Re: insighttoolkit vs tiff5
Okay let's do this. On Wed, May 9, 2012 at 6:02 PM, Dominique Belhachemi domi...@debian.org wrote: I think we should use libtiff-dev only and file bugs against the consuming package if build errors appear. -Dominique On Wed, May 9, 2012 at 10:58 AM, Mathieu Malaterre ma...@debian.org wrote: Hi there, With ref to #672242, does anyone see any reason to not go back and use libtiff4-dev in insighttoolkit. Upstream does not clearly support tiff 4.0.0 anyway. My only fear is that libtiff5-dev and libtiff4-dev will conflicts at some point in a package trying to use them both. Comments welcome -M -- 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/ca+7wusyzx7qb4prnj2b2jprpxi4c8ulbfmq7-mzurnkwrw6...@mail.gmail.com -- Mathieu -- 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/ca+7wusy7yls41zsl5n9toubs5rsx+dr0nhgrjzuydlgjkzt...@mail.gmail.com
Build issue when building with gcc-4.7
Hi, when building libhmsbeagle using gcc version 4.7 you get a build error which can be easily fixed (see patch in Debian Med SVN[1]) Before I upload a package featuring this patch I would like to clarify something which remains not clear to me. The first thing is that I'm a bit unsure what version you might consider as stable for Debian release. The homepage[2] is featuring version 1.0. However, our watch file (containing the metainformation from where to download the source which needs to point to tagged SVN releases because you are not providing a downloadable source tarball) points to SVN tags[3] and finds version 1.1. So which one is the one you want Debian to distribute? BTW, questions like this will not occure if you would provide versioned a source tarball at the homepage directly. The second issue is about the problem which was discussed in the beginning of this year[4] about SSE support. I have noticed that you seem to have dealt with this but at least if I build not really successfully. I can not build on my amd64 machine if I do not at least add this patch: --- libhmsbeagle-1.1.orig/configure.ac +++ libhmsbeagle-1.1/configure.ac @@ -211,6 +211,9 @@ if test $enable_sse = yes; then SSE_CFLAGS+=-DENABLE_SSE AM_CXXFLAGS=$AM_CXXFLAGS -msse2 +AM_CONDITIONAL(HAVE_SSE2,true) +else +AM_CONDITIONAL(HAVE_SSE2,false) fi # -- Otherwise automake is claimin missing AM_CONDITIONAL statement for HAVE_SSE2. Moreover I think the way you changed libhmsbeagle/CPU/Makefile.am is not sufficiently preventing that the build system tries to build libhmsbeagle-cpu-sse.la on non-Intel architectures. The first line says: lib_LTLIBRARIES=libhmsbeagle-cpu.la libhmsbeagle-cpu-sse.la and thus libhmsbeagle-cpu-sse.la is an unconditional target which is not handled by the HAVE_SSE2 conditional. It might be that the HAVE_SSE2 condition has a completely different purpose than the patch from Debian[5] which was using HAVE_SSE and thus I would like to make sure I have understood things properly first before I upload. Kind regards and thanks for providing libhmsbeagle as Free Software Andreas. [1] http://anonscm.debian.org/viewvc/debian-med/trunk/packages/libhmsbeagle/trunk/debian/patches/gcc-4.7.patch?view=markup [2] http://code.google.com/p/beagle-lib/ [3] http://beagle-lib.googlecode.com/svn/tags/ [4] http://bugs.debian.org/656755 [5] http://anonscm.debian.org/viewvc/debian-med/trunk/packages/libhmsbeagle/trunk/debian/patches/disable_cpu_sse_plugin.patch?revision=9433view=markup -- 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/20120510095938.gg3...@an3as.eu
Re: Fix for Bug#672090: bowtie2: ftbfs with GCC-4.7
On 05/09/2012 03:57 PM, Andreas Tille wrote: Hi Alex, On Wed, May 09, 2012 at 03:15:04PM +0200, Alex Mestiashvili wrote: I've prepared patch to fix #672090. Could you please check upload it. Uploaded. As I said in BTS IMHO also #668123 is fixed. We will see how the just uploaded version builds on other architectures and might close the bug manually afterwards. Thanks for working on this Andreas. Thank you, As I see now, it fails to build on i386. I think problem comes from Makefile. I will get a real i386 box and try to fix it. In 32bit chroot on amd64 I could built it successfully. And it still fails on other architectures than amd64. 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/4faba2fd.4050...@biotec.tu-dresden.de
Re: Do we track releases or development versions [Was: r-bioc-cummerbund ... upstream/1.1.3-17-gae72ebb]
On Tue, May 8, 2012 at 3:22 PM, Andreas Tille andr...@an3as.eu wrote: On Tue, May 08, 2012 at 11:32:11AM -0400, Carlos Borroto wrote: I agree on following stable releases as a general rule. The reason I chose to use development version of cummeRbund was because at the time upstream was recommending it. The package was on heavy development and stable releases tied to Bioconductor were getting behind quite fast. I just checked the upstream website and now the recommendation is to use the stable version tied to Bioconductor. I just finish my semester yesterday and I plan to get up to speed with several TODOs I have with the packages I'm contributing to. Thanks for the clarification. I'll do this update right away. Just let us know if you need any help / sponsoring. Hi Andreas, I'm taking a look at this package and everything seems ready. I see you already fixed the watch file. Regarding citation, I haven't read yet how we are doing this, but I will soon. Do you wan't me to get the changelog ready and ask for sponsoring? Or do you have something else in mind that should be tackle before submission? Thanks, Carlos -- 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/CABgGhBLoz2DPcaM=g4RAjhzZ6uxf4uiP0_-PxG6VPK3tb=c...@mail.gmail.com
