Your message dated Wed, 21 Dec 2011 16:48:24 +0000
with message-id <[email protected]>
and subject line Bug#644237: fixed in ncbi-blast+ 2.2.25-7
has caused the Debian Bug report #644237,
regarding blast2: update_blastdb.pl should not default to stderr for output
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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--
644237: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=644237
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: blast2
Version: 1:2.2.18.20080302-4
Severity: minor
File: /usr/share/doc/blast2/examples/update_blastdb.pl.gz
Usertags: unige.ch-jmlab
Hi there!
The update_blastdb.pl example erroneously uses stderr for any output,
thus it is practically impossible to distinguish between normal output
and real errors:
=====
$ gunzip -c /usr/share/doc/blast2/examples/update_blastdb.pl.gz
>update_blastdb.pl
$ chmod a+x update_blastdb.pl
$ ./update_blastdb.pl swissprot >/dev/null
Connected to NCBI
Downloading swissprot.tar.gz... done.
$ ./update_blastdb.pl swissprot >/dev/null
$ rm swissprot.tar.gz
$ ./update_blastdb.pl swissprot 2>/dev/null
$ rm swissprot.tar.gz
$ ./update_blastdb.pl swissprot -verbose 2>/dev/null
$
=====
BTW1, reporting to the version in lenny because update_blastdb.pl is not
present in the squeeze version (2.2.21.20090809-2) for an unknown reason
(nothing in the Debian or upstream changelogs). Feel free to reassign
it to ncbi-blast+ (2.2.25-5) instead, which actually ships
update_blastdb in /usr/bin/.
BTW2, the fact that the error codes in the C++ version changed
completely is IMHO very bad:
EXIT CODES
[C] This script returns 0 on success and a non-zero value on errors.
[C++] This script returns 0 on successful operations that result in no
downloads, 1 on successful operations that downloaded files, and
2 on errors.
Thx, bye,
Gismo / Luca
-- System Information:
Debian Release: 5.0.8
APT prefers oldstable
APT policy: (500, 'oldstable')
Architecture: amd64 (x86_64)
Kernel: Linux 2.6.26-2-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/bash
Versions of packages blast2 depends on:
ii libc6 2.7-18lenny7 GNU C Library: Shared libraries
ii libncbi6 6.1.20080302-4 NCBI libraries for biology applica
blast2 recommends no packages.
Versions of packages blast2 suggests:
pn libvibrant6a <none> (no description available)
ii ncbi-tools-bin 6.1.20080302-4 NCBI libraries for biology applica
pn ncbi-tools-x11 <none> (no description available)
-- no debconf information
pgp01R6LmGnsO.pgp
Description: PGP signature
--- End Message ---
--- Begin Message ---
Source: ncbi-blast+
Source-Version: 2.2.25-7
We believe that the bug you reported is fixed in the latest version of
ncbi-blast+, which is due to be installed in the Debian FTP archive:
ncbi-blast+-legacy_2.2.25-7_all.deb
to main/n/ncbi-blast+/ncbi-blast+-legacy_2.2.25-7_all.deb
ncbi-blast+_2.2.25-7.debian.tar.gz
to main/n/ncbi-blast+/ncbi-blast+_2.2.25-7.debian.tar.gz
ncbi-blast+_2.2.25-7.dsc
to main/n/ncbi-blast+/ncbi-blast+_2.2.25-7.dsc
ncbi-blast+_2.2.25-7_amd64.deb
to main/n/ncbi-blast+/ncbi-blast+_2.2.25-7_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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated ncbi-blast+ 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: Wed, 21 Dec 2011 15:47:04 +0100
Source: ncbi-blast+
Binary: ncbi-blast+ ncbi-blast+-legacy
Architecture: source amd64 all
Version: 2.2.25-7
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
ncbi-blast+ - next generation suite of BLAST sequence search tools
ncbi-blast+-legacy - NCBI Blast legacy call script
Closes: 644237
Changes:
ncbi-blast+ (2.2.25-7) unstable; urgency=low
.
* Do not output everything to STDERR in
c++/src/app/blast/update_blastdb.pl
Closes: #644237
* debian/control: Depends s/${python:Depends}/python/ because
the python dependency of /usr/bin/windowmasker_2.2.22_adapter
is not detected obviosely
* debian/copyright: Indentation fixes to get DEP5 compatibility
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