Re: GDCM2 : An Open Source DICOM library
On Sun, 2 Mar 2008, Mathieu Malaterre wrote: Could someone correct: s/gdmc/gdcm/g on the page, thanks. Ups's sorry. Just fixed in SVN - will be available after next cron job. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Re: GDCM2 : An Open Source DICOM library
On Sun, 2 Mar 2008, Mathieu Malaterre wrote: Here is the list of supported packages file formats: http://www.cmake.org/Wiki/CMake:CPackPackageGenerators Well, reading this page I think we might draw something from the CPack stuff that might be helpful to build a real Debian package. Let me know if you have any further questions, Well, the best way to speed up moving some software to Debian is always to work on proper Debian packaging as it is described at http://www.debian.org/doc/devel-manuals (perhaps especially the New Maintainers Guide might be most helpful for the moment). You can get any help for detailed questions either at this list (because your package is medicine related and our goal is to support this as good as possible) or on debian-mentors mailing list which has the general goal to support newcomers. Unfortunately we have not the men power to be able to tackle every interesting project immediately and thus we greatly welcome and try to support as best if upstream developers work on the packaging stuff themselves which finally is not that hard at all. Some package examples might be helpful as well. You can easily have a view onto other package sources if you try apt-get source [other_package_name] and if you take a package that seems to be technically similar you have quite a good example for your own work if you are looking into the debian directory that is unpacked in the package source directory. Kind regards and thanks for your interest Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Re: [Debian-med-packaging] Infernal has arrived in experimental, AutoDock uploaded
On Sun, 2 Mar 2008, Steffen Moeller wrote: There are two ways to do so: 1. Fix your package description and it will be put onto the page 2. Fix debian-med source in SVN what I meant was that at some meta-level the page could possibly give the information that you just wrote in your mail. Yes. I do not consider the pages as ready. Feel free to propose a phrase paragraph that you think would apropriately express this for an outsider. (I'm personally "biased" and might think that something is obvious which isn't for others.) I think I would opt for "experimental Debian package available". Opting for something is cheap, but what about implementation? ;-) There are technical and textual problems. Regarding the content we would need a fourth category in our traffic light scheme which sounds broken to me. From a users point of view inofficial and experimental are very similar. Even if experimental is offcial Debian the user most probably has to add some extra line to sources.list and gets something which is potentially dangerous or at least not of the quality he could usually expect. Technically it is not that cheap to implement because I'm currently reading only the package list of unstable. It is on my todo list to add stable and testing as well and add some information about this but adding experimental would cause severe additional problems which I do not really want to risk for a use that is at best questionably concerning the content (as I explained above). That's why I suggested the workaround to mention experimental packages as inofficial which in my eyes is a proper solution (I discussed this with some random DDs at Chemnitzer LinuxTage and all agreed). I got feedback from upstream btw, the PDFs of Infernal are manually edited with Adobe Illustrator and thus the is no lower level that was omitted. The documentation for the user guide will be added with the next release. Well, if the only reason for using experimental as target distribution are questionable doc files I would leave them out in the binary package and link to upstream docs. This might serve our users more than "hiding" a package at a place where less people will seek. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Re: [Debian-med-packaging] Infernal has arrived in experimental, AutoDock uploaded
Le Mon, Mar 03, 2008 at 09:29:05AM +0100, Andreas Tille a écrit : > On Sun, 2 Mar 2008, Steffen Moeller wrote: > > >I think I would opt for "experimental Debian package available". > > That's why I suggested the workaround to mention experimental packages > as inofficial which in my eyes is a proper solution (I discussed this > with some random DDs at Chemnitzer LinuxTage and all agreed). Or rename the category "Experimental or inofficial". I also think that we never will have enough packages in `experimental' to nicely populate an "Experimental" category. Have a nice day, -- Charles -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Re: [Debian-med-packaging] Infernal has arrived in experimental, AutoDock uploaded
On Mon, 3 Mar 2008, Charles Plessy wrote: Or rename the category "Experimental or inofficial". I also think that Ahh, that sounds very reasonable. we never will have enough packages in `experimental' to nicely populate an "Experimental" category. Yep. Thanks for the hint Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Re: Build-dependency for rasmol: cbflib
