smile

2011-05-19 Thread Thorsten Alteholz
Hi, I did some work on smile (which I had to rename to biosmile, as there are other (not yet official) packages already named smile). From my point of view it is lintian clean and buildable by pbuilder. Can one of you please have a look and tell me what things can be improved? Thorsten

Re: smile

2011-05-20 Thread Thorsten Alteholz
On Fri, 20 May 2011, Nelson A. de Oliveira wrote: http://lists.debian.org/debian-infrastructure-announce/2011/05/msg0.html ;-) Oh great, thanks alot for that link. Thorsten -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble?

Re: [debian-med] Install on ubuntu 10.04.2 or debian 6

2011-05-25 Thread Thorsten Alteholz
On Wed, 25 May 2011, Sebastian Hilbert wrote: I think the cmake issue has been taken care of after an hint from upstream. Yes, at least it compiled with only a small patch under sid. But this is a huge beast, it needed more than an hour to build on my small VM... Thorsten -- To

Re: Ginkgo-CADx package - was: Install on ubuntu 10.04.2 or debian 6

2011-05-25 Thread Thorsten Alteholz
On Wed, 25 May 2011, Andreas Tille wrote: I'd say for a first shot on this package which might go to experimental this rpath issue might be ignorable. Are you sure that a package with such an error can be uploaded? Usually it is ugly to have upstream provided debian/ dirs and I always try

Re: Ginkgo-CADx package - was: Install on ubuntu 10.04.2 or debian 6

2011-05-26 Thread Thorsten Alteholz
On Wed, 25 May 2011, Andreas Tille wrote: Unfortunately I am not yet able to commit anything after the alioth rework. There is still an error: svn: Can't create directory '/svn/debian-med/db/transactions/6851-1.txn': Read-only file system Uhmm. :-( Any location for http download might do

Re: Ginkgo-CADx package - was: Install on ubuntu 10.04.2 or debian 6

2011-05-26 Thread Thorsten Alteholz
On Thu, 26 May 2011, Steffen Möller wrote: E: ginkgocadx: binary-or-shlib-defines-rpath usr/lib/ginkgocadx/Plugins/libvisualizator.so.2.4.1.1 /usr/lib/openmpi/lib So this is really an issue. But I think lintian is wrong here. The error should just be overridden. No, the rpath is really

Re: Ginkgo-CADx package - was: Install on ubuntu 10.04.2 or debian 6

2011-05-27 Thread Thorsten Alteholz
On Thu, 26 May 2011, Andreas Tille wrote: What exactly is the problem / error message if you try to commit? It is still something like: (...) Sendingtrunk/debian/rules Transmitting file data .svn: Commit failed (details follow): svn: Can't create directory

Re: Ginkgo-CADx package - was: Install on ubuntu 10.04.2 or debian 6

2011-05-27 Thread Thorsten Alteholz
On Fri, 27 May 2011, Steffen Möller wrote: They have somehow changed to some role based stuff ... strange ... I took the role away and added it. Give it a try, please. *sigh* that is really strange. I still get this error. Sounds great! I am just having some ssh key issue myself and will

Re: Ginkgo-CADx package - was: Install on ubuntu 10.04.2 or debian 6

2011-05-30 Thread Thorsten Alteholz
On Thu, 26 May 2011, Thorsten Alteholz wrote: Unfortunately I am not yet able to commit anything after the alioth rework. There is still an error: svn: Can't create directory '/svn/debian-med/db/transactions/6851-1.txn': Read-only file system Ok, it seems to be that I am back. As usual

Re: rev 6863 (Re: Ginkgo-CADx package - was: Install on ubuntu 10.04.2 or debian 6)

2011-05-30 Thread Thorsten Alteholz
On Mon, 30 May 2011, Andreas Tille wrote: Hoping for somebody who cares about the copyright file now ... There are about 1800 files to be checked. Are there any tools to make this task a bit easier? Thorsten -- To UNSUBSCRIBE, email to

Re: smile

2011-05-31 Thread Thorsten Alteholz
Hi everybody, from my point of view package smile is ready to be uploaded now. Although it might not be the most popular one, it is still on the tasks list and somebody else might want to use it. What will be the next steps? Shall I build the package and upload it somewhere? What about the

Re: smile

2011-06-01 Thread Thorsten Alteholz
Hi Andreas, On Wed, 1 Jun 2011, Andreas Tille wrote: to pay some respect to your efforts as a newcomer I spended some minuted (the package was really well prepared so it did not needed more than a small break from my usual work) to finally upload. great, thanks alot. Thorsten -- To

