Debian Bug report logs - #651983
qiime: Recommends: not available 'cd-hit' package

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Message #5 received at submit@bugs.debian.org (full text, mbox, reply):

From: Luca Capello <luca@pca.it>

To: Debian Bug Tracking System <submit@bugs.debian.org>

Subject: qiime: Recommends: not available 'cd-hit' package

Date: Tue, 13 Dec 2011 20:21:40 +0100

[Message part 1 (text/plain, inline)]

Package: qiime
Version: 1.3.0-2
Severity: normal
Usertags: unige.ch-jmlab

Hi there!

One colleague asked me to install CD-HIT [1][2] on the squeeze machine
we have in the lab and I wdiscovered that there is no Debian package, but
still it is referenced by qiime:
=====
(base-sid)root@gismo:/# cat /etc/apt/sources.list
deb http://cdn.debian.net/debian sid main contrib non-free

(base-sid)root@gismo:/# apt-get update
[...]

(base-sid)root@gismo:/# apt-cache search cd-hit

(base-sid)root@gismo:/# apt-cache search cdhit
qiime - Quantitative Insights Into Microbial Ecology
qiime-doc - Quantitative Insights Into Microbial Ecology (tutorial)

(base-sid)root@gismo:/# apt-cache show qiime | grep -e cdhit -e cd-hit
Recommends: blast2 | blast+-legacy, cd-hit, rdp-classifier,
 chimeraslayer, muscle, infernal, fasttree, ampliconnoise,
 python-matplotlib, python-numpy
  * OTU and representative set picking with uclust, cdhit, mothur, BLAST,

(base-sid)root@gismo:/# apt-get install cd-hit
Reading package lists... Done
Building dependency tree
Reading state information... Done
Package cd-hit is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source

E: Package 'cd-hit' has no installation candidate

(base-sid)root@gismo:/#
=====

This seems plain wrong to me...

Thx, bye,
Gismo / Luca

Footnotes:
[1] <http://weizhong-lab.ucsd.edu/cd-hit/>
[2] what a wonderful *generic* name...

-- System Information:
Debian Release: wheezy/sid
  APT prefers unstable
  APT policy: (990, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)

Kernel: Linux 3.1.0-1-amd64 (SMP w/2 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash

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Message #12 received at 651983-close@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <tille@debian.org>

To: 651983-close@bugs.debian.org

Subject: Bug#651983: fixed in cd-hit 4.5.7-1

Date: Thu, 22 Dec 2011 21:32:10 +0000

Source: cd-hit
Source-Version: 4.5.7-1

We believe that the bug you reported is fixed in the latest version of
cd-hit, which is due to be installed in the Debian FTP archive:

cd-hit_4.5.7-1.debian.tar.gz
  to main/c/cd-hit/cd-hit_4.5.7-1.debian.tar.gz
cd-hit_4.5.7-1.dsc
  to main/c/cd-hit/cd-hit_4.5.7-1.dsc
cd-hit_4.5.7-1_amd64.deb
  to main/c/cd-hit/cd-hit_4.5.7-1_amd64.deb
cd-hit_4.5.7.orig.tar.gz
  to main/c/cd-hit/cd-hit_4.5.7.orig.tar.gz



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 651983@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated cd-hit 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 ftpmaster@debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Format: 1.8
Date: Wed, 14 Dec 2011 14:39:32 +0100
Source: cd-hit
Binary: cd-hit
Architecture: source amd64
Version: 4.5.7-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description: 
 cd-hit     - suite of programs designed to quickly group sequences
Closes: 651983 652074
Changes: 
 cd-hit (4.5.7-1) unstable; urgency=low
 .
   * Initial release (Closes: #652074)
   * This package is recommended by the package qiime and thus it also
     Closes: #651983
Checksums-Sha1: 
 20ea7175e0c86e91dc327bbc6e288a0d774fa874 1343 cd-hit_4.5.7-1.dsc
 d5b2e9261e886bda9437b7320a9acc751c33fa54 393944 cd-hit_4.5.7.orig.tar.gz
 a11cc94205ce2faee04b1f016e10cf4e444a91e7 258816 cd-hit_4.5.7-1.debian.tar.gz
 9552d9b38392f9ab482fbf5c84fd4c4be657239e 684770 cd-hit_4.5.7-1_amd64.deb
Checksums-Sha256: 
 a3e80394e112d82a41e5c489ed4fbdcdbc49f71ccaf5ee2926148428fa742b1c 1343 cd-hit_4.5.7-1.dsc
 8416ddba5c0f39b1c1b8b620113e94d18ef8a681c20c6da767570919a9757659 393944 cd-hit_4.5.7.orig.tar.gz
 965067eb0ae7c6071a2b021261f6193080fbccf29256dbda463b840f31976083 258816 cd-hit_4.5.7-1.debian.tar.gz
 d46c74de2dd7e215fbbfbbe73de30b1838df3a2c5cc835a8c3b547fdf6e1a3e4 684770 cd-hit_4.5.7-1_amd64.deb
Files: 
 8b7aebf64cfa16b7a04ddc70090b7011 1343 science optional cd-hit_4.5.7-1.dsc
 1e1dec088dfb5b7b624a5f283e1ae208 393944 science optional cd-hit_4.5.7.orig.tar.gz
 c6d2416240f6e4edd0d90e2c452f8cda 258816 science optional cd-hit_4.5.7-1.debian.tar.gz
 698ee3436c94301462cd56c1a9149abb 684770 science optional cd-hit_4.5.7-1_amd64.deb

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