[Debian-med-packaging] Bug#644237: blast2: update_blastdb.pl should not default to stderr for output

[Luca Capello]

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
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