Your message dated Sat, 05 Dec 2015 23:43:11 +0000
with message-id <[email protected]>
and subject line Bug#772305: fixed in mafft 7.266-1
has caused the Debian Bug report #772305,
regarding mafft: 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.
(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 [email protected]
immediately.)
--
772305: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=772305
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: mafft
Severity: normal
Version: 7.205-1
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/lib/mafft/bin/mafft line 1768 (unsafe echo with
> backslash):
> echo "Warning: Sequence homologs of the
> structures given with the --pdbfilelist option cannot be collected.\n"
> 1>>"$progressfile"
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: mafft
Source-Version: 7.266-1
We believe that the bug you reported is fixed in the latest version of
mafft, 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 mafft 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: Sat, 05 Dec 2015 23:44:00 +0100
Source: mafft
Binary: mafft
Architecture: source amd64
Version: 7.266-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
mafft - Multiple alignment program for amino acid or nucleotide sequences
Closes: 772305
Changes:
mafft (7.266-1) unstable; urgency=medium
.
* New upstream version
* Fix bashism
Closes: #772305
Checksums-Sha1:
bdcaf8bf05024d9663789fe1c2d36a042fd4c0cb 1974 mafft_7.266-1.dsc
b17f9bd2083b26800bb9ac4f4a6c27a3e069e2eb 440576 mafft_7.266.orig.tar.gz
28a71815b2d7d37b46ab4f20c9100bf3ab499dc2 6556 mafft_7.266-1.debian.tar.xz
4d1938e26210aa9194531f61d6acbd4b3aa8d3b0 833894 mafft_7.266-1_amd64.deb
Checksums-Sha256:
a28454673811923119ef49714f9cbd14504f85a56f2cd68c7b30a3004a4f8f30 1974
mafft_7.266-1.dsc
59d4921e13377bb2c8e1f0a007e94b3e698e2c546ce8facc9daa530bc673e707 440576
mafft_7.266.orig.tar.gz
e414190c1f4c600739197c361ca0aa48215e0a9f04c42ac7e0e5b5becfef29da 6556
mafft_7.266-1.debian.tar.xz
ed822fb84d688e8f022f3e29e85b39caa59e3df61c5a7a80d33797be2f7bb959 833894
mafft_7.266-1_amd64.deb
Files:
313cb4d72e48e4d872109a90d907230b 1974 science optional mafft_7.266-1.dsc
96660947025c66c88afc73d42def6b73 440576 science optional
mafft_7.266.orig.tar.gz
d6c2b22779ce88786b5fb70668932d7a 6556 science optional
mafft_7.266-1.debian.tar.xz
90b9c292b12b3ceb508d712504969d3d 833894 science optional
mafft_7.266-1_amd64.deb
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1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=BUSu
-----END PGP SIGNATURE-----
--- End Message ---
