pasteur.fr Homepage: ftp://ftp.pasteur.fr/pub/gensoft/projects/squizz/ Description: Squizz is a sequence

Bug#623558: trivial error, pid not required anymore

2011-04-22 Thread Olivier Sallou
-BEGIN PGP SIGNED MESSAGE- Hash: SHA256 The pid file that biomaj.sh tries to create is not used anymore. A patch will remove its creation. Error does not prevent bank update. - -- gpg key id: 4096R/326D8438 (pgp.mit.edu) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D

Bug#624205: new version available GWT2

2011-04-26 Thread Olivier Sallou
Package: gwt Severity: wishlist GWT2 is available for quite a long time now, but GWT debian package is still at version 1.6 Version 2 adds new features and most of GWT based apps are based now on this version. Could you please update the package. Thanks Olivier -- gpg key id: 4096R/326D8438

Bug#624284: error in postrm prevent smooth package upgrades

2011-04-27 Thread Olivier Sallou
Package: biomaj Severity: normal An error in postrm file prevent the upgrade of the package. An upgrade will fail. Package will need removal then install of new package. This has no impact on installed data... -- gpg key id: 4096R/326D8438 (pgp.mit.edu) Key fingerprint = 5FB4 6F83 D3B9 5204

Bug#624284: change severity

2011-04-27 Thread Olivier Sallou
Severity: grave change severity to prevent going to testing -- gpg key id: 4096R/326D8438 (pgp.mit.edu) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble?

Bug#624394: ITP:ncbi-blast-plus

2011-04-28 Thread Olivier Sallou
Package: wnpp Severity: wishlist Owner: Olivier Sallou olivier.sal...@irisa.fr Package name: ncbi-blast-plus Version : 2.2.25 URL : http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=WebPAGE_TYPE=BlastDocsDOC_TYPE=Download License : public domain Programming Lang: C

Bug#632086: ITP:libmath-vecstat-perl --Some basic numeric stats on vectors

2011-06-29 Thread Olivier Sallou
Package: wnpp Severity: wishlist X-Debbugs-CC:debian-...@lists.debian.org Language: Perl Homepage: http://search.cpan.org/dist/Math-VecStat/ Description: This package offers some basic statistics on vectors (min,max,average,) Dependencies: None Upstream author: Andrea Spinelli -- Olivier

Bug#632174: ITP:circos -- software package for visualizing data and information in a circular layout

2011-06-30 Thread Olivier Sallou
/intro/circular_approach --- this makes Circos ideal for exploring relationships between objects or positions Upstream author: Martin Krzywinski mart...@bcgsc.ca -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R

Bug#632174: add license info

2011-06-30 Thread Olivier Sallou
License: GPL2+ -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (pgp.mit.edu) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-bugs-dist-requ

Bug#632174: set owner

2011-08-11 Thread Olivier Sallou
owner: olivier.sal...@irisa.fr -- gpg key id: 4096R/326D8438 (pgp.mit.edu) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438

Bug#639868: ITP: chado -- Chado is a relational database schema that underlies many GMOD installations.

2011-08-31 Thread Olivier Sallou
Package: wnpp Severity: wishlist Owner: Olivier Sallou olivier.sal...@irisa.fr * Package name: chado Version : 1.11 Upstream Author : GMOD * URL : http://gmod.org/wiki/Chado_-_Getting_Started * License : Artistic License 2.0 Programming Lang: Perl,SQL

Bug#642991: [Debian-med-packaging] Bug#642991: ncbi-blast+: should notify why some tools are missing

2011-09-26 Thread Olivier Sallou
-packaging mailing list debian-med-packag...@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging - -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (pgp.mit.edu

Bug#643000: antlr has newer major version (3.4)

2011-09-26 Thread Olivier Sallou
Package: antlr Version: 2.7.7-17 Severity: wishlist Antlr provides new major version (3.x), grammars for version 3.x do not compile with 2.x (not completly at least) Could you go for newer version? -- System Information: Debian Release: wheezy/sid APT prefers unstable APT policy: (500,

Bug#643000: antlr has newer major version (3.4)

