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

2011-06-03 Thread Andreas Tille
On Fri, Jun 03, 2011 at 11:30:12AM +0200, Alex Mestiashvili wrote: > > So if no one has objections against non-free than we can distribute it > in non-free . > > Btw there is a new upstream version , I'll add it to git later during > weekend . If there is a new upstream version this means upst

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

2011-06-03 Thread Sebastian Hilbert
Am Freitag, 3. Juni 2011, 12:03:07 schrieb Alex Mestiashvili: > On 06/03/2011 11:46 AM, Sebastian Hilbert wrote: > > Am Freitag, 3. Juni 2011, 11:30:12 schrieb Alex Mestiashvili: > >> On 05/30/2011 05:43 PM, Alex Mestiashvili wrote: > >>> On 05/29/2011 04:50 PM, Charles Plessy wrote: > Dear Al

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

2011-06-03 Thread Alex Mestiashvili
On 06/03/2011 11:46 AM, Sebastian Hilbert wrote: Am Freitag, 3. Juni 2011, 11:30:12 schrieb Alex Mestiashvili: On 05/30/2011 05:43 PM, Alex Mestiashvili wrote: On 05/29/2011 04:50 PM, Charles Plessy wrote: Dear Alex, I reviewed the licenses in the sources of Cufflinks and fo

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

2011-06-03 Thread Sebastian Hilbert
Am Freitag, 3. Juni 2011, 11:30:12 schrieb Alex Mestiashvili: > On 05/30/2011 05:43 PM, Alex Mestiashvili wrote: > > 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 fr

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

2011-06-03 Thread Alex Mestiashvili
On 05/30/2011 05:43 PM, Alex Mestiashvili wrote: 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/gitw

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

2011-05-29 Thread Charles Plessy
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/copyright;h=af50c87d0a97f9db7c35b77e7af3f9ee321d4f6

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

2011-05-26 Thread Alex Mestiashvili
On 05/27/2011 07:56 AM, Charles Plessy wrote: Hi Alex, I found that format-patch can be given a path, so that it only produces patch for it. Here is how I have prepared a new cufflinks repository: debcheckout -a git://git.debian.org/debian-med/cufflinks.git --git-track='*' cd cufflinks/

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

2011-05-26 Thread Charles Plessy
Hi Alex, I found that format-patch can be given a path, so that it only produces patch for it. Here is how I have prepared a new cufflinks repository: debcheckout -a git://git.debian.org/debian-med/cufflinks.git --git-track='*' cd cufflinks/ git format-patch 0b7256275dc8b8f7495a46b6b337395

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

2011-05-26 Thread Alex Mestiashvili
On 05/26/2011 08:19 AM, Charles Plessy wrote: 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

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

2011-05-25 Thread Charles Plessy
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

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

2011-05-25 Thread Alex Mestiashvili
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 too

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

2011-05-25 Thread Charles Plessy
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

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

2011-05-25 Thread Andreas Tille
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:

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

2011-05-25 Thread Alex Mestiashvili
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 da

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

2011-05-24 Thread Charles Plessy
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, -- Charles Plessy Debian Med packaging team