[Debian-med-packaging] Bug#707416: tophat: FTBFS: (.text+0x1732): undefined reference to `pthread_create'

[Lucas Nussbaum]

Source: tophat
Version: 2.0.8b-1
Severity: serious
Tags: jessie sid
User: debian-qa at lists.debian.org
Usertags: qa-ftbfs-20130509 qa-ftbfs
Justification: FTBFS on amd64

Hi,

During a rebuild of all packages in sid, your package failed to build on
amd64.

Relevant part:
> g++  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -I/usr/include  -I./SeqAn-1.3 -Wl,-z,relro   -Wl,-z,relro -o prep_reads prep_reads.o ../src/libtophat.a -lbam -lz 
> /usr/lib/gcc/x86_64-linux-gnu/4.7/../../../../lib/libbam.a(bgzf.o): In function `bgzf_mt':
> (.text+0x1732): undefined reference to `pthread_create'
> /usr/lib/gcc/x86_64-linux-gnu/4.7/../../../../lib/libbam.a(bgzf.o): In function `bgzf_close':
> (.text+0x1afa): undefined reference to `pthread_join'
> collect2: error: ld returned 1 exit status

The full build log is available from:
   http://people.debian.org/~lucas/logs/2013/05/09/tophat_2.0.8b-1_unstable.log

A list of current common problems and possible solutions is available at 
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.