2011-09-26 Thread Olivier Sallou
-BEGIN PGP SIGNED MESSAGE- Hash: SHA256 Thanks, I had not seen that package had different packages per major version. Olivier Le 9/26/11 2:46 PM, Miguel Landaeta a écrit : reassign 643000 antlr3 thanks On Mon, Sep 26, 2011 at 01:44:41PM +0200, Olivier Sallou wrote: Antlr provides

Bug#632174: Fwd: font pointers license

2011-08-02 Thread Olivier Sallou
I tried to clarify license on pointers fonts embedded in upstream software. Author is ok to allow modifications on sources. - Mail transféré - De: Russ Rowlett rowl...@email.unc.edu À: Olivier Sallou olivier.sal...@irisa.fr Envoyé: Lundi 1 Août 2011 23:04:46 Objet: RE: font pointers

Bug#632174: Fwd: RE: font pointers license

2011-08-02 Thread Olivier Sallou
Message original Sujet: RE: font pointers license Date : Tue, 2 Aug 2011 12:36:41 + De :Rowlett, Russ rowl...@email.unc.edu Pour : Olivier Sallou olivier.sal...@irisa.fr Yes, that would be OK. Russ From: Olivier Sallou

Bug#637109: ITP: pycaptcha -- collection of Python modules implementing CAPTCHAs

2011-08-08 Thread Olivier Sallou
Package: wnpp Severity: wishlist Owner: Olivier Sallou olivier.sal...@irisa.fr * Package name: pycaptcha Version : 2.4 Upstream Author : Micah Dowty micah at navi cx * URL : http://pypi.python.org/pypi/PyCAPTCHA/0.4 * License : MIT Programming Lang: Python

Bug#637230: ITP: mobyle -- Mobyle is a wbe portal and framework to provide web interfaces to command-line tools. It is designed though not limited for bioinfomatics.

2011-08-09 Thread Olivier Sallou
Package: wnpp Severity: wishlist Owner: Olivier Sallou olivier.sal...@irisa.fr * Package name: mobyle Version : 1.0.0 Upstream Author : Herve Menager herve.mena...@pasteur.fr * URL : https://projets.pasteur.fr/wiki/mobyle/download * License : GPL Programming

Bug#632174: set owner to myself

2011-08-10 Thread Olivier Sallou
Owner: olivier.sal...@irisa.fr -- gpg key id: 4096R/326D8438 (pgp.mit.edu) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org

Bug#642991: [Debian-med-packaging] Bug#642991: ncbi-blast+: should notify why some tools are missing

2011-09-27 Thread Olivier Sallou
Hi, according to the previous discussions, I suggest to move the bug to wishlist severity: 1) people seem to agree that we should not modify extensions from upstream 2) other tools that could be usefull should be splitted to an other packet. Do other involved people agree? Olivier gpg key

Bug#643641: swi-prolog: pldoc not available

2011-09-28 Thread Olivier Sallou
Package: swi-prolog Version: 5.10.4-2+b1 Severity: normal pldoc is not integrated in swi-prolog package. pldoc is delivered with upstream code, this missing tool prevents from generating the prolog documentation on Debian system. -- System Information: Debian Release: wheezy/sid APT prefers

Bug#642991: [Debian-med-packaging] Bug#642991: ncbi-blast+: should notify why some tools are missing

2011-10-01 Thread Olivier Sallou
- Mail original - De: Aaron M. Ucko u...@debian.org À: Luca Capello l...@pca.it Cc: debian-...@lists.debian.org, 642...@bugs.debian.org Envoyé: Vendredi 30 Septembre 2011 21:02:18 Objet: [Debian-med-packaging] Bug#642991: ncbi-blast+: should notify why some tools are missing Luca

Bug#644136: ITP: ruby-text -- collection of text match and analysis algorithms

2011-10-03 Thread Olivier Sallou
Package: wnpp Severity: wishlist Owner: Olivier Sallou olivier.sal...@irisa.fr * Package name: ruby-text Version : 1.1.2 Upstream Author : Paul Battley, Michael Neumann, Tim Fletcher * URL : https://rubygems.org/gems/Text * License : GPL Programming Lang

Bug#644137: ITP: ruby-cassiopee -- provide methods to search exact match or approximate matches with Hamming or edit distance

