Your message dated Fri, 11 May 2012 10:10:20 +0000
with message-id <e1ssmnk-0008sc...@franck.debian.org>
and subject line Bug#671813: fixed in tophat 2.0.0-2
has caused the Debian Bug report #671813,
regarding Bashism in tophat2 that prevents to run on systems where dash is
default.
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 ow...@bugs.debian.org
immediately.)
--
671813: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=671813
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: tophat
Version: 2.0.0-1
Severity: grave
Hi all,
/usr/bin/tophat2 is a shell script (#!/bin/sh), but uses command(s?) available
only with bash.
$ tophat2
/usr/bin/tophat2: 13: [[: not found
This is probably easy to solve, but I did not have time to choose
which is the most ecosystem-friendly solution.
Cheers,
-- Charles
-- System Information:
Debian Release: wheezy/sid
APT prefers stable
APT policy: (910, 'stable'), (900, 'testing'), (800, 'unstable'), (500,
'stable-updates'), (1, 'experimental')
Architecture: amd64 (x86_64)
Kernel: Linux 2.6.39-bpo.2-amd64 (SMP w/8 CPU cores)
Locale: LANG=en_GB.utf8, LC_CTYPE=en_GB.utf8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Versions of packages tophat depends on:
ii bowtie2 2.0.0-beta5-1 ultrafast memory-efficient short r
ii dpkg 1.16.0.3 Debian package management system
ii libboost-thread1.49.0 1.49.0-2 portable C++ multi-threading
ii libc6 2.13-21 Embedded GNU C Library: Shared lib
ii libgcc1 1:4.7.0-6 GCC support library
ii libstdc++6 4.7.0-6 GNU Standard C++ Library v3
ii python 2.6.6-14 interactive high-level object-orie
ii zlib1g 1:1.2.6.dfsg-1 compression library - runtime
tophat recommends no packages.
Versions of packages tophat suggests:
ii bowtie 0.12.7-3 ultrafast memory-efficient short r
ii cufflinks 1.3.0-1 Transcript assembly, differential
-- no debconf information
--- End Message ---
--- Begin Message ---
Source: tophat
Source-Version: 2.0.0-2
We believe that the bug you reported is fixed in the latest version of
tophat, which is due to be installed in the Debian FTP archive:
tophat_2.0.0-2.debian.tar.gz
to main/t/tophat/tophat_2.0.0-2.debian.tar.gz
tophat_2.0.0-2.dsc
to main/t/tophat/tophat_2.0.0-2.dsc
tophat_2.0.0-2_amd64.deb
to main/t/tophat/tophat_2.0.0-2_amd64.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 671...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated tophat 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...@debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Format: 1.8
Date: Sun, 06 May 2012 13:26:38 +0200
Source: tophat
Binary: tophat
Architecture: source amd64
Version: 2.0.0-2
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
tophat - fast splice junction mapper for RNA-Seq reads
Closes: 671813
Changes:
tophat (2.0.0-2) unstable; urgency=low
.
* debian/upstream: BibTeX conform author syntax
* debian/patces/bashism_in_shell_script.patch: Fix bashism in shell script
Closes: #671813
* debhelper 9 (control+compat)
* debian/rules: Create some manpages using help2man
Checksums-Sha1:
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40b13f41713603cd537ef38d20d01156c88a29c9 5566 tophat_2.0.0-2.debian.tar.gz
4632384f69c3f598ffb9e565d9e458325a6dc223 668988 tophat_2.0.0-2_amd64.deb
Checksums-Sha256:
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tophat_2.0.0-2.dsc
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tophat_2.0.0-2.debian.tar.gz
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tophat_2.0.0-2_amd64.deb
Files:
204e8c0af52071feb9d809530df5bd53 1498 science optional tophat_2.0.0-2.dsc
651cf6a67f89390a349f7c3d9c253c4c 5566 science optional
tophat_2.0.0-2.debian.tar.gz
754f59f1240ceb794338cf1e38b44881 668988 science optional
tophat_2.0.0-2_amd64.deb
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--- End Message ---
