Re: Sumarizing Amide packaging status

On Fri, 2007-07-20 at 15:50 +0200, Andreas Tille wrote: On Fri, 20 Jul 2007, Karsten Hilbert wrote: Thanks, I see. Unfortunately, it won't install on Debian testing (I am not complaining, just stating a fact) due to dependancies not being up to the necessary version. I'll keep an

Re: Sumarizing Amide packaging status

On Fri, 2007-07-20 at 20:31 +0200, Andreas Tille wrote: On Fri, 20 Jul 2007, Dominique Belhachemi wrote: Yes this is probably possible. But if you choose this way you will get a version without xmedcon support. Any reason why you decided against xmedcon? The issue described above

Re: Request to Join Project Debian-Med

, [EMAIL PROTECTED] a écrit : Dominique Belhachemi has requested to join your project. You can approve this request here: http://alioth.debian.org/project/admin/?group_id=30063. Dear Dominique, the Debian-Med project is always happy to welcome new members. Apparently, you have some

Re: Request to Join Project Debian-Med

On Tue, 2007-10-09 at 13:46 +0200, Andreas Tille wrote: On Tue, 9 Oct 2007, Dominique Belhachemi wrote: i want to support debian-med in imaging and simulation. My next objective is to integrate SOFA: http://www.sofa-framework.org/ This seems to be a really valuable package. I would like

Re: pacs

Hi Eduardo, you can find a nice evaluation of 3 different DICOM/PACS Frameworks here: http://www.dcm4che.org/confluence/download/attachments/271/ossdicom.pdf They compare DCMTK, DCM4CHE and CONQUEST. The main advantage is the availability of packages in Debian for two of them. It could be

Re: Working on BioImage Suite 2.5 beta source tree

Hi, you can put my email address on that list. Cheers, Dominique On Sun, 2007-12-09 at 12:39 +0100, Andreas Tille wrote: Hello, I've got a private e-mail from Xenophon Papademetris of BioImageSuite who gave reasons for working on Debian packaging of BioImageSuite version 2.5 in a closed

Re: It's time for finding a logo

On Fri, 2007-12-07 at 14:24 +0100, Andreas Tille wrote: Feel free to start a logo wiki page. http://wiki.debian.org/DebianMedLogo It is a wiki page. Anyone is invited to contribute ;-) Cheers, Dominique -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble?

FW: BioImage Suite 2.5 released

Suite 2.5 released Since there was some discussion (and misunderstandings) on BioImage Suite posted on Debian-med late last year, I am forwarding on the release announcement for BioImage Suite 2.5. With some help (and prodding) of Dominique Belhachemi we have made all the changes necessary

Re: Extremadura 2008 Debian Work Meetings (fwd)

Hi all, i think it is a very good idea. This is a good chance to bring most of the Debian-Med team together. Last week in March and first week in April works best for me. Cheers Dominique On Fri, 2008-02-08 at 08:16 +0100, Andreas Tille wrote: Hi, for those who might not have noticed the

Re: Fwd: GDCM 2.0.7 is out !

On Tue, 2008-08-05 at 22:26 +0200, Mathieu Malaterre wrote: I must be doing something wrong, but I do not understand where the entry for Dicomnifti is coming from: At least on my computer I can see a duplicate entry for this software: http://debian-med.alioth.debian.org/tasks/imaging.html

Re: [med-svn] r2443 - in trunk/packages/sofa/trunk: . debian debian/patches

On Mon, 2008-09-01 at 22:41 +0900, Charles Plessy wrote: thank you for your work on sofa. I am a bit affraid that the name is too generic. In bionformatics for instance, there is another sofa: http://sofa.projects.semwebcentral.org/overview.html I guess that there are many other sofas in

Re: trying to build the image.deb

On Tue, 2008-09-23 at 13:27 +0200, Paolo Ariano wrote: i know, nor gcj is ok for the work (as openjdk) so i continue to use the sun jdk the /debian/rules script use to to set the JAVA_HOME this line: /usr/sbin/update-java-alternatives -l | head -1 | cut -d' ' -f 3 that gives me:

Re: plink package in NEW

On Tue, 2008-09-30 at 13:12 -0400, Faheem Mitha wrote: Dear Debian Med Developers, Can you point me to the Debian sources for the plink Debian package that is currently sitting in NEW? Sure. ;-) Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/plink/trunk/?rev=0sc=0

