Re: [MoM] Any progress?
Hi Andreas, Good news in the front of packaging fis-gtm: We can now build a set of libraries and most of the executables through a cmake-based configuration. The updates are in the branch: https://github.com/luisibanez/fis-gtm/tree/cmakeified The result of the build for a 64bits system is reported in the following dashboard. http://my.cdash.org/index.php?project=fis-gtm The partition of libraries is not the same as the standard fis-gtm build, and since this is the first pass, there is certainly room for improvement. I have compared the size of the executables, and it is also clear that I'm over linking them. A second pass is needed to better redistribute the .o files into the libraries, so we get the original size of executables, or at least, closer to them. I ran into some trouble compiling the assembly files, for the library in sr_x86_64/CMakeLists.txt I was getting this error message: /usr/bin/ld: CMakeFiles/fisgtmx64.dir/call_dm.s.o: relocation R_X86_64_PC32 against symbol `opp_dmode' can not be used when making a shared object; recompile with -fPIC but couldn't figure out how to pass the equivalent of the fPIC flag to the as compiler so I cowardly made the library static..., all the other libraries are shared. There is probably a better way to address that error... Next step, is to review the composition of the libraries, make sure that the executables are of reasonable size (close to the original build system of fis-gtm), and then start exploring the post-build process. I'll check with Bhaskar (upstream) to get their advice on the current status. BTW, They have released version 5.5: http://sourceforge.net/projects/fis-gtm/files/GT.M-x86-Linux-src/V5.5-000/ I'll be tempted to finished the packaging first using 5.4, but I'm happy to look at 5.5 if there is a preference for the newer version. Thanks Luis -- 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/CABAUzPqmCvJPO=gvz7cqcre2nrg5txi93ac97jmp3gswbhz...@mail.gmail.com
Patch for Qiime to comply with ghc 7.4.2
Hi Greg, we in the Debian Med team have got a patch for Qiime to build with ghc 7.4.2. You can find it in our SVN. Here you can see a web view what needs to be changed: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/qiime/trunk/debian/patches/ghc_7.4.2_compatibility.patch?view=markup To check out all current patches we are using in the Debian packaged version you can do svn co svn://svn.debian.org/svn/debian-med/trunk/packages/qiime/trunk/debian/patches Kind regards and thanks for maintaining Qiime as free software 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/20120321074253.ga1...@an3as.eu
Re: [MoM] Any progress?
Hi Luis, On Wed, Mar 21, 2012 at 03:12:26AM -0400, Luis Ibanez wrote: Good news in the front of packaging fis-gtm: We can now build a set of libraries and most of the executables through a cmake-based configuration. Sounds good! The partition of libraries is not the same as the standard fis-gtm build, and since this is the first pass, there is certainly room for improvement. ... I was getting this error message: /usr/bin/ld: CMakeFiles/fisgtmx64.dir/call_dm.s.o: relocation R_X86_64_PC32 against symbol `opp_dmode' can not be used when making a shared object; recompile with -fPIC but couldn't figure out how to pass the equivalent of the fPIC flag to the as compiler so I cowardly made the library static..., all the other libraries are shared. There is probably a better way to address that error... In case of such trouble I sometimes ask for advise at debian-mentors list but I guess your workaround should do for the moment. Next step, is to review the composition of the libraries, make sure that the executables are of reasonable size (close to the original build system of fis-gtm), and then start exploring the post-build process. I'll check with Bhaskar (upstream) to get their advice on the current status. Good. Please make pretty sure that upstream has a positive feeling about your new build system. To me it sounds pretty promising and probably very helpful also for other users of fis-gtm (even when not involved into Debian). So I hope they will consider taking this over upstream for a future version. BTW, They have released version 5.5: http://sourceforge.net/projects/fis-gtm/files/GT.M-x86-Linux-src/V5.5-000/ I'll be tempted to finished the packaging first using 5.4, but I'm happy to look at 5.5 if there is a preference for the newer version. I personally would go for the Debian packaging with what seems to be the most straightforeward way to package it. If this is the case for 5.4 we should do this and upgrade later. Many thanks for your work and the status update. Keep on the good work 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/20120321115913.ga6...@an3as.eu
Re: new link for http://www.hpc.unm.edu/~aroberts/main/free.htm
Hi Arthur, I hope that this address would reach the destination and hopefully I haven't mixed you up with someone else now in the search for your new email address. I have originally emailed to arth...@wsunix.wsu.edu which was listed on your UNM pages (Hi from another UNM alumni btw ;) ). So here it goes - my original email with the follow up from Andreas. If you still maintain those pages to some degree... : On Tue, 20 Mar 2012, Andreas Tille wrote: On Tue, Mar 20, 2012 at 01:40:10PM -0400, Yaroslav Halchenko wrote: I have ran into your page http://www.hpc.unm.edu/~aroberts/main/free.htm and wanted to share the resource you seems have still missing: Debian Med project: http://www.debian.org/devel/debian-med/ which takes care about integrating related free and open source software for medical imaging, bioinformatics, clinic IT infrastructure, and others within Debian OS. As a result we provide a rich variety of FOSS for various fields, e.g. have a look at tasks pages: http://debian-med.alioth.debian.org/tasks which seems to list lots of software of interest for you. Thanks to Yaroslav for pointing to Debian Med. When browsing the biotech-resource site I noticed that also chemistry related software is linked to. So in addition it might be interesting to know that there is a team inside Debian which in the same manner as we do care for biological software is enriching Debian with chemical software. Just have a look at http://blends.alioth.debian.org/debichem/tasks for a list of packages prepared by the DebiChem team. Kind regards Andreas. -- =--= Keep in touch www.onerussian.com Yaroslav Halchenko www.ohloh.net/accounts/yarikoptic -- 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/20120321142236.gb22...@onerussian.com
Re: [MoM] Any progress?