Re: rev 6863 (Re: Ginkgo-CADx package - was: Install on ubuntu 10.04.2 or debian 6)

2011-06-04 Thread Thorsten Alteholz
Hi everybody, thanks for all your tips. I think I am almost finished now with the copyright file. The only open issue is with file src/cadxcore/xmlrpc/base64.h The author of this file is listed but there is no license mentioned. Strictly speaking one may not do anything with such a file. So

Re: rev 6863 (Re: Ginkgo-CADx package - was: Install on ubuntu 10.04.2 or debian 6)

2011-06-04 Thread Thorsten Alteholz
On Fri, 3 Jun 2011, Sebastian Hilbert wrote: Is there any special formatting or is it more or less mention license(s) for any file distributed in the package ? It should be in some kind of DEP-5 format. I am not sure whether this format has to be applied yet. Is this enough or is there a

Re: rev 6863 (Re: Ginkgo-CADx package - was: Install on ubuntu 10.04.2 or debian 6)

2011-06-04 Thread Thorsten Alteholz
On Sat, 4 Jun 2011, Steffen Möller wrote: Formally there may be a problem. But I'd say it is fair to assume the dominating license of the package or of that folder. Is it the only contribution from that author? Yes, it is only one file. Just come up with your

dotur

2011-06-04 Thread Thorsten Alteholz
Hi, as I really don't like incomplete stuff, I did some work on dotur. In case it shall become a real package, we need an ITP. In case this software is useless now, it can be removed from the list of tasks. What are your opinions? Thorsten -- To UNSUBSCRIBE, email to

Re: svn alioth issue

2011-06-06 Thread Thorsten Alteholz
Hi Olivier, On Mon, 6 Jun 2011, Olivier Sallou wrote: I tried to rename one dir (ncbi-blast-plus to ncbi-blast+) with svn rename. On commit I have an error: can you please check whether you try to commit to alioth.debian.org or svn.debian.org? In case it is alioth, you will get this error.

Re: Bug#629344: ITP: plastimatch -- medical image reconstruction and registration

2011-06-06 Thread Thorsten Alteholz
Hi Gregory, On Sun, 5 Jun 2011, Gregory Sharp wrote: Finally I got the Alioth ssh keys to work, but I had a trouble uploading the directory into debian-med. Any idea what I did wrong? from which host did you checkout your repository? If it is alioth, you need to 'svn switch' to

Re: dotur

2011-06-07 Thread Thorsten Alteholz
On Sat, 4 Jun 2011, Andreas Tille wrote: it is included in BioLinux is a sign that it is used in practice. So if nobody insists filing an ITP bug seems reasonable. Ok, the bugnumber of the ITP is added to debian/changelog now. Thorsten -- To UNSUBSCRIBE, email to

Re: First upload of ncbi-blast+

2011-06-07 Thread Thorsten Alteholz
Hi Olivier, On Tue, 7 Jun 2011, Olivier Sallou wrote: Can someone have a look and upload to ftp master ? I have to admit that I am not a blast expert so please excuse if I am asking strange questions. While building your package I got some output that I don't understand completely. Could

Re: Ginkgo-CADx arrived in Debian

2011-06-18 Thread Thorsten Alteholz
On Sat, 18 Jun 2011, Sebastian Hilbert wrote: architecture seems to be amd64. No, it is not. Is there a reason why architecture is not 'all' From the control-file: Architecture: any But amd64 is the only architecture where this package builds up to now. Or in other words, due to the

Wiki

2011-06-21 Thread Thorsten Alteholz
Hi, on http://www.debian.org/devel/debian-med/index.en.html in the Links section is something written about Wikiomics. Is the link to that website really added intentionally? Thorsten -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble?

Re: Fwd Fed-Med: toothchart has been packaged

2011-07-06 Thread Thorsten Alteholz
Hi, On Mon, 4 Jul 2011, Andreas Tille wrote: I'm not specifically convinced that this is one that we should rank high on top of our priority list. Anybody wants to prove me wrong? it is just one index.php and some images of teeth. If you want to add a date of a new tooth, you have to

ITP: vcftools -- designed for working with VCF files

2011-07-08 Thread Thorsten Alteholz
Package: wnpp Severity: wishlist * Package name: vcftools Version : 0.1.5 Upstream Author : Adam Auton, Petr Danecek * URL : http://vcftools.sourceforge.net * License : GPL-3.0 Description : designed for working with VCF files VCFtools is a program

