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
Hi Charles, On Fri, 20 May 2011, Charles Plessy wrote: first of all, welcome to Debian Med and thanks for your contribution ! thanks for the welcoming. I hope there will be lots of contributions to follow. You can probably simplify a lot debian/rules by using the dh command from Debhelper.

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? Cont

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

2011-05-22 Thread Thorsten Alteholz
On Sun, 22 May 2011, Steffen Möller wrote: There are just too many other bits for me to finish first ... is anybody on this list prepared to jump at it, possibly? At least I will have a look at it. Thorsten

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, Sebastian Hilbert wrote: Indeed an initial package is already there. I applied some patch, but lintian still complain about a rpath for mpi. Apparently rpath is needed to go pass a lintian error already... Could you please elaborate on what that means ? Is this something up

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 UNSUBS

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 to

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 fo

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 adde

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 '/svn/debian-med/db/

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 (if

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

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 debian-med-requ...@lists.d

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 svn

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 UNSUB

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 whe

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

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 in

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 debian-med-requ...@lis

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. On

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 svn.debian.or

Re: svn alioth issue

2011-06-06 Thread Thorsten Alteholz
On Mon, 6 Jun 2011, Olivier Sallou wrote: I have: URL: svn+ssh://osallou-gu...@scm.alioth.debian.org/svn/debian-med/trunk/packages Repository Root: svn+ssh://osallou-gu...@scm.alioth.debian.org/svn/debian-med Everything.alioth.debian.org is equal to alioth.debian.org and now points to wagne

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 debian-med-requ...@list

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 the

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 manuall

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 packa

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 listmas.

Re: License of Prism

2011-07-14 Thread Thorsten Alteholz
(I would love if some volunteer would prove me wrong and starts That is my prompt. I sticked by the user reference manual and ignored the requirement of Allegro Common Lisp. I used clisp and was able to load the config file. During (mk:compile-system :prism) lots of warnings like: ;

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 - th

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 som

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 subject

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 n

Re: fis-gtm

2011-07-21 Thread Thorsten Alteholz
Hi Bhaskar, On Wed, 20 Jul 2011, Bhaskar, K.S wrote: I manage the upstream FIS GT.M project. good to have you here on the list, so I can pelt you with questions :-). One of our developers, Laurent Parenteau (a member of Debian Med) has volunteered to

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 changed

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 vers

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. Pe

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 th

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 `src/cadxcore/libCADxCore.so.2

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? Ma

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 p

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 REA

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 pa

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 VCS

Re: [med-svn] [Debian Wiki] Update of "DebianMedQAWorkflow" by ThorstenAlteholz

2011-10-24 Thread Thorsten Alteholz
Hi Charles, On Sat, 22 Oct 2011, Charles Plessy wrote: this is a nice documentation. I feel however that there are some part that are redundant with our group policy yes, definitely. How about merging ? I think this would be too early now. I still need to change one or two things. Beside

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 debian-med-requ..

workflow for Debian Med packages

2011-10-31 Thread Thorsten Alteholz
Hi, can everybody please have a look at: http://wiki.debian.org/DebianMedQA http://wiki.debian.org/DebianMedQAWorkflow and tell me your opinions. During my work on Debian Med packages I stumbled over one or another problem. With these documents I want to make things easier for everybody an

Debian Med Advent Calendar

2011-11-27 Thread Thorsten Alteholz
Hi everybody, days are closing in, the year is drawing to an end and the Christmas season starts. Most of us will spend this time within the family circle. But we should also think of all those, that are not in such a fine situation. All around the world volunteers track down those poor souls

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 to

Re: Debian Med Advent Calendar

2011-11-30 Thread Thorsten Alteholz
On Mon, 28 Nov 2011, Andreas Tille wrote: Even if I do not fully understand the calendar procedure If a bug is closed in december, this is noted behind the door of the calendar. So instead of getting something out, this calendar is filled with stuff. At Christmas I hope we have a well fille

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 (Was: Processed (with 1 errors): tagging as pending bugs that are closed by packages in NEW)

2011-12-02 Thread Thorsten Alteholz
On Thu, 1 Dec 2011, Andreas Tille wrote: Sure. While I do not like to turn this into a competition I would love to loose it in case it would come to such a situation!!! oh, no, I didn't want to start a competition. I just wanted to encourage the others to follow your example! Thorsten

