[Debian-med-packaging] Bug#606004: [Samtools-devel] SAMtools fails to build with ld --as-needed.

[John Marshall]

On 10 Dec 2010, at 11:57, Charles Plessy wrote:
> SAMtools fails to build when passing the option --as-needed to ld.
[...]
> calDepth:../libbam.a calDepth.c
> -		gcc -g -Wall -O2 -I.. calDepth.c -o $@ -lm -lz -L.. -lbam
> +		gcc -g -Wall -O2 -I.. calDepth.c -o $@ -L.. -lbam -lm -lz

Applied, and similarly in bcftools/Makefile and the main Makefile.   
(I'm a little surprised those other two built for you -- it wasn't  
hard to break those in r891 by building with gcc -static.)   
Makefile.mingw appears to be close to correct, but perhaps someone  
should check it properly.

> The behaviour of the linker is changing in Ubuntu and Fedora and  
> will change in
> Debian, rendering this patch necessary for building SAMtools on  
> these platforms.

As there is no down-side, it's really simply good hygiene to put the  
system libraries last in the link command.  I made similar fixes in  
svn r519, but problems had since sneaked back in.

Thanks,

     John


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