2011-10-03 Thread Olivier Sallou
Package: wnpp Severity: wishlist Owner: Olivier Sallou olivier.sal...@irisa.fr * Package name: ruby-cassiopee Version : 0.1.8 Upstream Author : Olivier Sallou olivier.sal...@irisa.fr * URL : https://rubygems.org/gems/cassiopee * License : GPL Programming

Bug#644272: ITP: libdbix-dbstag-perl

2011-10-04 Thread Olivier Sallou
Package: libdbix-dbstag-perl Version: 0.12 Owner: olivier.sal...@irisa.fr Creation of package libdbix-dbstag-perl, e.g. DBIx::DBStag from CPAN for Debian. This module is for mapping between relational databases and Stag objects (Structured Tags -

Bug#633523: biomaj: package should depends on default-jdk OR openjdk rather than forcing openjdk

2011-07-11 Thread Olivier Sallou
available) pn ncbi-tools-binnone (no description available) -- Configuration Files: /etc/biomaj/db_properties/global.properties changed [not included] -- debconf information excluded -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel

Bug#674269: waiting for source versioning

2012-06-27 Thread Olivier Sallou
I have sent an email to upstream author to get a versioning between binaries and sources. Sources are not delivered, only in SVN, and not tagged. We can watch new version via download page on binaries but we cannot match a binary with a source SVN commit or tag. -- gpg key id: 4096R/326D8438

Bug#680116: swi-prolog: seg fault on Sparc and IA64

2012-07-03 Thread Olivier Sallou
Package: swi-prolog Version: 5.10.4-3 Severity: important Dear Maintainer, * What led up to the situation? My package logol fails to build on IA64 and Sparc, some tests are failing while ok on other archs * What exactly did you do (or not do) that was effective (or ineffective)?

Bug#680116: swi-prolog: seg fault on Sparc and IA64

2012-07-04 Thread olivier sallou
on debian servers and adm cannot install experimental package. I gonna try for the trace. Olivier Regards, Eugeniy Meshcheryakov 3 липня 2012 о 19:44 +0200 Olivier Sallou написав(-ла): Package: swi-prolog Version: 5.10.4-3 Severity: important Dear Maintainer, * What led up

Bug#680116: swi-prolog: seg fault on Sparc and IA64

2012-07-04 Thread olivier sallou
Here are gdb logs: Program received signal SIGSEGV, Segmentation fault. 0x4007ce21 in into_relocation_chain () (gdb) backtrace #0 0x4007ce21 in into_relocation_chain () #1 0x40088370 in garbageCollect () #2 0x4008a3a0 in ensureGlobalSpace () #3

Bug#678242: qa.debian.org: Package with a problem link to a broken link: check why

2012-06-20 Thread Olivier Sallou
Package: qa.debian.org Severity: minor Dear Maintainer, I was lookig at one of my packages netlib-java (http://packages.qa.debian.org/n/netlib-java.html) and web interface shows a problem section with content: The package has not yet entered testing even though the 10-day delay is over. Check

Bug#678373: ITP: logol -- Pattern matching tool for biological sequences

2012-06-21 Thread Olivier Sallou
Package: wnpp Severity: wishlist Owner: Olivier Sallou osal...@debian.org * Package name: logol Version : 1.5.0 Upstream Author : Olivier Sallou olivier.sal...@irisa.fr * URL : http://logol.genouest.org * License : CeCILL Programming Lang: Java, Prolog

Bug#674265: ITP: biojava3 -- Java API to develop tools for bioinformatics research rewrote from biojava1

2012-05-24 Thread Olivier Sallou
Package: wnpp Severity: wishlist Owner: Olivier Sallou osal...@debian.org * Package name: biojava3 Version : 3.0.4 Upstream Author : BioJava team * URL : http://www.biojava.org/ * License : LGPL Programming Lang: Java Description : Java API to develop

Bug#674269: ITP: libforester-java -- library for phylogenomics and evolutionary biology research

2012-05-24 Thread Olivier Sallou
Package: wnpp Severity: wishlist Owner: Olivier Sallou osal...@debian.org * Package name: forester Version : 0.955 * URL : http://code.google.com/p/forester/ * License : LGPL Programming Lang: Java Description : library for phylogenomics