On Thu, Feb 28, 2008 at 4:12 PM, Andreas Tille <[EMAIL PROTECTED]> wrote: > [I take the freedom to quote your private mail to Debian-Med list and > hope you don't mind about ignorance of the netiquette in this special > case.] No problem, and sorry for not following up sooner. >0. Think about group maintenance in DebiChem or Debian-Med > as well. Group maintenance would be ok, but as mentioned in the ITP (#467655), I'm not a big fan of maintaining patch stacks under debian/. I will look into the merge mode in svn-buildpackage and see if I can integrate it to my workflow easily, but this will take some time. >1. If it is a library you should probably follow the library > packaging guide. This includes providing a package containing > the dynamical library as well as a -dev package with static > library and *.h files. > Hint: The most easiest way to build both is making usage of > automake and libtools. If you have problems with this > you could ask on debian-devel. If you decide to do so > it is a very good idea to talks to upstream about this first. Policy 8.3 gives three reasons for making static-only libraries. CBFlib scores two out of these three, namely * libraries whose interfaces are in flux or under development (commonly the case when the library's major version number is zero, or where the ABI breaks across patchlevels) * libraries which are explicitly intended to be available only in static form by their upstream author(s) I think the earliest time to start thinking about CBFlib shared libraries is when there's another package besides Rasmol in Debian depending on it. >2. I see large chunks of documentation in the source package > but no separate doc package. I would strongly advise to > build a separate doc package. Ok, I'll revise the package soonish. > BTW, did rasmol upstream accepted your GTK version? Yes, the code is in the CVS, but maybe not in the next release. Best, Teemu -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Re: Build-dependency for rasmol: cbflib
On Mon, 3 Mar 2008, Teemu Ikonen wrote: Group maintenance would be ok, but as mentioned in the ITP (#467655), I'm not a big fan of maintaining patch stacks under debian/. Well the URL you quotet there[1] inspired myself to start a discussion at debian-devel[2]. This initial mail leaded to a longish discussion and is not yet finished. Moreover the opinions diverged heavily so there is for the moment to change the policy we once defined for the Debian-Med project. I would not say that we are doing "The Right Thing" (TM) but there is no hard evidence that we are doing something terribly wrong. So for the moment there is no real need to change what we considered useful for those people who are working in the Debian-Med team. (It took in fact some time until I was really convinced to start using a patch system and learning quilt was finally quite easy thanks to Davids policy document. ;-)) I will look into the merge mode in svn-buildpackage and see if I can integrate it to my workflow easily, but this will take some time. I'm sure that people here on this list are more than willing to answer your questions if you have some specific problem. Policy 8.3 gives three reasons for making static-only libraries. CBFlib scores two out of these three, namely * libraries whose interfaces are in flux or under development (commonly the case when the library's major version number is zero, or where the ABI breaks across patchlevels) * libraries which are explicitly intended to be available only in static form by their upstream author(s) I think the earliest time to start thinking about CBFlib shared libraries is when there's another package besides Rasmol in Debian depending on it. Well, I agree for you that durrently there is no visible reason to build a dynamic library. I just learned over the years that users allways will ask for such a functionality - even if you never thought it might be possible. Do finally you are the maintainer (well, the ITP is yours - and I would like to spend my time currently with other things) and so you decide. I just wanted to give you reasons to think twice about it. 2. I see large chunks of documentation in the source package but no separate doc package. I would strongly advise to build a separate doc package. Ok, I'll revise the package soonish. That's fine. In this case I have a stronger opinion than in the library issue (where I wrote "you should probably" - here it is "strongly advise"). BTW, did rasmol upstream accepted your GTK version? Yes, the code is in the CVS, but maybe not in the next release. Grmpf, I would like to have this settled down. Thanks for supporting upstream anyway! Kind regards and thanks for your work on this Andreas. [1] http://kitenet.net/~joey/blog/entry/dpatch_dbs_etc_etc_etc_etc_considered_harmful/ [2] http://lists.debian.org/debian-devel/2008/01/msg00837.html -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Re: [Debian-med-packaging] Infernal has arrived in experimental, AutoDock uploaded
On Mon, Mar 03, 2008 at 06:07:38PM +0900, Charles Plessy wrote: > Le Mon, Mar 03, 2008 at 09:29:05AM +0100, Andreas Tille a écrit : > > On Sun, 2 Mar 2008, Steffen Moeller wrote: > > > > >I think I would opt for "experimental Debian package available". > > > > That's why I suggested the workaround to mention experimental packages > > as inofficial which in my eyes is a proper solution (I discussed this > > with some random DDs at Chemnitzer LinuxTage and all agreed). > > Or rename the category "Experimental or inofficial". Folks, Despite being listed in the online 1913 Webster dictionary, "inofficial" is not commonly used in English today. I humbly suggest "Experimental or unofficial". Thanks, -Steve signature.asc Description: Digital signature
