Re: libbam-dev ships sam.h in /usr/include/samtools
On 05/25/2011 04:35 AM, Charles Plessy wrote: Dear Alex, As the Perl transition is over, I have updated libbam to serve its headers in /usr/include/samtools, and libbio-samtools-perl to search for them there. You can go ahead with a similar change in cufflinks any time you like. Have a nice day, Hello , Thank you . Cufflinks in the git repository appears to be lintian clean . The manual pages were missing , but each tool provides a help , so I converted them with help2man and edited a bit for the better appearance . http://anonscm.debian.org/gitweb/?p=debian-med/cufflinks.git Best regards , Alex -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/4ddd1341.7020...@biotec.tu-dresden.de
Re: libbam-dev ships sam.h in /usr/include/samtools
Hi Alex, On Wed, May 25, 2011 at 04:33:37PM +0200, Alex Mestiashvili wrote: > Cufflinks in the git repository appears to be lintian clean . > The manual pages were missing , but each tool provides a help , so I > converted them with help2man and edited a bit for the better appearance . > > http://anonscm.debian.org/gitweb/?p=debian-med/cufflinks.git thanks for working on this. Is this a "call for sponsoring" of this package and if yes I'd welcome if Charles could do this because you both seemed to have some cooperation about this package. Just drop me a note if I should have a look. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110525150854.ga15...@an3as.eu
Fwd: [fedora-medical] dcm4che-test package review
FYI: Despite being RPM maybe it can be helpful when preparing Debian packages. Sebastian -- Weitergeleitete Nachricht -- Betreff: [fedora-medical] dcm4che-test package review Datum: Mittwoch, 25. Mai 2011, 18:23:48 Von: Ankur Sinha An: medical-...@lists.fedorahosted.org Hi folks, I just submitted the dcm4che-test-images package for review[1]. Could someone please begin to review it? dcm4che is dependent on this package, and therefore, so is mayan. [1] https://bugzilla.redhat.com/show_bug.cgi?id=707613 Thanks, Ankur ___ Medical-sig mailing list medical-...@lists.fedorahosted.org https://fedorahosted.org/mailman/listinfo/medical-sig - -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/201105251905.34850.sebastian.hilb...@gmx.net
Re: Medical Icons.
Dear All, Wise words indeed. However, when younger I was amazed to learn that 'Seneca' was not a wise old Iroquois Indian Chief. The benefits of a secondary US Education. But time has convinced me that there are many 'Seneca' wise people. Cheers! to Hamzamu a real Doctor! to Regards! -Thomas Clark On Sun, May 22, 2011 at 9:01 PM, Heddle Weaver wrote: > Hello, > > Free medical icons, anybody? > > > http://www.goomedic.com/free-60-medical-icons-for-medical-apps-developers-and-designers.html?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+Goomedic+%28GooMedic.com%29 > > Done up by my friend, Hamzamu, an Egyptian doctor caring for the Libyan > rebels at present, on his Ubuntu laptop, in what little spare time he has. > Regards, > > Weaver. > > -- > > Religion is regarded by the common people as true, > by the wise as false, > and by the rulers as useful. > > — Lucius Annæus Seneca. > > Terrorism, the new religion. > > >
Re: [debian-med] Install on ubuntu 10.04.2 or debian 6
Am Dienstag, 24. Mai 2011, 08:59:59 schrieb Andreas Tille: > On Mon, May 23, 2011 at 08:48:04PM +0200, Sebastian Hilbert wrote: > > > Once alioth is back, please create a > > > debian-med/trunk/packages/gingko-cadx folder with it all. It is > > > definitely a most rewarding spare-time activity. There are just too > > > many other bits for me to finish first ... is anybody on this list > > > prepared to jump at it, possibly? > > > > ? There is such a folder already, isn't there? > > Yes, there is (and it is called gingkocadx - with out the '-' ... feel > free to rename if you feel this is better). I'm just (not fully) back > from vaccation and might have missed a notice when Alioth might be back. > For those who are interested I can provide a copy of the content > somewhere. > > > I was under the impression that > > Andreas and Mathieu have prepared everything and now it takes someone to > > upload this. Did I miss something ? > > There is some preparation but I was blocked by some cmake issues where I > needed help (something should be in the mailing list archive ...). > I think the cmake issue has been taken care of after an hint from upstream. Sebastian -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/201105251913.13834.sebastian.hilb...@gmx.net
Ginkgo-CADx package - was: Install on ubuntu 10.04.2 or debian 6