Re: teem package

understand what to do. Apparently the teem package was assigned to Dominique Belhachemi: http://qa.debian.org/developer.php?login=domi...@cs.tu-berlin.de Comments ? Thanks, -- Mathieu -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact

Re: software for tasks/imaging

Hi Steve, I've added your suggestion to the imaging tasks. It should be visible shortly after the next tasks page generation cycle. Cheers Dominique On Mon, 23 Mar 2009, Steve M. Robbins wrote: Hi, Here's a suggestion for the imaging task [1]: an MRI simulator. mrisim is a simple MRI

Re: Fwd: GDCM

The build process of the package is not thread-safe. I get the error only if i use the -j2 flag. Dominique On Wed, 8 Apr 2009, Mathieu Malaterre wrote: Hi there, Could anyone comment on the problem Dominique is having. I do not understand the error message... Thanks. --

Re: GDCM package: Undefined symbols / VTK misconfiguration

On Mon, 18 May 2009, Mathieu Malaterre wrote: I get on the one hand: $ grep USE_64 ./usr/include/vtk-5.2/vtkConfigure.h #define VTK_USE_64BIT_IDS $ grep USE_64 usr/lib/vtk-5.2/VTKConfig.cmake SET(VTK_USE_64BIT_IDS ON) Ok so far so good, VTK was configured with 64 bits ON (thus vtkIdType will

Re: gdcm: No rule to make target `/usr/lib/jvm/default-java/lib/libjawt.so', needed by `bin/libvtkgdcmJava.so'. Stop.

Hi Mathieu, On Tue, 2009-09-22 at 22:31 +0200, Mathieu Malaterre wrote: For reason beyond my understanding, I am still getting the same error on armel (it disappear on powerpc) https://buildd.debian.org/~luk/status/package.php?p=gdcm The build on armel is 15 days old. You only have to wait

Bug#601180: ITP: ctk -- software for medical image analysis

Package: wnpp Severity: wishlist X-Debbugs-CC: debian-med@lists.debian.org Package name: ctk Upstream Author : ctk-developers ctk-develop...@commontk.org URL : http://www.commontk.org/ License : Apache License, Version 2.0 Description : software to provide support code

Re: Looking for a DD to upload log4qt/pythonqt

Hi Mathieu, thanks for helping with CTK. It is a great project. Are you aware of the CTK ITP? http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=601180 log4qt seems to be upstream dead, but a fork is maintained within CTK. So I think it is better not to package it separately from CTK. I will have

Re: Looking for a DD to upload log4qt/pythonqt

On Tue, Mar 8, 2011 at 11:38 AM, Mathieu Malaterre mathieu.malate...@gmail.com wrote: Dominique, On Tue, Mar 8, 2011 at 5:28 PM, Dominique Belhachemi lists4...@gmail.com wrote: thanks for helping with CTK. It is a great project. Are you aware of the CTK ITP? http://bugs.debian.org/cgi

Re: Looking for a DD to upload log4qt/pythonqt

On Tue, Mar 8, 2011 at 6:19 PM, Mathieu Malaterre mathieu.malate...@gmail.com wrote: BTW did you manage to get the CTK/dicom plugin to compile ? Not yet, I turned off all plugins and will turn them on one after another. With the new dcmtk/VTK packages the dicom plugin might work.

Re: ginkgocadx-2.5.1.0.tgz released. was: (ginkgocadx-2.5.0.1.tgz released)

On Sun, Jul 24, 2011 at 3:22 PM, Andreas Tille andr...@an3as.eu wrote: On Sun, Jul 24, 2011 at 07:06:22PM +0200, Thorsten Alteholz wrote: It does not build here. /usr/lib/libpng.so is needed but only /usr/lib/i386-linux-gnu/libpng.so is available. The multiarch support was added on 19.07. in

Re: Plastimatch fixes

Hi Greg, I don't think this can be re-distributed. From ./plastimatch-1.5.2/libs/specfun/readme : All the programs and subroutines contained in this diskette are copyrighted. However, we give permission to the reader who purchases this book to incorporate any of these programs into his or

debian-med svn checkout

Hi, Does the following description work for anyone since the changes on alioth? http://debian-med.alioth.debian.org/docs/policy.html#source = To check sources out from our repositories, please do: * If you are a member of Debian Med or a Debian