Re: [Debian-med-packaging] Infernal has arrived in experimental, AutoDock uploaded
On Mon, 3 Mar 2008, Steve M. Robbins wrote: "inofficial" is not commonly used in English today. Ahh, my fault - David did it correctly and I changed it because I found inofficial listed higher in a dictionary. I humbly suggest "Experimental or unofficial". Feel free to not humbly to suggest but rudely change in SVN next time you see /me making this kind of errors. Many thanks Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Re: pkg-emboss
Le Mon, Mar 03, 2008 at 05:22:27PM +0100, Markus Kiefer a écrit : > > One more question: > Is jemboss included in the package? Or is there a "jemboss" package out > there somewhere...? Dear Markus, I send a copy of my answer on our public mailing list, because your question is of general interest. jemboss is currently not packaged in Debian, because we have difficulties to handle java programs. If we want to support jemboss with Sun's Java, we would have to depend on a package distributed by Debian in its non-free section, and this would prevent us to distribute EMBOSS in the main section. On the other hand, we have no experience with free alternatives. Our current strategy is simple: wait that the free Sun Java is packaged for Debian; this is under way but requires time for integration. If you have experience that could help us, please feel free to share it! Have a nice day, -- Charles Plessy Debian-Med packaging team Wakō, Saitama, Japan -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Re: pkg-emboss
On Tue, 4 Mar 2008, Charles Plessy wrote: If you have experience that could help us, please feel free to share it! Please do not relay on the information very much - I just heard some Debian people saying that IceTea (the free Java part using the missing bits from classpath) might enter Debian in the not so far distance. Unfortunately we do not have much Java experience in the Debian-Med team but there is always the chance to ask on debian-java list about chances to integrate Java programs. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
[Debian Wiki] Update of "DebianMedTodo" by AndreasTille
Dear Wiki user, You have subscribed to a wiki page or wiki category on "Debian Wiki" for change notification. The following page has been changed by AndreasTille: http://wiki.debian.org/DebianMedTodo New page: = How to contribute to Debian-Med? This page is for people who wonder how they could help the [http://www.debian.org/devel/debian-med Debian-Med] project. == Users = == Developers
[Debian Wiki] Update of "DebianMedTodo" by AndreasTille
Dear Wiki user, You have subscribed to a wiki page or wiki category on "Debian Wiki" for change notification. The following page has been changed by AndreasTille: http://wiki.debian.org/DebianMedTodo -- == Users = + * If you know a Free Software project that might be useful for health care in any aspect and is not yet listed in our [http://debian-med.alioth.debian.org/tasks/ task list] just inform us by writing an e-mail to our [http://lists.debian.org/debian-med mailing list]. + == Developers =
[Debian Wiki] Update of "DebianMedTodo" by AndreasTille
Dear Wiki user, You have subscribed to a wiki page or wiki category on "Debian Wiki" for change notification. The following page has been changed by AndreasTille: http://wiki.debian.org/DebianMedTodo -- == Users = - * If you know a Free Software project that might be useful for health care in any aspect and is not yet listed in our [http://debian-med.alioth.debian.org/tasks/ task list] just inform us by writing an e-mail to our [http://lists.debian.org/debian-med mailing list]. + * If you know a Free Software project that might be useful for health care in any aspect and is not yet listed in our [http://debian-med.alioth.debian.org/tasks/ task list] just inform us by writing an e-mail to our [http://lists.debian.org/debian-med mailing list]. + * If you have some language Skills you can help to translate package descriptions for teh packages we maintain in Debian. To do this go to our [http://debian-med.alioth.debian.org/ddtp.php translation status page] and pick a project you would like to translate. Translation marked by a red "x" are not yet available. Click on the package you might like to translate the description and then pick your language. '''Warning''': ''Currently our page lists also packages that are not yet available in Debian. The reason is a bug in the script that generates this page. Those packages that have at least one translation are most probably included. We are working on this.'' == Developers =
[Debian Wiki] Update of "DebianMedTodo" by AndreasTille
Dear Wiki user, You have subscribed to a wiki page or wiki category on "Debian Wiki" for change notification. The following page has been changed by AndreasTille: http://wiki.debian.org/DebianMedTodo -- == Developers = + * Package one of the most wanted packages from each section + * Biology: [http://debian-med.alioth.debian.org/tasks/bio.php#mauve Mauve] + * Epidemiiology: [http://debian-med.alioth.debian.org/tasks/epi.php#netepi-analysis NetEpi] + * Watch the [http://debian-med.alioth.debian.org/bugs.php list of bugs] and fix bugs or try to provide a patch. +
How to contribute to Debian-Med?
