[Debian-med-packaging] Bug#813262: python-biopython: FTBFS: ApplicationError: Non-zero return code 255 from 'phyml -i Phylip/interlaced2.phy -d aa'

[Chris Lamb]

Source: python-biopython
Version: 1.66+dfsg-1
Severity: serious
Justification: fails to build from source
User: reproducible-builds at lists.alioth.debian.org
Usertags: ftbfs
X-Debbugs-Cc: reproducible-builds at lists.alioth.debian.org

Dear Maintainer,

python-biopython fails to build from source in unstable/amd64:

  [..]

  ======================================================================
  ERROR: test_phyml (test_phyml_tool.AppTests)
  Run PhyML using the wrapper.
  ----------------------------------------------------------------------
  Traceback (most recent call last):
    File "/home/lamby/temp/cdt.20160130233124.nsZ8IkBTDh/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/test_phyml_tool.py", line 46, in test_phyml
      out, err = cmd()
    File "/home/lamby/temp/cdt.20160130233124.nsZ8IkBTDh/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Application/__init__.py", line 517, in __call__
      stdout_str, stderr_str)
  ApplicationError: Non-zero return code 255 from 'phyml -i Phylip/interlaced2.phy -d aa', message 'beignet-opencl-icd: no supported GPU found, this is probably the wrong opencl-icd package for this hardware'
  
  ----------------------------------------------------------------------
  Ran 229 tests in 103.372 seconds
  
  FAILED (failures = 1)
  Skipping any tests requiring internet access
  Python version: 2.7.11 (default, Jan 11 2016, 21:04:40) 
  [GCC 5.3.1 20160101]
  Operating system: posix linux2
  E: pybuild pybuild:274: test: plugin custom failed with: exit code=1: set -e; \
                               mkdir -p /home/lamby/temp/cdt.20160130233124.nsZ8IkBTDh/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/home; \
                               mkdir -p /home/lamby/temp/cdt.20160130233124.nsZ8IkBTDh/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Doc/examples; \
                               cp -a Doc/Tutorial.tex /home/lamby/temp/cdt.20160130233124.nsZ8IkBTDh/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Doc; \
                               cp -a Doc/Tutorial /home/lamby/temp/cdt.20160130233124.nsZ8IkBTDh/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Doc; \
                               cp -a Doc/examples /home/lamby/temp/cdt.20160130233124.nsZ8IkBTDh/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Doc; \
                               cp -a Tests /home/lamby/temp/cdt.20160130233124.nsZ8IkBTDh/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build; \
                               cd /home/lamby/temp/cdt.20160130233124.nsZ8IkBTDh/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Tests; \
                               env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/home/lamby/temp/cdt.20160130233124.nsZ8IkBTDh/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/home python2.7 run_tests.py --offline
  dh_auto_test: pybuild --test -i python{version} -p 2.7 --test --system=custom --test-args=set -e; \
                               mkdir -p {build_dir}/home; \
                               mkdir -p {build_dir}/Doc/examples; \
                               cp -a Doc/Tutorial.tex {build_dir}/Doc; \
                               cp -a Doc/Tutorial {build_dir}/Doc; \
                               cp -a Doc/examples {build_dir}/Doc; \
                               cp -a Tests {build_dir}; \
                               cd {build_dir}/Tests; \
                               env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} run_tests.py --offline --dir . returned exit code 13
  debian/rules:67: recipe for target 'override_dh_auto_test' failed
  make[1]: *** [override_dh_auto_test] Error 25
  make[1]: Leaving directory '/home/lamby/temp/cdt.20160130233124.nsZ8IkBTDh/python-biopython-1.66+dfsg'
  debian/rules:49: recipe for target 'build' failed
  make: *** [build] Error 2

  [..]

The full build log is attached.


Regards,

-- 
      ,''`.
     : :'  :     Chris Lamb
     `. `'`      lamby at debian.org / chris-lamb.co.uk
       `-
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