Re: License of Prism

2011-07-14 Thread Thorsten Alteholz
On Wed, 13 Jul 2011, Karsten Hilbert wrote: I do see packages compiling Lisp in postinst. Can you please give me an example and do you know why they do it? Thorsten -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact

Re: Prism build attempts

2011-07-15 Thread Thorsten Alteholz
On Thu, 14 Jul 2011, Ira Kalet wrote: I'm responding to Thorsten's attempt to build Prism in CLISP. It has been done, but at this point you have to really know more about Lisp. Ok, so I will help as far as I can and hope that there is a LISP expert who can step in. I will work on this -

fis-gtm

2011-07-20 Thread Thorsten Alteholz
Hi everybody, it should be possible to build three packages for fis-gtm now. One is just a meta-package, one is a package with the initial (precompiled) software and one is a package that allows the binaries to be built from source. If anybody wants to have a look, I would be happy to get

Re: fis-gtm

2011-07-21 Thread Thorsten Alteholz
On Thu, 21 Jul 2011, Bhaskar, K.S wrote: I replied on-list to Thorsten's e-mail yesterday, but my reply never showed up in my Inbox. Did others receive it? No, your first attempt didn't arrive here. Thorsten -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a

Re: fis-gtm

2011-07-21 Thread Thorsten Alteholz
Hi Andreas, On Thu, 21 Jul 2011, Andreas Tille wrote: For the packaging itself I wonder if there is really a need for asking for a user and group name for the fisgtm user. I'd say this is not common (apache uses www-data, postgresql is using postgres both without asking the user for a

Re: fis-gtm

2011-07-21 Thread Thorsten Alteholz
On Thu, 21 Jul 2011, Andreas Tille wrote: Well, there is no written law that we have to stick to this. While it is a usual thing to do to follow upstream with his file layout of the release tarballs, there are several examples where we derive from this. There just should be good reasons to do

Re: fis-gtm

2011-07-22 Thread Thorsten Alteholz
Hi Laurent, On Thu, 21 Jul 2011, Laurent Parenteau wrote: I think it would be better if the packages would have the version number in the name, and maybe have fis-gtm depend on the latest release.  This way, one could install multiple different versions of GT.M if needed. you could already do

Re: fis-gtm

2011-07-22 Thread Thorsten Alteholz
On Fri, 22 Jul 2011, Andreas Tille wrote: I do not know about examples, but I think the watch file would be perfectly the same. Just fetch the amd64 file in the get-orig-source as well. Ok, I committed my first attempt of a combined package. If everything works, the root dir has to be

Re: fis-gtm

2011-07-23 Thread Thorsten Alteholz
Hi Laurent, On Fri, 22 Jul 2011, Laurent Parenteau wrote: On Thu, 21 Jul 2011, Laurent Parenteau wrote: I think it would be better if the packages would have the version number in the name, and maybe have fis-gtm depend on the latest release. This way, one could install multiple different

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

2011-07-24 Thread Thorsten Alteholz
On Sun, 24 Jul 2011, Andreas Tille wrote: Thus pinging the list if it is important to you might always help. 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 libpng ... Thorsten -- To

Re: fis-gtm

2011-07-25 Thread Thorsten Alteholz
Hi Bhaskar, sorry that I have so much questions, but I really want to understand your philosophy. I copied paragraphs from some of your latest mails and put my question/comment below: [KSB] I am not sure what you mean by what other people choose. (...) So, there is no special GT.M user.

Re: fis-gtm

2011-08-02 Thread Thorsten Alteholz
Hi Bhaskar, On Mon, 25 Jul 2011, Bhaskar, K.S wrote: For Linux, root.root is preferred and bin.bin is acceptable. Also, the norm should be to allow world execution of GT.M. ok, finally I have got it ;-). [KSB2] I don't understand the part about calling the configure script twice. Oh, I

Re: Ginkgo-CADx - we are not there (Was: CMake library dependency files; ginkgocadx experimental build, testers wanted!)

2011-08-08 Thread Thorsten Alteholz
On Sun, 7 Aug 2011, Andreas Tille wrote: I just tried another test but things did not changed regarding the Socket.cpp.o -c /tmp/buildd/ginkgocadx-2.5.2.0/src/cadxcore/xmlrpc/XmlRpcSocket.cpp make[3]: *** No rule to make target `/usr/lib/libpng.so', needed by

Re: duplicate-changelog-files

2011-08-23 Thread Thorsten Alteholz
Hi Mathieu, On Tue, 23 Aug 2011, Mathieu Malaterre wrote: lintian /home/mathieu/debian/debian-med/trunk/packages/dcmtk/build-area/dcmtk_3.6.0-8_amd64.changes W: dcmtk: duplicate-changelog-files usr/share/doc/dcmtk/CHANGES.360.gz usr/share/doc/dcmtk/changelog.gz did you do an update lately?