Hi, I just setted up a wiki page http://wiki.debian.org/DebianMedTodo for those who want to help out but have no idea how to do this. I would like to post this URL each month to this mailing list to catch newcommers. (Does anybody know whether we could mailman tweak to do such a monthly posting?) The page is also featuring a "most wanted package". I added my favourites in Biology, Epidemiology and Imaging. I also have a favourite GNUmed-Server. My plan is to upload the stuff I did to experimental (because it does not do the job I want it to do), add it to the list of "Experimental and unofficial packages" and than put it onto the "most wanted" list in the Practice section. Feel free to add items to the list. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
[Debian Wiki] Update of "DebianMedTodo" by AndreasTille
Dear Wiki user, You have subscribed to a wiki page or wiki category on "Debian Wiki" for change notification. The following page has been changed by AndreasTille: http://wiki.debian.org/DebianMedTodo -- * Package one of the most wanted packages from each section * Biology: [http://debian-med.alioth.debian.org/tasks/bio.php#mauve Mauve] - * Epidemiiology: [http://debian-med.alioth.debian.org/tasks/epi.php#netepi-analysis NetEpi] + * Epidemiology: [http://debian-med.alioth.debian.org/tasks/epi.php#netepi-analysis NetEpi] + * Imaging: http://debian-med.alioth.debian.org/tasks/imaging.php#bioimagesuite BioImagesuite] * Watch the [http://debian-med.alioth.debian.org/bugs.php list of bugs] and fix bugs or try to provide a patch.
[Debian Wiki] Update of "DebianMedTodo" by AndreasTille
Dear Wiki user, You have subscribed to a wiki page or wiki category on "Debian Wiki" for change notification. The following page has been changed by AndreasTille: http://wiki.debian.org/DebianMedTodo -- * Package one of the most wanted packages from each section * Biology: [http://debian-med.alioth.debian.org/tasks/bio.php#mauve Mauve] * Epidemiology: [http://debian-med.alioth.debian.org/tasks/epi.php#netepi-analysis NetEpi] - * Imaging: http://debian-med.alioth.debian.org/tasks/imaging.php#bioimagesuite BioImagesuite] + * Imaging: [http://debian-med.alioth.debian.org/tasks/imaging.php#bioimagesuite BioImagesuite] * Watch the [http://debian-med.alioth.debian.org/bugs.php list of bugs] and fix bugs or try to provide a patch.
[Debian Wiki] Update of "DebianMedTodo" by AndreasTille
Dear Wiki user, You have subscribed to a wiki page or wiki category on "Debian Wiki" for change notification. The following page has been changed by AndreasTille: http://wiki.debian.org/DebianMedTodo -- * Epidemiology: [http://debian-med.alioth.debian.org/tasks/epi.php#netepi-analysis NetEpi] * Imaging: [http://debian-med.alioth.debian.org/tasks/imaging.php#bioimagesuite BioImagesuite] * Watch the [http://debian-med.alioth.debian.org/bugs.php list of bugs] and fix bugs or try to provide a patch. + * Make sure you [http://people.debian.org/~tille/cdd/ap-bts.en.html#s-howto_itp tagged your ITP bugs properly]
[Debian Wiki] Update of "DebianMedTodo" by AndreasTille
Dear Wiki user, You have subscribed to a wiki page or wiki category on "Debian Wiki" for change notification. The following page has been changed by AndreasTille: http://wiki.debian.org/DebianMedTodo -- * Epidemiology: [http://debian-med.alioth.debian.org/tasks/epi.php#netepi-analysis NetEpi] * Imaging: [http://debian-med.alioth.debian.org/tasks/imaging.php#bioimagesuite BioImagesuite] * Watch the [http://debian-med.alioth.debian.org/bugs.php list of bugs] and fix bugs or try to provide a patch. - * Make sure you [http://people.debian.org/~tille/cdd/ap-bts.en.html#s-howto_itp tagged your ITP bugs properly] + * Make sure you [http://people.debian.org/~tille/cdd/ap-bts.en.html#s-howto_itp tagged your ITP bugs properly]. + * Make sure that your package is listed in our [http://debian-med.alioth.debian.org/tasks/ task list].
