Re: proposed patch libbam-dev due to cufflinks configure script not picking up bam.h
On 12/04/2011 12:39 AM, Andreas Tille wrote: > On Sat, Dec 03, 2011 at 06:43:50PM +0100, Andreas Tille wrote: > >>> Does anybody know how to avoid this ? >>> >> I gave it a quick(!) try (see git) but failed. I'd suggest asking on >> debian-ment...@lists.debian.org because there are people with a lot of >> experience (gaining it yourself will take you hours). >> > After having some not so quick look I at least found the reaosn for the > problem: In debian/patches/0001-bam2samtools.patch the configure script > and the m4 files are tweaked to make sure it will find the bam.h header > file. However when in dh_auto_clean the configure script is called > again this patch is not active any more. > > Even if the root of the problem seems to be clear I'm not fully sure > what might be the best solution for this problem. Any ideas? (Perhaps > asking this really on debian-mentors?) > > Kind regards > > Andreas. > > Hi Andreas , thank you for the commits . I had to patch both files , because during the build process autoconf is called and if ax_bam.m4 isn't patched it rewrites the configure with wrong path ... I tried to override dh_auto_clean with : override_dh_auto_clean: dh_quilt_patch dh_auto_clean but this didn't work because patches can't be applied cleanly to configure script re-generated by autoconf . 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/4edb4885.8050...@biotec.tu-dresden.de
Re: proposed patch libbam-dev due to cufflinks configure script not picking up bam.h
On 12/04/2011 12:39 AM, Andreas Tille wrote: > On Sat, Dec 03, 2011 at 06:43:50PM +0100, Andreas Tille wrote: > >>> Does anybody know how to avoid this ? >>> >> I gave it a quick(!) try (see git) but failed. I'd suggest asking on >> debian-ment...@lists.debian.org because there are people with a lot of >> experience (gaining it yourself will take you hours). >> > After having some not so quick look I at least found the reaosn for the > problem: In debian/patches/0001-bam2samtools.patch the configure script > and the m4 files are tweaked to make sure it will find the bam.h header > file. However when in dh_auto_clean the configure script is called > again this patch is not active any more. > > Even if the root of the problem seems to be clear I'm not fully sure > what might be the best solution for this problem. Any ideas? (Perhaps > asking this really on debian-mentors?) > > Kind regards > > Andreas. > > I think I've found the proper dh_helper - dh_autoreconf . see git for changes . Best , 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/4edb8162.3090...@biotec.tu-dresden.de
Re: proposed patch libbam-dev due to cufflinks configure script not picking up bam.h
On Sun, Dec 04, 2011 at 03:19:14PM +0100, Alexander Mestiashvili wrote: > I think I've found the proper dh_helper - dh_autoreconf . > see git for changes . Looks very reasonable (even if I did not tested the build). Do you regard it ready for sponsering? 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/20111204211219.gb32...@an3as.eu
