[Debian-med-packaging] Bug#851466: khmer: autopkgtest is failing

[Andreas Tille]

Package: khmer
Severity: normal

Hi,

the autopkgtest of khmer is failing[1] with

...
+ c++ -o test-prog-static -std=c++11 /usr/share/doc/khmer-common/test-compile.cc /usr/lib/x86_64-linux-gnu/liboxli.a /usr/lib/x86_64-linux-gnu/libz.a /usr/lib/x86_64-linux-gnu/libbz2.a
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libbz2.a(bzlib.o): relocation R_X86_64_32S against symbol `BZ2_crc32Table' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libbz2.a(compress.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libbz2.a(decompress.o): relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libbz2.a(blocksort.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status
...

The solution probably would be to fix the makefile to include -fPIC.

Kind regards

       Andreas.

[1] https://ci.debian.net/data/packages/unstable/amd64/k/khmer/20170112_131441.autopkgtest.log.gz

-- System Information:
Debian Release: 8.6
  APT prefers stable-updates
  APT policy: (500, 'stable-updates'), (500, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 3.16.0-4-amd64 (SMP w/1 CPU core)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)