Re: Communication channels: Please raise your opinion

2011-08-24 Thread Thorsten Alteholz
Hi everybody, On Wed, 24 Aug 2011, Andreas Tille wrote: To see if this might work I would like to propose a first IRC meeting next Monday 29.8. at 17:00 GMT in #debian-med. I thought I could break with IRC but it seems to track me :-). Anyway, depending on the weather conditions on that day,

status of packages

2011-09-14 Thread Thorsten Alteholz
Hi, I just found out that package abyss is currently not maintained within Debian Med but still in the svn repository. As there are currently several methods to mark packages no longer within svn (MOVED, README_git, now_managed_via_git, REMOVED_FROM_DEBIAN.readme), I would like to restart a

Re: vmd packaging moved to debichem

2011-09-15 Thread Thorsten Alteholz
Hi Michael, On Thu, 15 Sep 2011, Michael Banck wrote: Should I remove the vmd directory from the debian-med repository, would somebody else like to do this, or should there be some svn:externals link? if you don't mind, I would take care of that. That would be a good candidate for the new

Re: status of packages

2011-09-15 Thread Thorsten Alteholz
Hi Charles, On Thu, 15 Sep 2011, Charles Plessy wrote: I sometimes use a debian/DRAFT file in the draft packages I upload, but would be happy to use debian/README.status instead. I would like to separate the debian directory from the README.status. One of my aims was to remove all unneeded

Re: status of packages

2011-09-19 Thread Thorsten Alteholz
Hi Charles, On Sat, 17 Sep 2011, Charles Plessy wrote: sorry to be a bit late to realise: I remember why I was putting files like trunk/debian/RETIRED in the Subversion repositories of packages I migrated to Git: deleting the trunk directory without waiting for a release cycle will break the

Re: debian-med_1.9_amd64.changes is NEW

2011-10-27 Thread Thorsten Alteholz
On Thu, 27 Oct 2011, Andreas Tille wrote: I wished we could make some progres in med-his (regarding fis-gtm Yes, next month I will continue with that project. Hopefully I will be able to upload the new package by myself by then ... Thorsten -- To UNSUBSCRIBE, email to

Re: Debian Med Advent Calendar

2011-11-30 Thread Thorsten Alteholz
Hi Charles, On Mon, 28 Nov 2011, Charles Plessy wrote: I like to start mornings reading emails like this ! ok, I try my best to repeat that at other times :-). I do not remember seing such and advent calendar before; I am sure it can inspire other teams as well. Out of curiosity, I tried

Re: Debian Med Advent Calendar (Was: Processed (with 1 errors): tagging as pending bugs that are closed by packages in NEW)

2011-11-30 Thread Thorsten Alteholz
On Tue, 29 Nov 2011, Andreas Tille wrote: while it is not yet clear to me how the Advent calendar might be filled by I would like to claim the next door (2.12.) for bug #639389. Ok, but it should be the Debian Med Advent calendar and not the Andreas Advent Calendar :-) Thorsten -- To

Re: Debian Med Advent Calendar

2011-12-02 Thread Thorsten Alteholz
On Thu, 1 Dec 2011, Andreas Tille wrote: Ahhh, OK. So I will see whether the upload to fix #648705 which I wanted to claim for 3.12. will count in here because it was a bit delayed when passing NEW (the package names have changed with this upload). The marked as done-email already arrived

Re: Debian Med Advent Calendar

2011-12-02 Thread Thorsten Alteholz
On Thu, 1 Dec 2011, Andreas Tille wrote: As the star is part of the image, here is the link to the source: http://debian-med.alteholz.de/advent-2011-original.tar.gz which also contains the original original. 403: Forbidden --- something is wrong with your server. Urgs, that was a

Re: [med-svn] r8804 - trunk/packages/mgltools/pmv/trunk/debian

2011-12-16 Thread Thorsten Alteholz
Hi Andreas, On Wed, 7 Dec 2011, Andreas Tille wrote: Resolved circular dependency by recommending autodocktools instead from depending from it. In case there *really* should be a strong dependency this is not the correct fix and we need further work to split up autodocktools in reasonable

Re: Some packages have no upstream tarball (attn: alteholz-guest)

2011-12-16 Thread Thorsten Alteholz
Hi Steve, sorry for any inconvenience. On Sat, 10 Dec 2011, Steve M. Robbins wrote: I'd like to point out that some packages on debian-med have NO upstream tarball, and thus the mergeWithUpstream property is not needed. In fact, that's too mild. The property is *forbidden*, because setting

Re: MglTools packaging (Was: r8804 - trunk/packages/mgltools/pmv/trunk/debian)

2011-12-20 Thread Thorsten Alteholz
On Mon, 19 Dec 2011, Andreas Tille wrote: I disagree. The build process is mostly automated and works. There are more important things to work on. Promised. My personal experience does not fit this statement. 1. Google: site:bugs.debian.org mgltools 'depends on python ( 2.6)' 2. Google:

Re: Droping med-doc?