Bug#679989: linked to

2012-07-17 Thread Olivier Sallou
I have created a bug on swi-prolog as it is the generated executable that generates core dumps. Ref: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=680116 -- gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438

Bug#599651: closure of the bug

2011-10-10 Thread Olivier Sallou
Hi, as package as been updated for a long time ago, couldn't this bug be closed? Olivier -- gpg key id: 4096R/326D8438 (pgp.mit.edu) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject

Bug#644882: package name

2011-10-10 Thread olivier sallou
Hi, maybe package name should be libtorque-drmaa. Debian contains torque-xxx packages for Torque stuff, and as drmaa is a library I think it should be name according to this scheme. drmaa lib for sge is libdrmaa(-xxx for java etc...), so it would also be coherent. Regards, Olivier -- gpg key

Bug#644962: cannot reproduce

2011-10-11 Thread Olivier Sallou
Hi, I unfortunatly cannot reproduce the problem. I would need the sequence that creates the issue, or a fake one reproducing the error. Could be a sequence format that raise an error (bad characters?, even if I tried to do so also). I tested with a fake sequence and a fake db the same input

Bug#644962: cannot reproduce

2011-10-13 Thread Olivier Sallou
-BEGIN PGP SIGNED MESSAGE- Hash: SHA256 Le 10/13/11 4:21 PM, Luca Capello a écrit : forwarded 644962 blasts...@ncbi.nlm.nih.gov thanks Hi there! For the BLAST folks at NCBI, please see http://bugs.debian.org/644962. On Tue, 11 Oct 2011 13:37:39 +0200, Olivier Sallou wrote: I

Bug#593325: will propose patch

2011-10-16 Thread Olivier Sallou
Hi, I am creating a patch for this bug to uncompress examples. I will send the patch today or tomorrow Olivier

Bug#593325: Patch to uncompress examples

2011-10-16 Thread Olivier Sallou
Tags: patch Here is patch to remove compression of examples in ruby-gtk2 Only impact is in debian/rules. Olivier diff -Nru ruby-gnome2-1.0.0/debian/rules ruby-gnome2-1.0.0/debian/rules --- ruby-gnome2-1.0.0/debian/rules 2011-10-16 17:01:52.0 +0200 +++

Bug#645861: pod errors in source code

2011-10-19 Thread Olivier Sallou
Package: gbrowse Severity: minor Tags: upstream Sources have several pod errors raising errors in packaging. A patch is provided in debian package, but upstream should fix this. Upstream issue reference is: https://github.com/GMOD/GBrowse/issues/10

Bug#647416: ITP: libbio-chado-schema-perl -- object-relational mapping layer for use with the GMOD Chado database schema

2011-11-02 Thread Olivier Sallou
Package: wnpp Severity: wishlist Owner: Olivier Sallou olivier.sal...@irisa.fr * Package name: libbio-chado-schema-perl Version : 0.09010 Upstream Author : Robert Bruels rbu...@cpan.org * URL : http://search.cpan.org/~rbuels/Bio-Chado-Schema/lib/Bio/Chado/Schema.pm

Bug#647417: ITP: libdbix-class-tree-nestedset-perl -- Manage trees of data using the nested set model

2011-11-02 Thread Olivier Sallou
Package: wnpp Severity: wishlist Owner: Olivier Sallou olivier.sal...@irisa.fr * Package name: libdbix-class-tree-nestedset-perl Version : 0.10 Upstream Author : Ian Docherty pa...@iandocherty.com * URL : http://search.cpan.org/~icydee/DBIx-Class-Tree-NestedSet-0.10

Bug#653408: [Debian-med-packaging] Bug#653408: biomaj: [debconf_rewrite] Debconf templates and debian/control review proposal

2011-12-28 Thread Olivier Sallou
I will include updated french translation in next update Thanks for support -- gpg key id: 4096R/326D8438 (pgp.mit.edu) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of

Bug#653408: [Debian-med-packaging] Bug#653408: [ITR] templates://biomaj/{templates}

2011-12-29 Thread Olivier Sallou
-to-date on Alioth SVN. Thank you for your attention. ___ Debian-med-packaging mailing list debian-med-packag...@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging -- Olivier Sallou IRISA

Bug#588278: suggested patch

2011-12-29 Thread Olivier Sallou
package paths. Last-Updated: 29/12/11 Author: Olivier Sallou olivier.sal...@irisa.fr --- a/applications/tutorials/tutorials.pro +++ b/applications/tutorials/tutorials.pro @@ -1,7 +1,7 @@ -SOFA_DIR=../.. +SOFA_DIR=/usr/share/sofa TEMPLATE = subdirs -include($${SOFA_DIR}/sofa.cfg) +include($${SOFA_DIR

Bug#588278: patch proposal for bug 588278 in sofa-framework

2011-12-29 Thread Olivier Sallou
directly. Kind regards and in any case thanks for the patch Andreas. -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (pgp.mit.edu) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D

Bug#653408: [Debian-med-packaging] Bug#653408: [RFR] templates://biomaj/{templates}

2011-12-30 Thread Olivier Sallou
. ___ Debian-med-packaging mailing list debian-med-packag...@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE

Bug#653408: [Debian-med-packaging] Bug#653408: [RFR] templates://biomaj/{templates}

2011-12-30 Thread Olivier Sallou
Le 12/30/11 12:43 PM, Andreas Tille a écrit : On Fri, Dec 30, 2011 at 08:56:45AM +0100, Olivier Sallou wrote: It does have a Depends: openjdk-6-jdk|default-jdk|sun-java6-jdk, so yes, this sounds like a job for policy and/or $JAVA_HOME. In fact, JDK path is required somewhere in configuration

Bug#624205: cannot access git directory

2012-01-03 Thread Olivier Sallou
Hi, your git url is not reachable at git clone http://sousmonlit.dyndns.org/~niol/repositories.git/gwt-debian.git/.git http://sousmonlit.dyndns.org/%7Eniol/repositories.git/gwt-debian.git/.git -- gpg key id: 4096R/326D8438 (pgp.mit.edu) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC

Bug#654603: ITP: gassst -- Global Alignment Short Sequence Search Tool

2012-01-04 Thread Olivier Sallou
Package: wnpp Severity: wishlist Owner: Olivier Sallou olivier.sal...@irisa.fr * Package name: gassst Version : 1.28 Upstream Author : Dominique Lavanier dominique.lavan...@irisa.fr * URL : http://www.irisa.fr/symbiose/projects/gassst/ * License : CeCILL v2

Bug#691736: interest

2012-10-29 Thread Olivier Sallou
I am interested by this topic too. I already had a look to create automatically images for Amazon but faced some issues at boot... :-( I am interested on Open Nebula/Amazon/Open Stack stuff. Olivier -- gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335

Bug#692565: libgwt-dev-java: compilation failure

2012-11-07 Thread Olivier Sallou
Package: libgwt-dev-java Version: 2.4.0-1 Severity: normal Dear Maintainer, I tried to gwt compile biomaj-watcher package from embedded GWT libraries to GWT package. I face a compilation error: gwtc: [java] Nov 7, 2012 3:16:33 PM java.util.prefs.FileSystemPreferences$2 run [java]

Bug#692565: [pkg-eucalyptus-maintainers] Bug#692565: libgwt-dev-java: compilation failure

2012-11-07 Thread olivier sallou
2012/11/7 Charles Plessy ple...@debian.org Le Wed, Nov 07, 2012 at 03:29:21PM +0100, Olivier Sallou a écrit : Package: libgwt-dev-java Version: 2.4.0-1 Severity: normal Dear Maintainer, I tried to gwt compile biomaj-watcher package from embedded GWT libraries to GWT package. I

Bug#670353: Some (minimal?) Java help needed (Was: Bug#670353: ITP: fastqc -- quality control for next generation sequencing data)

2012-11-07 Thread Olivier Sallou
generation sequencing data The Debian Med source code repository has some functional (not lintian clean) package in trunk/packages/babraham/fastqc. -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438

Bug#670353: Some (minimal?) Java help needed (Was: Bug#670353: ITP: fastqc -- quality control for next generation sequencing data)