Re: Do we track releases or development versions [Was: r-bioc-cummerbund ... upstream/1.1.3-17-gae72ebb]
On Thu, May 10, 2012 at 10:25:45AM -0400, Carlos Borroto wrote: I'm taking a look at this package and everything seems ready. I see you already fixed the watch file. Yep. I fixed it and afterwards I have read the comment. :-) This made me a bit unsure ... Regarding citation, I haven't read yet how we are doing this, but I will soon. See http://wiki.debian.org/UpstreamMetadata At very bottom you'll find a template. There are 100 examples in our Vcs (SVN+Git). Do you wan't me to get the changelog ready and ask for sponsoring? Or do you have something else in mind that should be tackle before submission? It would be reasonable if you ping me once you are finished. I do not have additional plans for changes. 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/20120510202033.gj3...@an3as.eu
Re: Fix for Bug#672090: bowtie2: ftbfs with GCC-4.7
On Thu, May 10, 2012 at 01:14:05PM +0200, Alex Mestiashvili wrote: As I see now, it fails to build on i386. I think problem comes from Makefile. :-( I will get a real i386 box and try to fix it. If you will not succeede getting such a box, you might like to use debian-med.debian.net. There is pbuilder and sbuild installed on this machine. In 32bit chroot on amd64 I could built it successfully. And it still fails on other architectures than amd64. :-( Is this a problem in the code or just a broken Makefile? 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/20120510202249.gk3...@an3as.eu
Re: MOM: Expression of Interest
Hi Ismail, thanks for your interest in MoM. At first it would be cool if you would confirm that you are reading the list debian-med@lists.debian.org which would enable me to leave out CC to you personally which is unusual on this list. On Thu, May 10, 2012 at 06:34:35PM +0100, ismail adegbenga wrote: Hi Andreas, I am a follower of the gnumed-devel mailig list. I just read your mail showing your intent to mentor a student on the above list. I really liked that Sebastian forewarded my mail and I'm happy to teach you about the things you need to work on the packages. I am not a programmer, although I am willing to learn and contribute something to the growth of FOSS. It does not harm if you have some coding skills but it is not required specifically not if the package in question you are targeting is basically packaged and just needs updates. I am a Debian-Sid user. I have noticed the relatively slow pace at which updates appear in Debian. Is this concerning the gnumed packages? Just to make sure we are talking about the same thing: I think we are quite good behind upstream GNUmed to package for Debian *unstable*. If you are concerned about getting these packages into Debian *stable* that's something else and would be only possible via backports. Could you go a bit more into detail what would you consider a faster pace (just to understand what you are gaining for - I'm by all means for an enhancement, just to make sure we adjust our time scale properly. :-)). I am assuming this is due to the few number of people involved in packaging upstream updates I am willing to learn and contribute if this will improve the general state of things. I'd be very happy if somebody else would update the GNUmed packages in SVN and I would just need to pull the status and upload. To start with the MoM poject I'd suggest you put your name on the Wiki page[1] and read the Debian Med policy which is linked under Helpful Links. This gives basic advise what to do to get commit permissions to the SVN repository. If you have any question about this - even if you think it might sound stupid just ask here in public. There are no such things like stupid questions - only not asking is stupid. We need this communication to adjust the mentoring topics. Kind regards and thanks again for your interest to help Debian Med Andreas. [1] http://wiki.debian.org/DebianMed/MoM -- 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/20120510205205.gn3...@an3as.eu
Re: MOM: Expression of Interest
On Thu, May 10, 2012 at 10:52:05PM +0200, Andreas (Debian) wrote: I am a follower of the gnumed-devel mailig list. I just read your mail showing your intent to mentor a student on the above list. I really liked that Sebastian forewarded my mail and I'm happy to teach you about the things you need to work on the packages. I would agree to serve as technical upstream contact. Karsten -- GPG key ID E4071346 @ gpg-keyserver.de E167 67FD A291 2BEA 73BD 4537 78B9 A9F9 E407 1346 -- 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/20120510210752.gg3...@hermes.hilbert.loc