On 03/21/2012 03:12 AM, Luis Ibanez wrote: Hi Andreas, Good news in the front of packaging fis-gtm: We can now build a set of libraries and most of the executables through a cmake-based configuration. [KSB] Excellent, Luis! ...snip... Next step, is to review the composition of the libraries, make sure that the executables are of reasonable size (close to the original build system of fis-gtm), and then start exploring the post-build process. I'll check with Bhaskar (upstream) to get their advice on the current status. [KSB] We'll discuss offline. BTW, They have released version 5.5: http://sourceforge.net/projects/fis-gtm/files/GT.M-x86-Linux-src/V5.5-000/ I'll be tempted to finished the packaging first using 5.4, but I'm happy to look at 5.5 if there is a preference for the newer version. [KSB] Perhaps it makes sense for you to finish building and releasing V5.4-002B in the package repositories, and then give me a set of instructions that I can use to build and release V5.5-000? Regards -- Bhaskar -- GT.M - Rock solid. Lightning fast. Secure. No compromises. _ The information contained in this message is proprietary and/or confidential. If you are not the intended recipient, please: (i) delete the message and all copies; (ii) do not disclose, distribute or use the message in any manner; and (iii) notify the sender immediately. In addition, please be aware that any message addressed to our domain is subject to archiving and review by persons other than the intended recipient. Thank you. -- 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/4f69e021.7010...@fisglobal.com
Re: [Debian-med-packaging] j2f package
I could go a little futher.
I think you also need jarpack,netlib-java and jlapack.
I could generate jarpack and netlib-java stuff (not packaged yet, from
source), but I cannot find anywhere jlapack source.
For jlapack, there are only binaries and no instructions on how to
generate those. I sent a mail upstream to have information, I will let
you know.
Olivier
Le 3/21/12 3:54 PM, Olivier Sallou a écrit :
Le 3/7/12 10:00 AM, Andreas Tille a écrit :
[Shamelessly quoting you on list because no private content and a
public explanetion seems to make sense.]
Hi Olivier,
thanks for pushing me! :-)
On Wed, Mar 07, 2012 at 09:26:23AM +0100, Olivier Sallou wrote:
Hi Andreas,
could you validate j2f package with the package you were preparing
(don't remember the name) ?
Finally it was the last unpackaged precondition for beast-mcmc package
and I injected my current packaging status now in SVN:
svn://svn.debian.org/debian-med/trunk/packages/libmtj-java/trunk
I've got some build result with the following patch:
$ diff -u build.xml.orig build.xml
--- build.xml.orig 2011-04-22 23:43:26.0 +0200
+++ build.xml 2012-01-23 16:08:21.0 +0100
@@ -16,4 +16,6 @@
zipfileset dir=.
excludes=**/lib/nblibraries-private.properties **/nbproject/private**
**/.ant-targets-build.xml dist/** build/** **/*.zip **/.svn**
prefix=mtj-${version} /
/zip
/target
+property name=src.dir value=src/
+property name=javac.classpath
value=/usr/share/java/junit.jar:lib/netlib-java/netlib-java-0.9.3.jar:lib/netlib-java/arpack_combo-0.1.jar/
/project
After installing f2j package, and setting /usr/share/java/f2jutil.jar
instead of lib/netlib-java/netlib-java-0.9.3.jar , we have lots of
compil errors less.
Remaining errors are with arpack_combo I think. I do not know how to
generate it, I gonna have a look.
Olivier
If yes I will upload it, else I will wait...
The problem is that I can't say. We somehow need to reproduce the JARs
in lib/netlib-java which somehow can be approached using f2j but I
somehow lost track how this could be done. So my answer to your
question is: may be. If you find a way to reproduce working the two
jars in lib/netlib-java I'd be more than thankful.
Kind regards
Andreas.
