Your message dated Tue, 16 Dec 2014 15:37:45 +0000
with message-id <[email protected]>
and subject line Bug#772392: fixed in trimmomatic 0.32+dfsg-2
has caused the Debian Bug report #772392,
regarding trimmomatic: bashism in /bin/sh script
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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--
772392: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=772392
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: trimmomatic
Severity: important
Version: 0.32+dfsg-1
User: [email protected]
Usertags: goal-dash
Hi,
I've ran checkbashisms (from the 'devscripts' package) over the whole
archive and I found that your package has a /bin/sh script that uses a
"bashism".
checkbashisms' output:
> possible bashism in ./usr/bin/TrimmomaticPE line 11 ($FUNCNAME):
> java -classpath "$JARVERSION" org.usadellab.$PKGNAME.$FUNCNAME $@
Not using bash (or a Debian Policy compliant shell interpreter that doesn't
provide such an extra feature) as /bin/sh is likely to lead to errors or
unexpected behaviours. Please be aware that dash is the default /bin/sh.
Please closely examine the above output and the script, and determine
what the proper severity of the bug is, and adjust it accordingly. If
it's important or greater please hurry to get this fixed for jessie.
Hints about how to fix bashisms can be found at:
https://wiki.ubuntu.com/DashAsBinSh
Thanks in advance,
Raphael Geissert
--- End Message ---
--- Begin Message ---
Source: trimmomatic
Source-Version: 0.32+dfsg-2
We believe that the bug you reported is fixed in the latest version of
trimmomatic, 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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated trimmomatic 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: SHA256
Format: 1.8
Date: Tue, 16 Dec 2014 15:59:41 +0100
Source: trimmomatic
Binary: trimmomatic
Architecture: source all
Version: 0.32+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
trimmomatic - flexible read trimming tool for Illumina NGS data
Closes: 772392
Changes:
trimmomatic (0.32+dfsg-2) unstable; urgency=medium
.
* Fix bashism in wrapper script
Closes: #772392
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