Re: proposed patch libbam-dev due to cufflinks configure script not picking up bam.h

[Alex Mestiashvili <alex@biotec.tu-dresden.de>]

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-mentors@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