Am Dienstag, 24. Mai 2011, 10:07:53 schrieb Mathieu Malaterre: > On Tue, May 24, 2011 at 8:59 AM, Andreas Tille wrote: > >> I was under the impression that > >> Andreas and Mathieu have prepared everything and now it takes someone to > >> upload this. Did I miss something ? > > > > There is some preparation but I was blocked by some cmake issues where I > > needed help (something should be in the mailing list archive ...). > > 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 upstream might be able to help with ? Sebastian -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/201105251914.50518.sebastian.hilb...@gmx.net
Re: Ginkgo-CADx package - was: Install on ubuntu 10.04.2 or debian 6
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 upstream might be able to help with ? This is something that can be done in debian/rules. Normally you can just delete the rpath. I would say that the use of its own sqlite library is more serious. I am not really sure whether the Debian package can/should be used. They provide a library consisting of one big file. Due to better compiler optimization this should gain some performance. I might have missed some of the previous discussions. Is there a reason why upstream provides its own debian directory? If it is of any use, maybe it can be renamed? Otherwise svn-buildpackage would mix everything together and lintian complains about lots of template files. Thorsten -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/pine.lnx.4.64.1105251933420.23...@tor.gallien.in-chemnitz.de
Re: [debian-med] Install on ubuntu 10.04.2 or debian 6
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 UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/pine.lnx.4.64.1105251930190.23...@tor.gallien.in-chemnitz.de
Re: Ginkgo-CADx package - was: Install on ubuntu 10.04.2 or debian 6
Hi, On Wed, May 25, 2011 at 07:43:05PM +0200, Thorsten Alteholz wrote: > 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... I'd say for a first shot on this package which might go to experimental this rpath issue might be ignorable. >> Could you please elaborate on what that means ? Is this something upstream >> might be able to help with ? > > This is something that can be done in debian/rules. Normally you can just > delete the rpath. Lintian usually gives a hint how to fix this when called with -i option. > I would say that the use of its own sqlite library is more serious. I am > not really sure whether the Debian package can/should be used. They > provide a library consisting of one big file. Due to better compiler > optimization this should gain some performance. We should always prefer the Debian packaged version. Usually this is quite easy to approach in debian/rules. > I might have missed some of the previous discussions. Is there a reason > why upstream provides its own debian directory? If it is of any use, > maybe it can be renamed? Otherwise svn-buildpackage would mix everything > together and lintian complains about lots of template files. Usually it is ugly to have upstream provided debian/ dirs and I always try to teach upstream to leave this out. Because upstream is known to be quite responsive this should be no problem (even if I have heard that source format 3.0 can handle this somehow I would prefer to get rid of it because it is at best confusing). Please let me know if the packaging is in a ready for sponsoring state. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110525192732.ga24...@an3as.eu
Re: [debian-med] Install on ubuntu 10.04.2 or debian 6
Am Mittwoch, 25. Mai 2011, 19:33:37 schrieb 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... > Thanks for taking the (cpu) time to work on it. Sebastian -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/201105252210.50687.sebastian.hilb...@gmx.net
Re: Ginkgo-CADx package - was: Install on ubuntu 10.04.2 or debian 6
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 teach upstream to leave this out. Because upstream is known to be quite responsive this should be no problem Ok, who is in contact with upstream? Please let me know if the packaging is in a ready for sponsoring state. 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 Thorsten -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/pine.lnx.4.64.1105252210460.27...@tor.gallien.in-chemnitz.de
Re: Ginkgo-CADx package - was: Install on ubuntu 10.04.2 or debian 6
