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

[Charles Plessy]

Dear Samtools developers,

SAMtools fails to build when passing the option --as-needed to ld. You can
find an example of build log at the following URL:

http://people.ubuntuwire.org/~lucas/ubuntu-nbs/64/samtools_0.1.10-1_lubuntu64.buildlog

Luckily, this is easily solved by re-ordering the build options:

--- samtools-0.1.12a.orig/examples/Makefile
+++ samtools-0.1.12a/examples/Makefile
@@ -40,11 +40,11 @@ ex1.bcf:ex1.bam ex1.fa.fai
 		(cd ..; make libbam.a)
 
 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


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.

You can find more information about linker changes at the following URL.

http://wiki.debian.org/ToolChain/DSOLinking

By the way, thank you for writing SAMtools. It is a great program.

Have a nice week-end,

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan