Your message dated Thu, 28 Apr 2011 06:47:14 +0000
with message-id <[email protected]>
and subject line Bug#623558: fixed in biomaj 1.1.0-2
has caused the Debian Bug report #623558,
regarding biomaj: Location of pid file
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.
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--
623558: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=623558
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: biomaj
Version: 1.1.0-1
Severity: minor
No problem during install and running the sample alu db.
But, I got a minor error
/usr/share/biomaj/bin/biomaj.sh: line 103: /usr/share/biomaj/tmp/.bmajpid_alu:
Aucun fichier ou dossier de ce type (for no french speaker => means no found or
directory found)
In fact /usr/share/biomaj/tmp doesn't exist, and I think is ok with the debian
policy.
The code in biomaj.sh is :
echo $$>$BIOMAJ_ROOT/tmp/.bmajpid_$arg
with $BIOMAJ_ROOT = /usr/share/biomaj
There is a tmp directory for biomaj (tmp.dir in /etc/biomaj/general.conf) but
it's use by the java code not the shell script starting biomaj.
I think that the pid file should go to /var/lib/biomaj/tmp or /var/run/biomaj
or either /tmp
/var/lib/biomaj/tmp is created by the package so it can be use, even if you
change the location in general.conf (like I did, to put databases on another
partition).
Thanks for the packaging.
Best regard,
Anthony.
-- System Information:
Debian Release: wheezy/sid
APT prefers unstable
APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: i386 (i686)
Kernel: Linux 2.6.38-2-686-bigmem (SMP w/1 CPU core)
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/bash
Versions of packages biomaj depends on:
ii ant 1.8.0-4 Java based build tool like make
ii ant-contrib 1.0~b3+svn177-2 collection of tasks, types and oth
ii debconf [debconf-2 1.5.38 Debian configuration management sy
ii junit4 4.8.2-2 JUnit regression test framework fo
ii libcommons-dbcp-ja 1.4-1 Database Connection Pooling Servic
ii libcommons-net-jav 1.4.1-2 internet protocol suite Java libra
ii libcommons-pool-ja 1.5.6-1 pooling implementation for Java ob
ii libgnujaf-java 1.1.1-5 free implementation of the javabea
ii libgnumail-java 1.1.2-5 free implementation of the javamai
ii libhsqldb-java 1.8.0.10-9 Java SQL database engine
ii libjcommon-java 1.0.16-1 General Purpose library for Java
ii libjdom1-java 1.1.1+dfsg-1 lightweight and fast library using
ii libjfreechart-java 1.0.13-3 Chart library for Java
ii libjgoodies-forms- 1.3.0-1 Framework to lay out and implement
ii libjsch-java 0.1.42-2 pure Java implementation of the SS
ii liblog4j1.2-java 1.2.15-11 Logging library for java
ii libmysql-java 5.1.10+dfsg-2 Java database (JDBC) driver for My
ii liboro-java 2.0.8a-7 Regular expression library for Jav
ii libregexp-java 1.5-2 Regular expression library for Jav
ii libsaxonb-java 9.0.0.4+svn20080322-3 The Saxon-B XSLT Processor
ii openjdk-6-jdk 6b18-1.8.7-2 OpenJDK Development Kit (JDK)
biomaj recommends no packages.
Versions of packages biomaj suggests:
ii blast2 1:2.2.24.20100808-2 Basic Local Alignment Search Tool
pn mysql-community-serv <none> (no description available)
ii ncbi-tools-bin 6.1.20100808-2 NCBI libraries for biology applica
-- Configuration Files:
/etc/biomaj/db_properties/global.properties changed [not included]
/etc/biomaj/general.conf changed [not included]
-- debconf information excluded
--- End Message ---
--- Begin Message ---
Source: biomaj
Source-Version: 1.1.0-2
We believe that the bug you reported is fixed in the latest version of
biomaj, which is due to be installed in the Debian FTP archive:
biomaj_1.1.0-2.debian.tar.gz
to main/b/biomaj/biomaj_1.1.0-2.debian.tar.gz
biomaj_1.1.0-2.dsc
to main/b/biomaj/biomaj_1.1.0-2.dsc
biomaj_1.1.0-2_all.deb
to main/b/biomaj/biomaj_1.1.0-2_all.deb
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.
Olivier Sallou <[email protected]> (supplier of updated biomaj 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: SHA1
Format: 1.8
Date: Fri, 22 Apr 2011 16:27:11 +0200
Source: biomaj
Binary: biomaj
Architecture: source all
Version: 1.1.0-2
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Olivier Sallou <[email protected]>
Description:
biomaj - Biological banks updater
Closes: 623558 623807 624284
Changes:
biomaj (1.1.0-2) unstable; urgency=low
.
* Add russian translation of debconf:
Thanks to Yuri Kozlov <[email protected]>
Closes: #623807
* debian/patches/fix623558_remove_pid:
Remove unnecessary pid file creation
Closes: #623558
* debian/postrm,debian/preinst:
Issue for smooth upgrade, require old package
removal then new package install
Closes: #624284
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biomaj_1.1.0-2.debian.tar.gz
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