Re: debian-med svn checkout

Thanks Nelson, svn co svn+ssh://svn.debian.org/svn/debian-med/trunk/ It still doesn't work for me. All I get is the following error message: svn: To better debug SSH connection problems, remove the -q option from 'ssh' in the [tunnels] section of your Subversion configuration file. svn:

Re: debian-med svn checkout

Thanks, It is working now. I used a wrong key for my *-guest account. Cheers Dominique On Thu, Aug 11, 2011 at 12:30 PM, Nelson A. de Oliveira nao...@gmail.com wrote: Hi! On Thu, Aug 11, 2011 at 1:25 PM, Dominique Belhachemi domi...@debian.org wrote: It still doesn't work for me. All I get

Re: ITK is too big for buildd

Maybe the buildd machines can be upgraded with some funding from the DPL? Best, Dominique On Tue, Aug 16, 2011 at 9:18 PM, Steve M. Robbins st...@sumost.ca wrote: Thanks, Michael Schutte, for fixing one of the ITK bugs! I have another problem that could really use some help, namely trying

Re: sofa-framework failing to build

Hi Nelson, Thanks for updating the SVN. From the build logs it seems that new qwt package doesn't contain the needed functionality anymore. Best, Dominique On Thu, Aug 18, 2011 at 7:09 PM, Nelson A. de Oliveira nao...@gmail.com wrote: Hi! After updating sofa-framework (both the build-deps

Re: Looking for a DD to upload ActiViz.NET

Very nice. I will review (and upload) the package tonight. Cheers Dominique On Thu, Nov 3, 2011 at 8:03 AM, Mathieu Malaterre mathieu.malate...@gmail.com wrote: Dear DDs,  I am looking for a debian-med DD to upload the ActiViz.NET package. It is packaged in the debian-med svn as usual. And I

Re: Looking for a DD to upload ActiViz.NET

On Thu, Nov 3, 2011 at 5:17 PM, Andreas Tille ti...@debian.org wrote: On Thu, Nov 03, 2011 at 04:25:08PM -0400, Dominique Belhachemi wrote: Very nice. I will review (and upload) the package tonight. It's good to have another pair or eyeballs.  Feel free to upload.  I just fixed a minor

Re: Removing the field::biology:bioinformatics and biology:: debtags ?

Sounds good to me. Hierarchical tags don't make much sense. Thanks -Dominique On Wed, Jan 4, 2012 at 9:17 PM, Charles Plessy ple...@debian.org wrote: Dear all, we have hundred of packages, and making sure that they are all comprehensively tagged takes time. As discussed earlier, the

Re: [MoM] Packaging fis-get

Hi Luis, Very nice progress! On Sun, Jan 22, 2012 at 6:12 PM, Luis Ibanez luis.iba...@kitware.com wrote: dpkg-checkbuilddeps: Unmet build dependencies: debhelper (= 8) For now (if you are using Lucid) you can change the debhelper version in debian/control to debhelper (= 7) and write a 7 in

Re: [MoM] Packaging fis-get

On Tue, Jan 24, 2012 at 6:48 PM, Luis Ibanez luis.iba...@kitware.com wrote: On Tue, Jan 24, 2012 at 5:55 PM, Andreas Tille andr...@an3as.eu wrote: On Tue, Jan 24, 2012 at 05:33:57PM -0500, Bhaskar, K.S wrote:         debuild [KSB]  Considering that the two files above are the binary

Re: Plans for ITK version 4

On Sat, Jan 28, 2012 at 4:43 AM, Steve M. Robbins st...@sumost.ca wrote: On Tue, Jan 24, 2012 at 08:38:44AM -0500, Dominique Belhachemi wrote: Steve, Thanks for all the work. It would be good to have ITK4 in 'experimental'. Having coexisting packages is nice to have but will cause probably

Re: insighttoolkit vs tiff5

I think we should use libtiff-dev only and file bugs against the consuming package if build errors appear. -Dominique On Wed, May 9, 2012 at 10:58 AM, Mathieu Malaterre ma...@debian.org wrote: Hi there,  With ref to #672242, does anyone see any reason to not go back and use libtiff4-dev in

Re: Any progress with FIS GT.M?