2012-01-09 Thread Thorsten Alteholz
On Sun, 8 Jan 2012, Andreas Tille wrote: I finally came to the conclusion that it makes no sense to pretend having a documentation package if it is not maintained at all. I guess the contentes should better go to some kind of Wiki. So up, up and away

Re: Debian Native Packages and README.Status

2012-01-23 Thread Thorsten Alteholz
Hi Steve, On Sat, 14 Jan 2012, Steve M. Robbins wrote: The trouble with this is that Source: unavailable does not describe the situation. The source *is*, indeed, available. The distinction, rather, is that there is no upstream tarball. oops, I wasn't aware that the cmake file is all that

Re: [med-svn] r9384 - trunk/packages/fis-gtm/fis-gtm-initial/trunk/debian

2012-01-23 Thread Thorsten Alteholz
On Sun, 22 Jan 2012, Andreas Tille wrote: +# obtain build architecture to detect the right binary for installation I guess that is not correct. Some times ago Bhaskar explained to me that there are reasons to let the user decide whether the 32bit or 64bit version shall be installed on

Re: Looking for a Debian packager for FIS-GT.M : Change the History of Healthcare !!

2012-01-23 Thread Thorsten Alteholz
Hi Luis, On Thu, 19 Jan 2012, Luis Ibanez wrote: I guess at some point we need to touch base with the Debian packagers who has been working in fis-gtm, to make sure that I'm not stepping in their toes..., no, just go on. Any help from somebody who knows better what to do is appreciated. I am

Re: [MoM] Regarding status of fis-gtm-initial package

2012-01-23 Thread Thorsten Alteholz
On Sun, 22 Jan 2012, Andreas Tille wrote: IMHO that's pretty useless and thus I changed debian/rules to only install the tar which matches the architecture that matches the build system. There has been a discussion about this some time ago ... (in my case

Re: [med-svn] r9384 - trunk/packages/fis-gtm/fis-gtm-initial/trunk/debian

2012-01-27 Thread Thorsten Alteholz
On Mon, 23 Jan 2012, Andreas Tille wrote: Just explaining my motivation - not insisting that this was correct: We are currently talking about / working on the initial package to bootstrap a real fid-gtm package. Yes, but I assumed that we only wanted to have one -initial package. So it

Re: [MoM] Packaging fis-get

2012-01-27 Thread Thorsten Alteholz
On Tue, 24 Jan 2012, Luis Ibanez wrote: Then went into the directory: cd debian-med/trunk/packages/fis-gtm/ cd fis-gtm-initial/trunk and got the source code with the command: make -f debian/rules get-orig-source Ok, let me introduce my workflow here: After doing

Re: How Debian Packaging practices could apply to VistA maintenance and distribution

2012-01-27 Thread Thorsten Alteholz
On Wed, 25 Jan 2012, Bhaskar, K.S wrote: [KSB] Are there packages that are (for example) pure shell scripts so that there is no difference between a source package and a binary package? A VistA Debian package would be like that. No, the source package always contains information on how to

Re: [MoM] Packaging fis-get

2012-01-27 Thread Thorsten Alteholz
On Wed, 25 Jan 2012, Andreas Tille wrote: This is because Thorsten decided to move the complete tarball straight into the *.deb package which is a very untypical decision and I was reasoning about this several times in this thread. I hope I answered everything satisfactorily (I have to catch

Re: [MoM] Packaging fis-get

2012-01-29 Thread Thorsten Alteholz
On Sun, 29 Jan 2012, Andreas Tille wrote: I admit I also stumbled about this $HOME/.fis-gtm issue but was to tired yesterday and forgot to bring this up in my response. (...) The alternatives system has the purpose to handle different alternative packages. However, in the GT.M case there