--
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
--
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/4f6a00eb.8020...@irisa.fr
blimps license
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jorja! I am Laszlo Kajan from Burkhard Rost's Lab, writing to you on behalf of the Debian Med Team. Debian Med is packaging bioinformatics software for Debian and Ubuntu. We have recently included blimps in the non-free section of the distribution, thanks to the fact that you make it available under the FHCRC NONCOMMERCIAL LICENSE. This is especially important because sift - an important tool to predict the phenotypic affects of point mutations - of Pauline Ng depends on blimps and so the packaging of sift requires a blimps package. While the FHCRC NONCOMMERCIAL LICENSE does allow packaging and royalty-free redistribution, its restrictions make it difficult to maintain /dependent/ software like sift in Debian/Ubuntu. Therefore I turn to you with the question: = Would it be possible at this point to change the license of blimps to a free license such as LGPL/GPL? Thank you very much for making blimps available to the bioinformatics community and for considering our question. Best regards, Laszlo Kajan Debian Med Team -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iQIcBAEBAgAGBQJPagalAAoJEJvS1kCaDFL6LrsQAKlHc5N2KwHpMgJO0vYDY9uU K3Y0k0tvLiDKJz2vTw2El7dQ8PeEHArE3MHbCjqUnBAThLH2uTZmwPsF/VNpNpAT Q4A4p2ejZ3oQm5ocyt7OqA2XlL5aBoPU1ODs09KPPunfzOQMwp0XAx+GN3y+IOAT sUuOETDgb51yIwPpAkOcgurA983a3mLh3wRHWsn4jwBJc8KmrZwLX3B54IjxaTp2 OoflyrFNSvFR8yVRkTas9O+EgkzSYTdIZrUo5gZ4THTJeWh5mxHduximg8Q9mMME b0GYfIOmqwxq97NKkN1XCpHmKO505DaFQ9YKXfGVqgJnmqzHTAii668/7FHFWAsG iViMYUePuuM2MMUa1KPbKjooRqfrn049OO9et6BquH6b5q5xUIiLc5LOZdQ2Ri+b w05NWJKOnxv7vTLgnJgJEdIxN++uvif9VOVakSaTN5OKz9u3YuNPfpAyvqPgJKh0 RmRywTzupG7cqaD9hwU43WaNVbGp1WLZuPIBdTOS+EAcAquPknbPLxq8ZojyKopL WaYJNEcTSUYFzSgwY53gght/woXe5532jdGb0LOuaGLT91/21Hw37Lmhg5cbs9xI ySsH+nV9MkUVq2pqWuOQvZrzNDMbltAVOEjMPY3D7U46pxWi/K6zAGE6LmGjPt0D 6UlRHo5tee1TDfRVrXA3 =Nkcc -END PGP SIGNATURE- -- 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/4f6a06aa.6080...@rostlab.org
Re: [Debian-med-packaging] j2f package
Hi Olivier, On Wed, Mar 21, 2012 at 05:25:15PM +0100, Olivier Sallou wrote: I could go a little futher. I think you also need jarpack,netlib-java and jlapack. I could generate jarpack and netlib-java stuff (not packaged yet, from source), but I cannot find anywhere jlapack source. For jlapack, there are only binaries and no instructions on how to generate those. I sent a mail upstream to have information, I will let you know. I think when we were in Southport I recieved som email of an author who pointed me to http://www.netlib.org/java/f2j/ providing a link saying filejlapack-0.8.tgz for JLAPACK source and class files (tgz archive) by Keith Seymour seym...@cs.utk.edu size1.3M but this is not really a source archive. I somehow have the suspicion that the sources would be the result of some F2J process. When digging deeper I've got another hint at http://icl.cs.utk.edu/f2j/faq/index.html#320 and the suggested cvs -d:pserver:anonym...@f2j.cvs.sourceforge.net:/cvsroot/f2j login cvs -z3 -d:pserver:anonym...@f2j.cvs.sourceforge.net:/cvsroot/f2j co -r jlapack0_8 -P f2j resulted in a f2j dir containing a subdirectory jlapack-3.1.1 which seems to contain the relevant Fortran code for the conversion to Java. The Fortran code seems to be some version of BLAS which shows differences to some Debian packaged sources I found (but I do not remember any more those details. Thanks for your work on this 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/20120321204630.gd6...@an3as.eu
Re: [MoM] Any progress?
Andreas, On Wed, Mar 21, 2012 at 4:37 PM, Andreas Tille andr...@an3as.eu wrote: Hi Luis, On Wed, Mar 21, 2012 at 10:05:21AM -0400, Bhaskar, K.S wrote: [KSB] Perhaps it makes sense for you to finish building and releasing V5.4-002B in the package repositories, and then give me a set of instructions that I can use to build and release V5.5-000? From a Debian perspective it makes sense to work on the latest upstream and if upstream is obviosely interested the motivation to work on the latest release and support your attempt in this would probably the highest. Perhaps you might like to check if your changes easily apply to the new code. - Yes, this certainly makes sense. I'll grab the 5.5 version and put it in a Git branch. This will make easier to evaluate how difficult it might be to port the current cmake files to V5.5. I'll double check on this with Bhaskar as well. Luis -- 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/CABAUzPpjcMUYDB_wV0VZ9jFLYt=fZbnt8JN=-eR3A3T=rze...@mail.gmail.com
