Re: blast+ packaging

2011-05-30 Thread Olivier Sallou
hi, after updating to your code, there is a compil (configure) error at build time: configure: error: Do not know how to build MT-safe with compiler /usr/bin/g++ Maybe a missing dependency, do you have any idea? Olivier Le 5/29/11 6:12 PM, Aaron M. Ucko a écrit : > Olivier Sallou writes: > >>

ubuntu backport on launchpad usage

2011-05-30 Thread Olivier Sallou
Hi, I have 2 questions on ubuntu backport on debian-med launchpad: 1) can we put a package, simply to get it available on current ubuntu version? (though deb package will be available on next ubuntu release). If yes, how do we manage it from version point of view ? If debian package has version xx

Re: ubuntu backport on launchpad usage

2011-05-30 Thread Steffen Möller
On 05/30/2011 10:49 AM, Olivier Sallou wrote: > Hi, > I have 2 questions on ubuntu backport on debian-med launchpad: > > 1) can we put a package, simply to get it available on current ubuntu > version? (though deb package will be available on next ubuntu release). > If yes, how do we manage it from

Re: ubuntu backport on launchpad usage

2011-05-30 Thread Charles Plessy
Le Mon, May 30, 2011 at 10:49:01AM +0200, Olivier Sallou a écrit : > > 1) can we put a package, simply to get it available on current ubuntu > version? (though deb package will be available on next ubuntu release). > If yes, how do we manage it from version point of view ? If debian > package has

Re: blast+ packaging

2011-05-30 Thread Aaron Ucko
That's a puzzling error; please send your c++/config.log, which should shed more light on it.  Thanks! -- Sent from my Palm Pre On May 30, 2011 3:44, Olivier Sallou wrote: hi, after updating to your code, there is a compil (configure) error at build time: configure

Re: blast+ packaging

2011-05-30 Thread Olivier Sallou
Here is config.log 25+-src/c++$ cat config.log This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by ncbi-tools++ configure 0.0, which was generated by GNU Autoconf 2.59. Invocation command line was $ .

Re: blast+ packaging

2011-05-30 Thread Aaron Ucko
It looks like you're trying to run the whole build under fakeroot, which is unnecessary.  I can improve debian/rules to allow for that, but would regardless recommend switching to debuild -rfakeroot. Sorry you ran into trouble!

Re: libbam-dev ships sam.h in /usr/include/samtools

2011-05-30 Thread Alex Mestiashvili
On 05/29/2011 04:50 PM, Charles Plessy wrote: Dear Alex, I reviewed the licenses in the sources of Cufflinks and found that the files under src/locfit are not free, because their license forbids to make benchmarks… http://anonscm.debian.org/gitweb/?p=debian-med/cufflinks.git;a=blob;f=debian/cop

Re: blast+ packaging

2011-05-30 Thread Aaron M. Ucko
Olivier Sallou writes: > configure: error: Do not know how to build MT-safe with compiler > /usr/bin/g++ Updating debian/rules to r6893 should fix that, though I'd still recommend using fakeroot only as needed (e.g., via debuild -rfakeroot). Once again, thanks for pointing out the problem and s

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 back. As usual the

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: rev 6863 (Re: Ginkgo-CADx package - was: Install on ubuntu 10.04.2 or debian 6)

2011-05-30 Thread Nelson A. de Oliveira
Hi! On Mon, May 30, 2011 at 6:07 PM, Thorsten Alteholz wrote: > There are about 1800 files to be checked. > Are there any tools to make this task a bit easier? licensecheck (from the devscripts package) can help you, but it's still highly recommended to manually review all the files (there are c

Re: Ginkgo-CADx package - was: Install on ubuntu 10.04.2 or debian 6

2011-05-30 Thread Andreas Tille
On Mon, May 30, 2011 at 07:44:27PM +0200, Thorsten Alteholz wrote: > Ok, it seems to be that I am back. :-) > As usual the problem sat in front of > the monitor. This is so embarrassing, let us cast a veil of silence over > it ... Silence? Hmmm, silence - everything has its price. In this

Debian packaging for plastimatch

2011-05-30 Thread Gregory Sharp
Hello, I am interested in Debian packaging for plastimatch (plastimatch.org). The procedure is more or less clear, and I have completed the tutorial to create debian directory, and make source and binary packages. So far, I have registered on Alioth and requested to join debian-med. It seems

Re: Debian packaging for plastimatch

2011-05-30 Thread Andreas Tille
Hi Greg, welcome on the Debian Med mailing list. On Mon, May 30, 2011 at 03:08:29PM -0700, Gregory Sharp wrote: > Hello, > > I am interested in Debian packaging for plastimatch (plastimatch.org). The > procedure is more or less clear, and I have completed the tutorial to create > debian direc

Re: Debian packaging for plastimatch

2011-05-30 Thread Mathieu Malaterre
Hi Greg ! On Tue, May 31, 2011 at 12:08 AM, Gregory Sharp wrote: > So far, I have registered on Alioth and requested to join debian-med.  It > seems that debian latest release of ITK is 3.18, so I think that a good next > step should be to implement ITK 3.20.  I appreciate any advice for this s