On Wed, May 25, 2011 at 10:18:40PM +0200, Thorsten Alteholz wrote: > 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? I have not built the package - but packages with lintian *warnings* can be uploaded (and IMHO the rpath issue is only a warning, but I might be wrong). Could anybody post the output of "lintian -i" ? >> Usually it is ugly to have upstream provided debian/ dirs and I always >> try to teach upstream to leave this out. Because upstream is known to >> be quite responsive this should be no problem > > Ok, who is in contact with upstream? Karsten and Sebastian Hilbert were in contact but IMHO anybody of Debian Med could just explain this to the address inside debian/copyright. >> Please let me know if the packaging is in a ready for sponsoring state. > > 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 for the moment - I need to check commit tomorrow. Thanks for your input Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110525203955.ge24...@an3as.eu
Re: libbam-dev ships sam.h in /usr/include/samtools
Le Wed, May 25, 2011 at 05:08:54PM +0200, Andreas Tille a écrit : > On Wed, May 25, 2011 at 04:33:37PM +0200, Alex Mestiashvili wrote: > > Cufflinks in the git repository appears to be lintian clean . > > The manual pages were missing , but each tool provides a help , so I > > converted them with help2man and edited a bit for the better appearance . > > > > http://anonscm.debian.org/gitweb/?p=debian-med/cufflinks.git > > thanks for working on this. Is this a "call for sponsoring" of this > package and if yes I'd welcome if Charles could do this because you > both seemed to have some cooperation about this package. Just drop > me a note if I should have a look. Hello everybody, I had a look, but spent one hour trying to fix the Git repository instead of doing a real review. Some commits are kind of duplicated, in particular merges and imports of upstream version 1.0.2, and I do not manage to remove them. Just rebasing and deleting the corresponding lines did not work. Does anybody has a suggestion ? Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110526050812.ga15...@merveille.plessy.net
Re: libbam-dev ships sam.h in /usr/include/samtools
On 05/26/2011 07:08 AM, Charles Plessy wrote: Le Wed, May 25, 2011 at 05:08:54PM +0200, Andreas Tille a écrit : On Wed, May 25, 2011 at 04:33:37PM +0200, Alex Mestiashvili wrote: Cufflinks in the git repository appears to be lintian clean . The manual pages were missing , but each tool provides a help , so I converted them with help2man and edited a bit for the better appearance . http://anonscm.debian.org/gitweb/?p=debian-med/cufflinks.git thanks for working on this. Is this a "call for sponsoring" of this package and if yes I'd welcome if Charles could do this because you both seemed to have some cooperation about this package. Just drop me a note if I should have a look. Hello everybody, I had a look, but spent one hour trying to fix the Git repository instead of doing a real review. Some commits are kind of duplicated, in particular merges and imports of upstream version 1.0.2, and I do not manage to remove them. Just rebasing and deleting the corresponding lines did not work. Does anybody has a suggestion ? Have a nice day, It's my fault , instead of doing git checkout upstream I was trying to create a new upstream branch and push it to remote ... Would it be possible just to roll back to latest commit done by you , and start over from that point with my changes and the new upstream 1.0.2 ? Alex -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/4dddee54.1040...@biotec.tu-dresden.de
Re: Ginkgo-CADx package - was: Install on ubuntu 10.04.2 or debian6
Am Mittwoch, 25. Mai 2011, 22:18:40 schrieb 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 teach upstream to leave this out. Because upstream is known to > > be quite responsive this should be no problem > > Ok, who is in contact with upstream? I am in contact with upstream. they are reading this list I think but I have served as contact in the past. Re the Debian dir. I believe they have indicated that they are going to remove this in the next release. > > > Please let me know if the packaging is in a ready for sponsoring state. > > 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 > Please let us know when there are packages ready to test. If Alioth is holding you back you might want to zip up the neccessary files and I can try to build it locally or on the OpenBuildService by Novell Sebastian -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/201105260816.27965.sebastian.hilb...@gmx.net
Re: libbam-dev ships sam.h in /usr/include/samtools
Le Thu, May 26, 2011 at 08:08:20AM +0200, Alex Mestiashvili a écrit : > > Would it be possible just to roll back to latest commit done by you > , and start over from that point with my changes and the new > upstream 1.0.2 ? Yes, this is something that I was considering: recover your changes with git-format-patches, reset (--hard) to the latest clean commit, and apply the relevant patches with git am. Cheers, -- Charles -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110526061922.gb15...@merveille.plessy.net