Once there is a minimalistic working fis-gtm package we should upload it to experimental. This allows us to pass the NEW queue time ahead and we can get some build logs for all the architectures. -Dominique On Thu, May 31, 2012 at 8:03 AM, Andreas Tille andr...@an3as.eu wrote: Hi Luis, On

Re: ITK 4.1 patches for gcc 4.7

ITK 3.20 is affected by this bug as well. A lot of tests in the plastimatch package are failing now on i386. e.g. itk::ExceptionObject (0x96f0b18) Location: virtual void itk::NrrdImageIO::ReadImageInformation() Full logs for the i386 build are here:

Re: plastimatch on i386 ?

Last time I checked I had the impression it has something to do with a bug in ITK3. http://lists.debian.org/debian-med/2012/06/msg00152.html -Dominique On Thu, Jul 26, 2012 at 5:49 AM, Mathieu Malaterre ma...@debian.org wrote: Greg, Could you comment on the test failure on i386 ? This

Re: Bug#692498: ITP: bamtools -- C++ API and toolkit for manipulating BAM (genome alignment) files

It is also possible to remove the third party code from the source tarball and from debian/copyright. Please take a look at the following two patches. They add out-of-source support to bamtools. https://github.com/domibel/bamtools/commit/5fc8c1928eaa46fb58618db8ecb93e40cfce54ba

Re: Bug#692498: ITP: bamtools -- C++ API and toolkit for manipulating BAM (genome alignment) files

On Thu, Nov 8, 2012 at 3:56 AM, Andreas Tille andr...@an3as.eu wrote: Would you consider to create a bamtools-tools (well, this sounds like a stupid name - perhaps only bam-tools or bamtools-utils - whatever might sound intuitive to you) package? For similarity issues I checked samtools

Re: Bug#692498: ITP: bamtools -- C++ API and toolkit for manipulating BAM (genome alignment) files

On Fri, Nov 9, 2012 at 9:43 AM, Andreas Tille andr...@an3as.eu wrote: Hi, On Fri, Nov 09, 2012 at 09:01:04AM -0500, Dominique Belhachemi wrote: Would you consider to create a bamtools-tools (well, this sounds like a stupid name - perhaps only bam-tools or bamtools-utils - whatever might

Re: Bug#692498: ITP: bamtools -- C++ API and toolkit for manipulating BAM (genome alignment) files

On Fri, Nov 9, 2012 at 10:38 AM, Andreas Tille andr...@an3as.eu wrote: On Fri, Nov 09, 2012 at 10:33:03AM -0500, Dominique Belhachemi wrote: So the last remaining questions are: 1. Can we fix the pristine-tar branch properly (to exclude third_party) or would it possibly

Re: Anybody up for packaging OpenIGTLink?

Already done. http://packages.qa.debian.org/o/openigtlink.html On Tue, Dec 18, 2012 at 10:13 AM, Andreas Tille andr...@an3as.eu wrote: Hi, I'm lurking on Fedora Medical list and I think this is also something for us. Any volunteer? Kind regards Andreas. - Forwarded message

Re: pysam package

Hi Diane, Running pysam tests during buildtime would be very helpful. I just run the tests manually and stumbled upon a bug in samtools. ( http://code.google.com/p/pysam/issues/detail?id=71 ) I wonder why this hasn't been fixed upstream, anyway, I am going to patch Debian's samtools package with

Re: Info for picard-tools

Hi Olivier, can you try their svn repository? # Non-members may check out a read-only working copy anonymously over HTTP. svn checkout *http*://cofoja.googlecode.com/svn/trunk/ cofoja-read-only See http://code.google.com/p/cofoja/source/checkout Cheers -Dominique On Thu, Mar 21, 2013 at

Re: [fis-gtm] ready for upload - needs sponsor

Yes, you can subscribe to the corresponding bug report http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=541239 -Dominique On Tue, Oct 22, 2013 at 5:22 PM, Laurent Parenteau laurent.parent...@gmail.com wrote: Is there any (automated) ways to be notified once the package will be available in

Re: Debian builds of ITK for non-x84/amd64 architectures

Hi Matt, Thank you for looking into this. Per Debian policy the build machines cannot submit any build reports, but you can get all build logs (with all failing tests) here: https://buildd.debian.org/status/logs.php?pkg=insighttoolkit4 I see that the ITK build time on Debian's build machines

Re: Debuild issue

On Tue, Dec 17, 2013 at 3:42 AM, Andreas Tille ti...@debian.org wrote: Hi Gregory, On Mon, Dec 16, 2013 at 04:10:29PM -0800, Gregory Sharp wrote: The source tarball should not contain the Debian revision number. The -1 in the end is the Debian package version which will be increased if