2012-11-08 Thread Olivier Sallou
Le 11/8/12 8:40 AM, Olivier Sallou a écrit : Le 11/7/12 3:29 PM, Andreas Tille a écrit : Hi, I stumbled upon this one and did some work on it in Vcs-Svn: http://svn.debian.org/debian-med/trunk/packages/babraham/fastqc/trunk/ It is close to lintian clean now but there is some

Bug#670353: Some (minimal?) Java help needed (Was: Bug#670353: ITP: fastqc -- quality control for next generation sequencing data)

2012-11-08 Thread Olivier Sallou
Le 11/8/12 8:40 AM, Olivier Sallou a écrit : Le 11/7/12 3:29 PM, Andreas Tille a écrit : Hi, I stumbled upon this one and did some work on it in Vcs-Svn: http://svn.debian.org/debian-med/trunk/packages/babraham/fastqc/trunk/ It is close to lintian clean now but there is some

Bug#690165: biomaj-watcher: postinst script change permissions on global.properties

2012-10-10 Thread Olivier Sallou
Package: biomaj-watcher Severity: normal global.properties contains sensitive configuration information owned by root or tomcat6. postinst script changes access permissions to read access for anyone. postinst should keep access permissions, only modifying the owner of the file. -- System

Bug#647902: libsqlite3-0: Error in DB connection after upgrade to v3.7.9-1

2011-11-07 Thread Olivier Sallou
Package: libsqlite3-0 Version: 3.7.9-1 Severity: important I am packaging a perl application using SQLite and DBD-SQLite3-perl I was using v3.7.8-1 and tests were fine. However pbuilder failed on tests (updated to latest). I updated my computer to latest version of libsqlite3-0, and tests now

Bug#647902: seems to be more perl related

2011-11-07 Thread Olivier Sallou
After some investigation and a few tests, my tests succeed if PERL_DL_NONLAZY is set to 0: osallou@debiansid:~/Desktop/libbio-chado-schema-perl$ PERL_DL_NONLAZY=1 perl -MExtUtils::Command::MM -e test_harness(0, 'blib/lib', 'blib/arch') t/001_basics.t t/001_basics.t ..

Bug#647902: sample script

2011-11-07 Thread Olivier Sallou
I tried to create a sample script to test, though I do not get same errors on output, I see that DBI-connect fails whe NONLAZY is set to 1. Script: #!/bin/bash sqlite3 foo.db ''; # Connect and run bad SQL PERL_DL_NONLAZY=0 perl -MDBI -le 'DBI-connect(dbi:SQLite:dbname=foo.db, ,

Bug#685900: unblock: circos/0.61-3

2012-08-26 Thread Olivier Sallou
Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: unblock Please unblock package circos I would like to ask to take into account circos 0.61-3 in stable release. The fix included in 0.61-3 fixes a bug preventing usage of the package (missing

Bug#686077: ITP: libsnappy1.0.3-java -- Fast Java compressor/decompressor, port of Snappy

2012-08-28 Thread Olivier Sallou
Package: wnpp Severity: wishlist Owner: Olivier Sallou osal...@debian.org * Package name: libsnappy1.0.3-java Version : 1.0.3-rc3 Upstream Author : Xerial.org * URL : https://code.google.com/p/snappy-java/downloads/list?can=4q=colspec=Filename+Summary+Uploaded

Bug#683291: ITP: soapdenovo -- short-read assembly method that can build a de novo draft assembly for the human-sized genomes

2012-07-30 Thread Olivier Sallou
Package: wnpp Severity: wishlist Owner: Olivier Sallou osal...@debian.org * Package name: soapdenovo Version : 1.0.5 Upstream Author : BGI-Shenzhen * URL : http://soap.genomics.org.cn/soapdenovo.html * License : GPL3+ Programming Lang: C Description

Bug#680116: swi-prolog: seg fault on Sparc and IA64

2012-08-01 Thread olivier sallou
2012/7/24 olivier sallou olivier.sal...@gmail.com Hi, I won t be able to do so before one week. However,the issue is only in a few archs i can't test. The issue occured in auto builds,and buildd servers for those archs could not be set with experimental. Logol shows some errors in build

Bug#680433: check with upstream

2012-09-20 Thread Olivier Sallou
Hi gonna contact upstream author to see if they can autodetect (with correct configure etc...) Olivier -- gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to

Bug#688433: analysing

2012-09-24 Thread Olivier Sallou
Hi, I gonna analyse this deeply, but looking at the code vs policy: - local changes are preserved during a package upgrade - configuration files is preserved when the package is removed, and only deleted when the package is purged. The package updates, indeed, the conf file at upgrades etc..

