packages not queued on Debian CI

2015-08-15 Thread Afif Elghraoui 


On الإثنين 10 آب 2015 20:39, Charles Plessy wrote:
 By the way, I do not understand why python-cobra does not show up on
 ci.debian.net, despite it seems to have every control field needed.

I thought this just needed a couple days, but it's been more than that
and python-cobra is still not listed there. This is also the case for
python-pbcore. I'm not sure what's going on.

Regards
Afif

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

Re: About backports.

2015-08-15 Thread Afif Elghraoui 
Hi, all,

On الثلاثاء 11 آب 2015 00:59, Andreas Tille wrote:
From my personal point of view its similar:  Debian has a quite
 sophisticated infrastucture.  Setting up something thats not even
 comparable would drain maintenance time I could use for more progressive
 things.  I for myself had even ignored backports in the past but I
 started to upload some selected packages recently since there might be
 some chance that it will be used in the foreseable future by my
 institute.  From my usage backports (with all the delay issues it might
 have) is sufficient - if not some local mirror will do to come over some
 delays.
 
From a strategic point of view I'm not sure that some extra
 infrastucture will support the idea of convergence to collect people
 behind a common idea.


Even with the current system in Debian, this can be somewhat
automated--for example, setting up a machine to respond to the testing
migration emails by triggering a rebuild of a package on a Stable chroot
and, if it succeeds and passes tests, to automatically prepare the
package and upload to backports. I could look into doing part of this,
but I obviously can't do any uploads, automated or otherwise. If I ever
get to become a DD, I could then look into taking care of this whole
process.

We would then just need to keep track of a list of packages that should
be backported.

regards
Afif

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

Re: Help needed to update to latest fastqc

2015-08-15 Thread olivier sallou 
I am starting csid base packaging from your work. I could build native libs, 
adding some autotools script to avoid using upstream scripts (one per arch).
I am adding auto test to check cisd java with native libs. Still need some 
patching.

I am quite confident to get package soon. Once ready i will look at jhfd5 
package. I won t focus immediatly on polishing ( control desc ...).

Oliviet

Envoyé depuis mon smartphone Sony Xperia™ via le réseau SFR

 Tim Booth a écrit 

Hi Olivier,

Looks like Bernd Rinn is making positive noises regarding a DFSG version
of the library, so hopefully once he provides code you can take what I
have done and make use of it.  I committed to SVN because it's so much
easier than pushing to GIT and I'm lazy, sorry.

In my libsis-jhdf5-java package I created a small test
ReadWriteTest.java which I confirmed works correctly when used with
the binary libhdf5.so supplied by upstream.  Also my patches
fix_dodgy_cast.patch and remove_ch_rinn_imports.patch should be sound
but the others are junk caused by me trying to kick the code into
submission.

If for some reason we can't get this working then you could very easily
patch out FAST5 support in FastQC for now.  My impression is that it's
something of an alpha feature in any case.  I can't even find a .fast5
format file to test with!

PATCH for FASTQC
This patch disables support for FAST5 format until we get the library built.
Most users won't need this anyway, and those that do can convert the file
to FASTQ using other tools.

Note you also need to completely remove the file
uk/ac/babraham/FastQC/Sequence/Fast5File.java, which I can't do in a quilt 
patch.

Tim Booth - 13th Aug 2015
--- a/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
+++ b/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
@@ -100,7 +100,8 @@
   return new BAMFile(file,false);
   }
   else if (file.getName().toLowerCase().endsWith(.fast5)) {
-  return new Fast5File(file);
+  //return new Fast5File(file);
+  throw new SequenceFormatException(Support for FAST5 
files has not been enabled in this build of FastQC.);
   }
   else {
   return new FastQFile(config,file);
PATCH

I'm done with this for now.  Off to debug some Python code.

Best,

TIM

Bug#793392: marked as done (ITP: dcmtkpp -- Wrappers around DCMTK to have an easier API)

2015-08-15 Thread Debian Bug Tracking System 
Your message dated Sat, 15 Aug 2015 16:00:16 +
with message-id e1zqdsw-0006mt...@franck.debian.org
and subject line Bug#793392: fixed in dcmtkpp 0.2.1-1
has caused the Debian Bug report #793392,
regarding ITP: dcmtkpp -- Wrappers around DCMTK to have an easier API
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 ow...@bugs.debian.org
immediately.)


-- 
793392: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=793392
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
---BeginMessage---
Package: wnpp
Severity: wishlist
Owner: Debian Med team debian-med@lists.debian.org

* Package name: dcmtkpp
  Version : 0.2.1
  Upstream Author : Julien Lamy l...@unistra.fr
* URL : https://github.com/lamyj/dcmtkpp
* License : CeCILL-B
  Programming Lang: C++
  Description : Wrappers around DCMTK to have an easier API

DCMTK++ is a set of wrappers around DCMTK, leveraging C++ constructs to have 
an easier API, notably for the networking part. Included are exception-based
error handling, generic access to datasets elements, standard JSON 
representation of datasets, explicit messages and generic implementation of
SCU and SCP.
---End Message---
---BeginMessage---
Source: dcmtkpp
Source-Version: 0.2.1-1

We believe that the bug you reported is fixed in the latest version of
dcmtkpp, 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 793...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Julien Lamy l...@unistra.fr (supplier of updated dcmtkpp 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: Thu, 16 Jul 2015 15:18:46 +0200
Source: dcmtkpp
Binary: libdcmtkpp0 libdcmtkpp0-dev libdcmtkpp0-doc
Architecture: source amd64 all
Version: 0.2.1-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team 
debian-med-packag...@lists.alioth.debian.org
Changed-By: Julien Lamy l...@unistra.fr
Description:
 libdcmtkpp0 - C++ wrapper library for the DCMTK DICOM toolkit
 libdcmtkpp0-dev - C++ wrapper library for the DCMTK DICOM toolkit (development 
file
 libdcmtkpp0-doc - C++ wrapper library for the DCMTK DICOM toolkit 
(documentation)
Closes: 793392
Changes:
 dcmtkpp (0.2.1-1) unstable; urgency=low
 .
   * Initial release (Closes: #793392)
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Files:
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 f90a49ecfdc399a75a46c14e3e2299a5 125911 science optional 
dcmtkpp_0.2.1.orig.tar.gz
 f32aeed623955e73eb772d4a939161a4 9472 science optional 
dcmtkpp_0.2.1-1.debian.tar.xz
 1c50845f4fff3c6e055bb8a037a22a05 51416 libdevel optional 
libdcmtkpp0-dev_0.2.1-1_amd64.deb
 b0bbdad4ff9c6f0845e3fbeb7a6fc5ac 231094 doc optional 
libdcmtkpp0-doc_0.2.1-1_all.deb
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