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 fault

Re: Debian Med Advent Calendar

2011-12-08 Thread Thorsten Alteholz
On Sun, 27 Nov 2011, Thorsten Alteholz wrote: Maybe we can hide at least one number of a closed case behind every door. Wow, I am really impressed. After 8 days of hard work, 19 bugs could be closed :-). Keep it up! Thorsten -- To UNSUBSCRIBE, email to debian-med-requ

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 pie

Re: Debian Med Advent Calendar

2011-12-16 Thread Thorsten Alteholz
Hi Andreas, On Mon, 12 Dec 2011, Andreas Tille wrote: and after there should be half the doors open I wonder if the open doors could not show at least the number of bugs closed on this day. A usual advent calendar changes its look evry day and the doors remain somehow opened. hmm, if you look

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

2011-12-20 Thread Thorsten Alteholz
On Sun, 18 Dec 2011, Andreas Tille wrote: I actually very much in favour of building mgltools from plain upstream source as it is provided upstream in one source package and create different source packages. When doing this refactoring a package -common could be created which is needed by more

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: Debian Med Advent Calendar

2011-12-27 Thread Thorsten Alteholz
Hi everybody, I am really impressed. As I started the Advent Calendar, I expected only one closed bug every day. But after 24 days of hard work 63 bugs are able to pass to the retirement community in the Archive. Unfortunately some new bugs have been detected but still the number of bugs assig

Re: Debian Med Advent Calendar

2011-12-28 Thread Thorsten Alteholz
Hi Andreas, On Wed, 28 Dec 2011, Andreas Tille wrote: Seems we could do with only "one bug of the week" in 2012 to bring it down to zero. :-) ok, so let's go :-) BTW, the calendar does not seem to work any more. Ooops, sorry, fat finger alert. Now it should work again. I hope it even surv

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 amd64

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 the

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: A VistA Debian package is like a Linux installer ISO image. It's a tool that will let you create new VistA environments on your computer, So we only need one VistA Debian package, that contains just this 'installer' and everything else is done by KID

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 shou

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 get-orig-sour

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 b

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 the

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 listmas...@l

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 listmas...@lists.debia

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 usr/

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 usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/Transla

Re: libsbml5

2012-04-02 Thread Thorsten Alteholz
On Mon, 2 Apr 2012, Ivo Maintz wrote: I think, it's ready... Hmm, without matlab on my computer: dh_strip --dbg-package=libsbml5-dbg strip --remove-section=.comment debian/libsbml5-matlab/usr/lib/*.mexa64 strip: 'debian/libsbml5-matlab/usr/lib/*.mexa64': No such file make: *** [binar

Re: Please upload NEW r-cran-deal

2012-04-02 Thread Thorsten Alteholz
On Mon, 2 Apr 2012, Ivo Maintz wrote: r-cran-deal should be ready for upload... Hmm, got fresh version from svn, only installed packages from Depends: and got an error while building. Did you use pbuilder or something like that? Thorsten mkdir -p "." fakeroot debian/rules binary awk:

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 (-> $(MODULES

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 $(CURDIR)/debian/$(BINPKG)/usr/$(GTM_INSTALL_DIR)/g

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 tracke

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 rule

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 bugrep

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 tha

Re: end of the year

2012-12-27 Thread Thorsten Alteholz
Hi everybody, as Christmas time is over now here are some statistics about this year's bug squashing. We started with about 100 bugs for debian-med and could resolve 15 bugs for debian-med packages. Additionally 12 release critical bugs have been resolved by our members. So we haven't been as

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 o

Re: Hint for some imaging software from Fedora Medical SIG

2013-05-16 Thread Thorsten Alteholz
Hi everybody, On Thu, 16 May 2013, Andreas Tille wrote: You might like to check this Wiki page for further interesting programs besides Seg3D[2] and msvtk[3]. I might consider creating a packaging skeleton if this helps. Any takers for packaging? shouldn't we begin with an entry in the task

Re: FreeMedForms new upstream

2013-07-08 Thread Thorsten Alteholz
On Sun, 7 Jul 2013, Andreas Tille wrote: I have put Thorsten Alteholz explicitly in CC - perhaps he might be able to verify and upload before I can do. it builds here and I uploaded it. But according to lintinan this package still needs a lot of care ... Thorsten -- To UNSUBSCRIBE

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 global_resources/package_helpers/freemed

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

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