Bug#688661: [Debian-med-packaging] Bug#688684: ncbi-blast+: trying to overwrite '/usr/bin/seedtop', which is also in package blast2 1:2.2.26.20120620-2

2012-09-25 Thread Olivier Sallou
Fixed in SVN -- gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org

Bug#688684: [Debian-med-packaging] Bug#688684: ncbi-blast+: trying to overwrite '/usr/bin/seedtop', which is also in package blast2 1:2.2.26.20120620-2

2012-09-25 Thread Olivier Sallou
(or for there scripts). Olivier -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-bugs-dist-requ

Bug#693094: RFH: cloud-init -- configuration and customization of cloud instances

2012-11-12 Thread olivier sallou
2012/11/13 Charles Plessy ple...@debian.org Package: wnpp Severity: normal I request assistance with maintaining the cloud-init package. The package description is: System to handle early initialization of a cloud instance. Cloud-init can for example set a default locale and a host

Bug#682490: file permissions

2012-08-06 Thread Olivier Sallou
The biomaj-watcher is a web application (tomcat6). To do so, application must be able to write in a number of files/directories of the biomaj package. I will investigate dpkg-statoverride usage. Olivier -- gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9

Bug#684977: missing runtime dependency

2012-08-15 Thread olivier sallou
Package: circos Version: 0.61-1 Severity: normal File: circos Circos needs libclone-perl as runtime dependency and is missing in control file -- System Information: Debian Release: wheezy/sid APT prefers unstable APT policy: (500, 'unstable'), (500, 'testing') Architecture: amd64 (x86_64)

Bug#656066: mauvais fichier, en attente de réceptionner le fichier correct

2012-01-17 Thread Olivier Sallou
Le fichier joint n'est pas correct, en attente de recevoir la bonne traduction -- gpg key id: 4096R/326D8438 (pgp.mit.edu) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of

Bug#656066: update french translation file after review

2012-01-20 Thread Olivier Sallou
update french translation file after review -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (pgp.mit.edu) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 French translation

Bug#656755: [Debian-med-packaging] Bug#656755: Help with architecture not supporting SSE (Was: Bug#656755: libhmsbeagle FTBFS on everything except amd64)

2012-01-23 Thread Olivier Sallou
look like they fail whilst building libhmsbeagle_cpu_sse_la-BeagleCPUSSEPlugin.lo. Regards, Adam -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (pgp.mit.edu) Key fingerprint = 5FB4 6F83 D3B9 5204 6335

Bug#657184: ITP: j2f -- Java Application Programming Interfaces (APIs) to numerical libraries originally written in Fortran

2012-01-24 Thread Olivier Sallou
Package: wnpp Severity: wishlist Owner: Olivier Sallou olivier.sal...@irisa.fr * Package name: j2f Version : 0.8.1 Upstream Author : Keith Seymour (seym...@cs.utk.edu) * URL : http://sourceforge.net/projects/f2j/ * License : GPL Programming Lang: C

Bug#656066: biomaj: Update french translation after template update

2012-01-16 Thread Olivier Sallou
. # Copyright (C) 2011 Olivier Sallou # This file is distributed under the same license as the PACKAGE package. # Olivier Sallou olivier.sal...@irisa.fr, 2011. # #, fuzzy msgid msgstr Project-Id-Version: biomaj 1.1.0\n Report-Msgid-Bugs-To: bio...@packages.debian.org\n POT-Creation-Date: 2012-01-16 07

Bug#659295: post-inst error

2012-02-22 Thread olivier sallou
Hi, would you have more info on the error occuring? The installation worked fine on my computer, so I think it is a matter of context/setup. I do not see any hint in the attached logs on the failed command. Thanks Olivier -- gpg key id: 4096R/326D8438 (pgp.mit.edu) Key fingerprint = 5FB4