Re: Build logs

2012-03-10 Thread Thorsten Alteholz
Hi Eric, On Fri, 9 Mar 2012, Eric MAEKER wrote: May I suggest to add a startup date in the build logs available from sure, would it be sufficient to add a line at the beginning of the logfile? Just out of curiosity, at the end of the top page most of the time there is a line telling when

package bagphenotype

2012-03-13 Thread Thorsten Alteholz
Hi everybody, according to http://valdarlab.unc.edu/software.html bagphenotype is no longer maintained and shall be replaced by bagpipe. What shall we do? Thorsten -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact

Re: Please review Bits from Debian Med proposal

2012-03-13 Thread Thorsten Alteholz
On Tue, 13 Mar 2012, Andreas Tille wrote: Thanks in advance for any commitment I am mentioned at the beginning, so everything is perfect :-). Thorsten -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact

Re: libsbml5

2012-03-28 Thread Thorsten Alteholz
Hi Ivo, On Wed, 28 Mar 2012, Ivo Maintz wrote: But now it should be ready for upload (also to close bug #665837). after building the package, I got some I:-lines from lintian: I: libsbml5-dev: package-contains-empty-directory usr/lib/jni/ I: libsbml5-dev: package-contains-empty-directory

Re: libsbml5

2012-03-29 Thread Thorsten Alteholz
Hi Ivo, On Thu, 29 Mar 2012, Ivo Maintz wrote: I: libsbml5-octave: binary-has-unneeded-section usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/OutputSBML.mex .comment I: libsbml5-octave: binary-has-unneeded-section

Re: Please upload NEW r-cran-deal

2012-04-04 Thread Thorsten Alteholz
On Tue, 3 Apr 2012, Ivo Maintz wrote: I use sbuild. I tested it just in an absolutely fresh setup; it works. yes, sorry, my mistake :-(. Thorsten -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org

Re: libsbml5

2012-04-04 Thread Thorsten Alteholz
On Tue, 3 Apr 2012, Ivo Maintz wrote: I fixed this. strip is now only called for this libs, if libsbml5 is build with matlab. Hmm, there seems to be a problem with dependencies (no swig found if swig2.0 is installed). The logs are at: https://buildd.debian.org/status/package.php?p=libsbml

Re: Please upload NEW r-cran-deal

2012-04-04 Thread Thorsten Alteholz
On Wed, 4 Apr 2012, Charles Plessy wrote: this is a typical symptom of mergeWithUpstream not being set. *blush* you are right. Thorsten -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive:

meme

2012-06-27 Thread Thorsten Alteholz
Hi, could somebody with more perl experience please have a look whether perl-include.patch of meme really is as desired? Or is there another way how things should be done in such a case? Further the meme documentation (to be exact: overview.html) talks about lots of small tools (-

Re: Any progress with FIS GT.M?

2012-07-01 Thread Thorsten Alteholz
On Sun, 1 Jul 2012, Luis Ibanez wrote: It turned out to be easier to remove the COPYING file as a final step in the installation: override_dh_auto_install: @echo I: Fixing up permissions for setuid rights -- we aren't done yet! chmod u+s

end of the year

2012-11-30 Thread Thorsten Alteholz
Hi everybody, now it is the time again. The days are closing in, the year is drawing to an end and the Christmas season starts. As last year we should think of all those, that are not around with their own kind. Again, during the last few months, lots of volunteers all around the world

Re: end of the year

2012-12-01 Thread Thorsten Alteholz
On Fri, 30 Nov 2012, Andreas Tille wrote: If I understood you correctly that you are collecting the bugs manually (and not straight automatically from UDD which would set hard technical criterion) yes, it is still done manually. I would suggest the following extention of the

Re: end of the year

2012-12-01 Thread Thorsten Alteholz
Hi Eric, On Fri, 30 Nov 2012, Eric Maeker wrote: Thanks for the bug list. I found one for the freemedforms project http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=686677 It can be easily corrected, but I don't really know how to send the patch. I just had a short look at the

Re: end of the year

2012-12-03 Thread Thorsten Alteholz
On Mon, 3 Dec 2012, Eric Maeker wrote: All dependencies are corrected. Ok We just need to patch the control file and add a bug close in the changelog. SVN files are actually for the 0.8.0, so we have to patch tagged 0.7.6 files. Hmm, as 0.8.0 is already in experimental, I don't think

Re: Apache clinical Text Analysis and Knowledge Extraction System (cTAKES)

2013-04-11 Thread Thorsten Alteholz
On Thu, 11 Apr 2013, Mathieu Malaterre wrote: Good luck with maven/java... See 693234#23 Hmm, and the ctakes-resources consist of 1GB of data ... Is there an upper limit of tolerated package size? Thorsten -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject

Re: freemedforms rpath

2013-07-10 Thread Thorsten Alteholz
Hi Eric, On Wed, 10 Jul 2013, Eric Maeker wrote: I've commited the rpath issue correction. Please, if anyone can make a small test. Just compil, install, and run /usr/bin/freemedforms (or by the menu entry). doing a svn-buildpackage results in: cp -a

Advent calendar

2013-11-25 Thread Thorsten Alteholz
Hi, in order to keep an old tradition, I want to remind everybody of our combined efforts to take care of some poor souls at this time of the year. As the years before we should think of all those, that are not around with their own kind. Again, during the last few months, lots of volunteers

Re: Bug#728797: ITP: python-mne -- Python modules for MEG and EEG data analysis

2013-11-28 Thread Thorsten Alteholz
Hi Yaroslav, On Thu, 28 Nov 2013, Andreas Tille wrote: H, this information is new to me. If I have understood NEW queue correctly than it is better not to touch packages which are in the queue. Otherwise you might confuse ftpmaster or influence the position of your package to get handled

Re: Bug#728797: ITP: python-mne -- Python modules for MEG and EEG data analysis

2013-11-29 Thread Thorsten Alteholz
On Thu, 28 Nov 2013, Yaroslav Halchenko wrote: in case an ftp trainee has checked the -1 version and now sees a new one, he would not be delighted by this, as his previous work would be just a waste of time. is that from personal experience? I just wanted to mention an argument from a

Re: Advent calendar

2013-12-25 Thread Thorsten Alteholz
Hi everybody, thanks alot for closing so much bugs. After taking care of 64 bugs in 2011 and 27 bugs in 2012, we reached a new all time high of 73 bugs this year, BRAVO! The oldest bug that could be closed was #541207 [1] which was the RFP of fis-gtm dated from 2009 :-). Season's Greetings

Re: [MoM] snp-sites (Was: I would like to submit a package to debian-med)

2014-01-15 Thread Thorsten Alteholz
On Wed, 15 Jan 2014, Andreas Tille wrote: Uploaded ... waiting for acception by ftpmaster. So this is my moment to ask questions :-) debian/copyright says: Files: * License: GPL-2+ But the accompanying commentary says something about GPLv3+ (as do the headers of the src/* files). On

Re: [MoM] snp-sites (Was: I would like to submit a package to debian-med)

2014-01-15 Thread Thorsten Alteholz
Hi Jorge, On Wed, 15 Jan 2014, Jorge Sebastião Soares wrote: GPL wise it's all done I think. It's all committed including the new pristine tar 1.3. wow, that was fast. Please let me know if you find any other weirdness. From my point of view everything is fine now. @Andreas: I am waiting

Re: MIRA 4.0 released at SourceForge

2014-02-04 Thread Thorsten Alteholz
Hi, On Mon, 3 Feb 2014, Andreas Tille wrote: Thanks to Thorsten mira is no uploaded while I was sleeping my last night in Stonehaven. I was watching Super Bowl and due to the really boring game I had some spare time :-). Any clue how to adapt the watch file to fetch version 4.0? Today

Re: Updating fis-gtm package to 6.1

2014-02-10 Thread Thorsten Alteholz
Hi everybody, the whole project has the systemd-discussion and we discuss about the packaging of fis-gtm :-). So let me ask some questions and I hope they haven't been asked before ... More precisely we are talking about versions: fis-gtm-6.0 (currently in Debian)

Re: Updating fis-gtm package to 6.1

2014-02-11 Thread Thorsten Alteholz
On Tue, 11 Feb 2014, Andreas Tille wrote: As far as I have read Dominique's (and more importantly Thorsten's mail who was perhaps partly wearing his ftpmaster hat, thanks Thorsten - I was hoping for input like this) the question was rather rhetorically. Oh, no, it was not meant to be

Re: Updating fis-gtm package to 6.1

2014-02-11 Thread Thorsten Alteholz
On Mon, 10 Feb 2014, Dominique Belhachemi wrote: There is no big difference to all the other packages in Debian. Transitions happen all the time. Compared to other transitions, a transition from 6.0 to 6.1 to 6.2 within one release cycle sounds really different to me. Besides, the older

Re: Updating fis-gtm package to 6.1

2014-02-11 Thread Thorsten Alteholz
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 reflect that, so that someone installing fis-gtm always gets the latest release. My concern is just to make sure that installing the latest release

