Your message dated Sun, 19 Jun 2016 16:19:58 +0000
with message-id <e1befs2-0003iu...@franck.debian.org>
and subject line Bug#826903: fixed in biomaj 1.2.3-8
has caused the Debian Bug report #826903,
regarding biomaj: installation with skipping mysql database configuration
breaks package manager
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
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
826903: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=826903
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: biomaj
Version: 1.2.3-7
Severity: critical
Tags: d-i
Justification: breaks the whole system
Dear Maintainer,
I installed a fresh debian testing using net installer.
I have used advanced graphical setup.
I selected DebianScience. When asked to configure MySQL database connection
for BioMAJ, I chose to don't configure it.
The installer preceeds some hours configuring other packages.
When configuring BioMAJ, it broke up. At this moment, GRUB has not been
installed.
>From this point, apt-get did not do anything. It just told me it could not
>connect to the server.
I had to reboot without grub and install grub manually in recovery mode.
sudo has not been installed at this moment. I had to apt-get purge biomaj
in recovery mode to get sudo working (I had disabled the root user).
-- System Information:
Debian Release: stretch/sid
APT prefers testing
APT policy: (500, 'testing')
Architecture: amd64 (x86_64)
Kernel: Linux 4.5.0-2-amd64 (SMP w/8 CPU cores)
Locale: LANG=de_DE.utf8, LC_CTYPE=de_DE.utf8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
Versions of packages biomaj depends on:
ii ant 1.9.7-3
ii ant-contrib 1.0~b3+svn177-7
ii ant-optional 1.9.7-3
ii debconf [debconf-2.0] 1.5.59
ii default-jre [java6-runtime] 2:1.8-57
ii junit4 4.12-4
ii libcommons-cli-java 1.3.1-3
ii libcommons-codec-java 1.10-1
ii libcommons-dbcp-java 1.4-5
ii libcommons-httpclient-java 3.1-12
ii libcommons-logging-java 1.2-1
ii libcommons-net-java 3.4-2
ii libcommons-pool-java 1.6-2
ii libhsqldb-java 2.3.4-1
ii libjcommon-java 1.0.16-5
ii libjdom1-java 1.1.3-1
ii libjets3t-java 0.8.1+dfsg-2
ii libjgoodies-forms-java 1.6.0-4
ii libjsch-java 0.1.53-1
ii liblog4j1.2-java 1.2.17-7
ii libmail-java 1.5.5-1
ii libmysql-java 5.1.38-1
ii liboro-java 2.0.8a-11
ii libregexp-java 1.5-3
ii libsaxonhe-java 9.5.1.1+dfsg-1
ii mysql-client 5.6.30-1
ii openjdk-8-jre [java6-runtime] 8u91-b14-2
ii perl 5.22.2-1
biomaj recommends no packages.
Versions of packages biomaj suggests:
ii blast2 1:2.2.26.20120620-10+b1
pn mysql-server <none>
ii ncbi-tools-bin 6.1.20120620-10+b1
-- debconf information:
biomaj/mysql_host:
* biomaj/mysql: false
biomaj/mysql_login:
--- End Message ---
--- Begin Message ---
Source: biomaj
Source-Version: 1.2.3-8
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.
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 826...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Olivier Sallou <osal...@debian.org> (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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Fri, 17 Jun 2016 13:10:13 +0200
Source: biomaj
Binary: biomaj biomaj-properties
Architecture: source all
Version: 1.2.3-8
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Olivier Sallou <osal...@debian.org>
Description:
biomaj - biological data-bank updater
biomaj-properties - biological data-bank updater - example properties files
Closes: 826903
Changes:
biomaj (1.2.3-8) unstable; urgency=medium
.
* Allow mysql skip at install (Closes: #826903).
Checksums-Sha1:
9fd230c5fb5c5446aac9f58255bd6f9e1b419e65 2451 biomaj_1.2.3-8.dsc
805de809048e402875b673254c24946d2fd6ea34 24280 biomaj_1.2.3-8.debian.tar.xz
36fb108457e19166b72735be7190739e1badc6ac 26972
biomaj-properties_1.2.3-8_all.deb
b4b56f41ac04d81edf8e3d00aca6789fc23ea9bc 4278678 biomaj_1.2.3-8_all.deb
Checksums-Sha256:
6c07ca08678320ae62e8c9cfcf8ccb2c682f5960629747fe9b8cec3d1e5e758e 2451
biomaj_1.2.3-8.dsc
3bdf7fd74ca50eb6113f61a41f32fa6d67cfc46ad52a88792ad199923a444826 24280
biomaj_1.2.3-8.debian.tar.xz
a19dcc26f505ec3204e474ee9eb15e95ac367e97c086ce51301c15ced9a28359 26972
biomaj-properties_1.2.3-8_all.deb
9eedea2b8bae23df58559da5809690f83e442a1d332b57dfec46bab8aedb8ef7 4278678
biomaj_1.2.3-8_all.deb
Files:
ab60a9821a25749a899fa63cc2694277 2451 science optional biomaj_1.2.3-8.dsc
32c0c07c5925103c7e63a5727448bae8 24280 science optional
biomaj_1.2.3-8.debian.tar.xz
b0f0392c96fb4c625837f0aee29cd52a 26972 science optional
biomaj-properties_1.2.3-8_all.deb
d4f870915fff6af0b71f498e15271f89 4278678 science optional
biomaj_1.2.3-8_all.deb
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--- End Message ---