Bug#659295: almost fixed

2012-02-22 Thread olivier sallou
I could find the issue. Some Perl depends were not set by the perl:Depends. I added dependencies in control file. While testing locally with piuparts, I still have however an error at purge: 4m39.2s ERROR: FAIL: Package purging left files on system: /var/lib/ucf/hashfile.1 not owned

Bug#661793: bioperl: Error in berkeleydb3.pm while creating Temp file

2012-03-01 Thread Olivier Sallou
Package: bioperl Version: 1.6.901-2 Severity: important Tags: upstream When using bp_seqfeature_load.pl I have an error at build_summary_statistics call time of berkeleydb3.pm: Couldn't create temporary file for sorting: Inappropriate ioctl for device It occurs in berkeleydb3.pm line 500

Bug#661793: [Debian-med-packaging] Bug#661793: bioperl: Error in berkeleydb3.pm while creating Temp file

2012-03-02 Thread Olivier Sallou
Le 3/3/12 10:26 AM, Florent Angly a écrit : On 02/03/12 18:28, Olivier Sallou wrote: So it is upstream that put parameters in the wrong order. Ah, yes, of course. I failed to notice that. It turns out that I am involved with the Bioperl project. So, I fixed this issue upstream: https

Bug#662922: gbrowse: Upstream bug issue with make test target

2012-03-07 Thread Olivier Sallou
Package: gbrowse Version: 2.48~dfsg-1 Severity: normal Tags: upstream Upstream bug https://github.com/GMOD/GBrowse/issues/12 has been created for this issue. It impacts the make test target where renderfarm relate tests fail. It does not impact runtime. -- System Information: Debian

Bug#658828: biomaj-watcher: [INTL:fr] French Debconf translation

2012-02-06 Thread Olivier Sallou
) 2011 Olivier Sallou # This file is distributed under the same license as the biomaj-watcher package. # Olivier Sallou olivier.sal...@irisa.fr, 2011. # msgid msgstr Project-Id-Version: biomaj-watcher 1.0\n Report-Msgid-Bugs-To: biomaj-watc...@packages.debian.org\n POT-Creation-Date: 2012-01-16 11:51

Bug#658833: biomaj: Missing file for console help

2012-02-06 Thread Olivier Sallou
Package: biomaj Version: 1.2.0-3 Severity: normal The package does not include file console_help.txt. This file is used by the program to display default help and --help parameter. The result is help console is not available -- System Information: Debian Release: wheezy/sid APT prefers

Bug#658833: Ubuntu reference

2012-02-06 Thread Olivier Sallou
Bug originated from Ubuntu bug #915316. This bug was set as invalid because it referred to an install/upgrade issue, not relevant, but the missing help appeared as a side effect. This bug is created to refer directly the missing help issue. -- gpg key id: 4096R/326D8438 (pgp.mit.edu) Key

Bug#657478: biomaj-watcher: diff for NMU version 1.2.0-3.1

2012-02-10 Thread Olivier Sallou
:49 PM, gregor herrmann a écrit : tags 657478 + patch tags 657478 + pending thanks Dear maintainer, I've prepared an NMU for biomaj-watcher (versioned as 1.2.0-3.1) and uploaded it to DELAYED/2. Please feel free to tell me if I should delay it longer. Regards. - -- Olivier Sallou IRISA

Bug#653408: update of translations

2012-02-01 Thread Olivier Sallou
I gonna update all translation with included patch and update biomaj package. Thanks to all trnasation teams for their help Olivier -- gpg key id: 4096R/326D8438 (pgp.mit.edu) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to

Bug#652031: ITP: clustalo -- Clustal Omega is the latest addition to the Clustal family

2011-12-14 Thread Olivier Sallou
Package: wnpp Severity: wishlist Owner: Olivier Sallou olivier.sal...@irisa.fr * Package name: clustalo Version : 1.0.3 Upstream Author : clust...@ucd.ie * URL : http://www.clustal.org/omega/ * License : GPL Programming Lang: C Description : Clustal

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