Re: readseq2 upstream unresponsive

2014-02-20 Thread Thorsten Alteholz
On Wed, 19 Feb 2014, olivier sallou wrote: after several mails to upstream to clarify some license issue, I think we will have to put readseq2 in non-free. I didn't follow the previous discussion. Is it the file that is available at: http://iubio.bio.indiana.edu/soft/molbio/readseq/java/

Re: [MoM] incorporating phyutility into the packages

2014-03-17 Thread Thorsten Alteholz
Hi Stephen, On Sun, 16 Mar 2014, Stephen Smith wrote: I would be happy to take a look at the copyright contents. However, I am a bit new to this so not exactly sure which bits are missing. In debian/copyright the maintainer must document the copyright holder and license of all files in the

Re: [MoM] incorporating phyutility into the packages

2014-04-01 Thread Thorsten Alteholz
Hi Stephen, lintian tells me something about: W: phyutility: incompatible-java-bytecode-format Java7 version (Class format: 51 I am not a Java expert, but wouldn't this make the package unusable on standard Debian? Do you need src/jade/lib/libmatrixExp.so for anything? Thorsten -- To

Re: force bowtie2 transition to testing

2014-04-09 Thread Thorsten Alteholz
On Wed, 9 Apr 2014, Andreas Tille wrote: On Wed, Apr 09, 2014 at 05:42:22PM +0200, Alex Mestiashvili wrote: bowtie2 has stuck in unstable because of change in supported architectures. I've opened #742614, but haven't received any reaction so far. Is there anything else one can do to force

Re: Set of R preliminary packages towards (r-bioc-)BioSeqClass - 2Upload!2U

2014-07-10 Thread Thorsten Alteholz
Hi Steffen, On Thu, 10 Jul 2014, Steffen Möller wrote: package, which is all much about machine learning on biological sequences. Those packages work, but are not nice, yet, in particular those are not necessarily DFSG clean at the very moment. It is mostly about PDFs shipping with the source

Re: Updating the fis-gtm package to V6.2-000

2014-09-29 Thread Thorsten Alteholz
On Mon, 29 Sep 2014, Andreas Tille wrote: [amul:4] V6.2-000 is ready for upload! And so I did. Thanks for your work on this Hmm, AGPL code without exception linked with openssl doesn't look well .. Thorsten -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a

Re: Updating the fis-gtm package to V6.2-000

2014-09-30 Thread Thorsten Alteholz
Hi Bhaskar, On Mon, 29 Sep 2014, Bhaskar, K.S wrote: GT.M does not require OpenSSL, does not statically link to it, and does not in a strict sense, depend on OpenSSL. But there is a looser relationship / dependency. hmm, while looking at the Debian package, I found the following comment:

Re: Updating the fis-gtm package to V6.2-000

2014-10-06 Thread Thorsten Alteholz
Hi Bhaskar, On Thu, 2 Oct 2014, Bhaskar, K.S wrote: [KSB] Those *openssl* files are versions of the reference implementation of the plugin compiled with #include, #if, etc. configured to call call OpenSSL.  They are not actually linked to OpenSSL or other libraries - linking happens

Re: Updating the fis-gtm package to V6.2-000

2014-10-09 Thread Thorsten Alteholz
On Mon, 6 Oct 2014, Bhaskar, K.S wrote: [KSB2] Adding a license exception to the COPYING file would probably require me to go through Legal and that may add delays that increase the risk of pushing us past the deadline. Aah, ok. Would removing the claim of copyright to the reference

Re: Updating the fis-gtm package to V6.2-000

2014-10-09 Thread Thorsten Alteholz
On Thu, 9 Oct 2014, Andreas Tille wrote: Does it matter that the bug was submitted against 6.1-000 and we are working on V6.2-000? No. We *could* have fixed 6.1-000 before (and it would have migrated to testing then) but since you immediately started working on 6.2 I considered it more

Re: Updating the fis-gtm package to V6.2-000

2014-10-09 Thread Thorsten Alteholz
Hi Andreas, On Thu, 9 Oct 2014, Andreas Tille wrote: No. We *could* have fixed 6.1-000 before (and it would have migrated to testing then) but since you immediately started working on 6.2 I considered it more sensible to fix it in 6.2 which can close the bug in the same manner. Hmm, strictly

Re: Updating the fis-gtm package to V6.2-000

2014-10-10 Thread Thorsten Alteholz
Hi Andreas, On Thu, 9 Oct 2014, Andreas Tille wrote: really sense - I'm no fis-gtm user. However, we agreed that for a low popcon package it is not possible to maintain several versions officially. Does this clarify my idea why fixing the licensing issue in fis-gtm-6.2-000 would be

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