Re: Re: Updating fis-gtm package to 6.1

On Thu, Feb 6, 2014 at 10:52 PM, Luis Ibanez luis.iba...@kitware.comwrote: On Thu, Feb 6, 2014 at 10:30 PM, Dominique Belhachemi domi...@debian.orgwrote: It comes down to a simple question: Which fis-gtm version is most useful in the next Debian release? I think the best way

Re: Updating fis-gtm package to 6.1

There is no big difference to all the other packages in Debian. Transitions happen all the time. Just let the latest stable release propagate into testing. Luis is setting up the git packaging infrastructure to make a transition from one release to another release as smooth as possible. We can

Re: Updating fis-gtm package to 6.1

On Tue, Feb 11, 2014 at 6:08 PM, Bhaskar, K.S ks.bhas...@fisglobal.comwrote: On 02/11/2014 04:35 PM (US Eastern Time), Thorsten Alteholz wrote: On Tue, 11 Feb 2014, Bhaskar, K.S wrote: Dominique's suggestion makes sense. There's no issue changing the latest release and having fis-gtm

Re: Which version of Samtools for Jessie ?

Hi Charles, I suggest to ship with samtools 0.1.19 . The new samtools 1.1 version isn't quiet ready yet, and htslib needs some upstream work too. -Dominique On Tue, Sep 30, 2014 at 6:17 AM, Charles Plessy ple...@debian.org wrote: Dear all, as Samtools users know, a major update happened

Re: Which version of Samtools for Jessie ?

On Tue, Sep 30, 2014 at 6:39 AM, Einar Ryeng ein...@pvv.org wrote: On Tue, Sep 30, 2014 at 07:17:05PM +0900, Charles Plessy wrote: Version 1.1 should be backwards-compatible, but there are probably corner cases lurking around, such as other tools expecting a version number starting with

Re: Please check new version of tophat

On Sat, Oct 4, 2014 at 4:30 PM, Andreas Tille andr...@an3as.eu wrote: Hi folks, I tried to adapt the patches of the new version of tophat (2.0.13). While the package build it creates an extra executable which is installed to /usr/bin/samtools_0.1.18 which IMHO should be prevented. Since I'm

Re: Please check new version of tophat

On Sun, Oct 5, 2014 at 7:59 PM, Charles Plessy ple...@debian.org wrote: Le Sun, Oct 05, 2014 at 01:21:57PM -0400, Dominique Belhachemi a écrit : Based on the changelog I would say that you can skip the 2.0.13 release. TopHat 2.0.13

Re: [python-pysam] - 4 packages built and all lintian clean

On Sun, Dec 7, 2014 at 6:09 AM, Andreas Tille andr...@an3as.eu wrote: Finally I found several lintian infos (lintian -i -I): I: python-pysam source: wildcard-matches-nothing-in-dep5-copyright samtools/kseq.h (paragraph at line 10) I: python-pysam source:

Re: About CommonTK (CTK) and Slicer4

Hi Gert, As a Slicer user I recommend to use their pre-built binaries [ http://download.slicer.org/] or to build the program from git master. The project is fast moving, and it is essential to use up-to-date builds to take advantage of all available modules and 3rd party extensions. Best

Re: Putting tvc under Debian Med team maintenance

On Fri, Jan 13, 2017 at 5:06 AM, Andreas Tille wrote: > Hi Dominique, > > I wonder why tvc is not under Debian Med team maintenance. It somehow > went in under my radar and I just noticed it when checking rdepends of > libbamtools. Since I simply assume that you are fine with

Re: RFS: bowtie/1.2.1.1+dfsg-1

On Sat, Oct 21, 2017 at 11:44 AM, Alex Mestiashvili < ames...@rsh2.donotuse.de> wrote: > On 10/20/2017 06:46 PM, Dominique Belhachemi wrote: > > On Thu, Oct 19, 2017 at 12:16 PM, Alex Mestiashvili < > > ames...@rsh2.donotuse.de> wrote: > > > >> Hello, &g

Re: RFS: bowtie/1.2.1.1+dfsg-1

On Thu, Oct 19, 2017 at 12:16 PM, Alex Mestiashvili < ames...@rsh2.donotuse.de> wrote: > Hello, > > I've worked a bit on bowtie in git [0] and think that it is ready for > upload. It also presumably closes #864439. One of the issues I run > during package building is that bowtie unit tests fail