Bug#904735: libbio-samtools-perl: FTBFS: recompile with -fPIC

[Niko Tyni]

Control: retitle -1 libbam-dev: no longer built with -fPIC
Control: reassign -1 libbam-dev 0.1.19-3

On Fri, Jul 27, 2018 at 01:12:01PM +0300, Niko Tyni wrote:
> Source: libbio-samtools-perl
> Version: 1.43-1
> Severity: serious
> Tags: ftbfs
> Control: block 902557 with -1
> 
> This package fails to build on sid/amd64:
> 
>   x86_64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -shared -L/usr/local/lib -fstack-protector-strong -o blib/arch/auto/Bio/DB/Sam/Sam.so lib/Bio/DB/Sam.o c_bin/bam2bedgraph.o -L/usr/lib -lbam -lpthread -lz
>   /usr/bin/ld: /usr/lib/libbam.a(bam_aux.o): relocation R_X86_64_PC32 against symbol `bam_verbose' can not be used when making a shared object; recompile with -fPIC
>   /usr/bin/ld: final link failed: bad value
>   collect2: error: ld returned 1 exit status
>   error building blib/arch/auto/Bio/DB/Sam/Sam.so from lib/Bio/DB/Sam.o c_bin/bam2bedgraph.o at /usr/share/perl/5.26/ExtUtils/CBuilder/Base.pm line 321.
>   dh_auto_build: perl Build returned exit code 2
>   make: *** [debian/rules:4: build] Error 2
>   dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2

This is because libbam-dev is no longer built with -fPIC, even though
/usr/share/doc/libbam-dev/README.Debian still claims so. Reassigning.

> It seems to have built OK on test.reproducible-builds.org on 2018-07-12,
> so could be a binutils regression rather than libbam-dev?

This was on i386, where missing -fPIC doesn't cause a link error (I think),
so a bad guess on my part.

BTW, the Vcs-* entries of samtools-legacy don't seem to allow
unauthenticated access.  Could you please fix this.

 https://salsa.debian.org/med-team/samtools-legacy
-- 
Niko Tyni   ntyni at debian.org