Re: mips/mipsel in samtools and pysam

2015-07-27 Thread Afif Elghraoui
Hi, Andreas,

The build logs for the current versions of samtools and pysam (without
contributed patches provided for the older release) show that building
was successful on mipsel [1-2]. Building on mips has not been attempted
for these two packages since htslib has apparently failed to  [3] build
there.

Perhaps mips will work as well if htslib becomes available there. At
least for pysam, the provided patches no longer apply cleanly, but maybe
they will not be needed anymore..

Regards
Afif

1. https://buildd.debian.org/status/package.php?p=python-pysam
2. https://buildd.debian.org/status/package.php?p=samtools&suite=sid
3.
https://buildd.debian.org/status/logs.php?pkg=htslib&ver=1.2.1-1&arch=mips



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Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name


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Bug#784863: marked as done (ITP: kmer-tools -- suite of tools for DNA sequence analysis)

2015-07-27 Thread Debian Bug Tracking System
Your message dated Mon, 27 Jul 2015 22:00:25 +
with message-id 
and subject line Bug#784863: fixed in kmer-tools 0~20150520+2004-1
has caused the Debian Bug report #784863,
regarding ITP: kmer-tools -- suite of tools for DNA sequence analysis
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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immediately.)


-- 
784863: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=784863
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---

Package: wnpp
Severity: wishlist
Owner: Debian Med Team 

* Package name: kmer-tools
  Version : 20141114+1994
  Upstream Author : Brian Walenz 
* URL : http://kmer.sourceforge.net
* License : GPL
  Programming Lang: C
  Description : suite of tools for DNA sequence analysis

The kmer package is a suite of tools for DNA sequence analysis.
It provides tools for searching (ESTs, mRNAs, sequencing reads);
aligning (ESTs, mRNAs, whole genomes); and a variety of analyses
based on kmers.

This package is a dependency of wgs-assembler (RFP #395843), both to be
built and maintained by the Debian Med team. This kmer-tools
package is under development at:
http://anonscm.debian.org/gitweb/?p=debian-med/kmer-tools.git
--- End Message ---
--- Begin Message ---
Source: kmer-tools
Source-Version: 0~20150520+2004-1

We believe that the bug you reported is fixed in the latest version of
kmer-tools, 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 784...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Afif Elghraoui  (supplier of updated kmer-tools 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 ftpmas...@ftp-master.debian.org)


-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Fri, 01 May 2015 19:20:00 -0700
Source: kmer-tools
Binary: kmer libkmer-dev meryl libmeryl-dev
Architecture: source amd64
Version: 0~20150520+2004-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team 

Changed-By: Afif Elghraoui 
Description:
 kmer   - suite of tools for DNA sequence analysis
 libkmer-dev - suite of tools for DNA sequence analysis (development lib)
 libmeryl-dev - in- and out-of-core kmer counting and utilities (development 
lib)
 meryl  - in- and out-of-core kmer counting and utilities
Closes: 784863
Changes:
 kmer-tools (0~20150520+2004-1) unstable; urgency=low
 .
   * Initial release (Closes: #784863)
Checksums-Sha1:
 af0ce2cbd2c20d2f018f0390a79474442c25625d 2159 kmer-tools_0~20150520+2004-1.dsc
 3cd96b007836982bbbfbd5a228157305cae01c6d 920604 
kmer-tools_0~20150520+2004.orig.tar.xz
 8614f7653e354dae07faed1bdcd34f03ff0d4b38 10088 
kmer-tools_0~20150520+2004-1.debian.tar.xz
 b8afe769950fbf0e60d7aed48d77f74b6cdfa14d 11736 kmer_0~20150520+2004-1_amd64.deb
 1cc47df535ebaf7aad73324a1cea65ad43bca07b 2084 
libkmer-dev_0~20150520+2004-1_amd64.deb
 967b0bd164502ad5f03a2bd936cbdd6c06e3de98 222510 
libmeryl-dev_0~20150520+2004-1_amd64.deb
 b6ac936ac8629edf7958d627177de04ab3af57f2 187428 
meryl_0~20150520+2004-1_amd64.deb
Checksums-Sha256:
 f3c87c854d92798b41ae6de2423514ad304b6e5b859d671305de3a830b76112e 2159 
kmer-tools_0~20150520+2004-1.dsc
 c5a06f74255d5e1ec4da8317908bb68e9a1bee994d63bdd43f6fee2c1503e2f1 920604 
kmer-tools_0~20150520+2004.orig.tar.xz
 981aae19024872999807a8c547c62014a67b04cfd416029d74d8efda5d0f284a 10088 
kmer-tools_0~20150520+2004-1.debian.tar.xz
 fa68f2449a5d635caddcbbe304a4f6288b5522fda80f5a12fea7c674a352b3ef 11736 
kmer_0~20150520+2004-1_amd64.deb
 7fcb60fda080fb4458bb2774a0678a78a48cb66e9fa02377757ffe8674aa68a3 2084 
libkmer-dev_0~20150520+2004-1_amd64.deb
 4b976277c48255ae3a4ef1a3f8f020aaa105d2178400073ca9b84d74a2d47502 222510 
libmeryl-dev_0~20150520+2004-1_amd64.deb
 29d3bc405add67e0d96b2d6f391663221e35c69532905eac6b7dbd64769cc425 187428 
meryl_0~20150520+2004-1_amd64.deb
Files:
 84e13369d84a3fd51138b3a82fc08907 2159 science optional 
kmer-tools_0~20150520+2004-1.dsc
 d74cfb4e67daefd520d7d5d8c0957528 920604 science optional 
kmer-tools_0~20150520+2004.orig.tar.xz
 8d65383cd8a1fe5e271a8b9baee1236d 10088 science optional 
kmer-tools_0~20150520+2004-1.debian.tar.xz
 bd01443c611215e44c5cc2e424f84dd0 11736 science optional 
kmer_0~20150520+2004-1_amd64.deb
 69a1b85a19702458fcd917edaf25ddb7 2084 libdevel optional 
libkmer-de

Processed (with 1 errors): Fix issues caused by bad email formatting

2015-07-27 Thread Debian Bug Tracking System
Processing commands for cont...@bugs.debian.org:

> block 787977 by 793763
Bug #787977 [wnpp] ITP: smrtanalysis -- software suite for single molecule, 
real-time sequencing
787977 was blocked by: 787982 787981 395843
787977 was not blocking any bugs.
Added blocking bug(s) of 787977: 793763
> owner 793763 Debian Med Packaging Team
Bug #793763 [wnpp] ITP: blasr -- mapping single-molecule sequencing reads
Ignoring request to set the owner of bug #793763 to the same value
> 
Unknown command or malformed arguments to command.
> --
Stopping processing here.

Please contact me if you need assistance.
-- 
787977: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=787977
793763: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=793763
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems


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