[Debian-med-packaging] Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
Jakub Wilk
jwilk at debian.org
Fri Jun 13 12:18:48 UTC 2014
* Scott Kitterman <debian at kitterman.com>, 2014-06-11, 12:46:
>All four archs fail with a similar error:
>
>E: pybuild pybuild:256: test: plugin custom failed with: exit code=1: mkdir -p /«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/Doc; \
> cp -a Doc/Tutorial.tex /«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/Doc; \
> cp -a Tests /«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build; \
> cd /«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/Tests; \
> env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/tmp python2.7 run_tests.py --offline
>dh_auto_test: pybuild --test -i python{version} -p 2.7 --test --system=custom --test-args=mkdir -p {build_dir}/Doc; \
> cp -a Doc/Tutorial.tex {build_dir}/Doc; \
> cp -a Tests {build_dir}; \
> cd {build_dir}/Tests; \
> env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/tmp {interpreter} run_tests.py --offline --dir . returned exit code 13
>make[1]: *** [override_dh_auto_test] Error 13
That's only dh_auto_* and pybuild exiting noisily. The actual reasons
for failures are elsewhere, and they vary with architecture:
On mips:
| ======================================================================
| ERROR: test_long (test_Muscle_tool.SimpleAlignTest)
| Simple muscle call using long file
| ----------------------------------------------------------------------
| Traceback (most recent call last):
| File "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/test_Muscle_tool.py", line 275, in test_long
| align = AlignIO.read(child.stdout, "clustal")
| File "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/AlignIO/__init__.py", line 427, in read
| raise ValueError("No records found in handle")
| ValueError: No records found in handle
|
| ======================================================================
| ERROR: test_align (test_Wise.TestWise)
| Call dnal with optional arguments, and do a trivial check on the output.
| ----------------------------------------------------------------------
| Traceback (most recent call last):
| File "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/test_Wise.py", line 45, in test_align
| temp_file = Wise.align(["dnal"], ("Wise/human_114_g01_exons.fna_01", "Wise/human_114_g02_exons.fna_01"), kbyte=100000, force_type="DNA", quiet=True)
| File "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Wise/__init__.py", line 111, in align
| return align(cmdline, pair, 0, force_type, dry_run, quiet, debug)
| File "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Wise/__init__.py", line 113, in align
| raise OSError("%s returned %s" % (" ".join(cmdline), status))
| OSError: dnal returned 36
|
| ----------------------------------------------------------------------
| Ran 211 tests in 10267.955 seconds
|
| FAILED (failures = 2)
| Skipping any tests requiring internet access
| Python version: 2.7.7 (default, Jun 4 2014, 17:09:48)
On mipsel:
| ======================================================================
| ERROR: test_align (test_Wise.TestWise)
| Call dnal with optional arguments, and do a trivial check on the output.
| ----------------------------------------------------------------------
| Traceback (most recent call last):
| File "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/test_Wise.py", line 45, in test_align
| temp_file = Wise.align(["dnal"], ("Wise/human_114_g01_exons.fna_01", "Wise/human_114_g02_exons.fna_01"), kbyte=100000, force_type="DNA", quiet=True)
| File "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Wise/__init__.py", line 111, in align
| return align(cmdline, pair, 0, force_type, dry_run, quiet, debug)
| File "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Wise/__init__.py", line 113, in align
| raise OSError("%s returned %s" % (" ".join(cmdline), status))
| OSError: dnal returned 36
|
| ----------------------------------------------------------------------
| Ran 211 tests in 1166.417 seconds
|
| FAILED (failures = 1)
| Skipping any tests requiring internet access
| Python version: 2.7.7 (default, Jun 4 2014, 00:11:03)
On powerpc and s390x:
| ======================================================================
| ERROR: test_clusterdistance (test_Cluster.TestCluster)
| ----------------------------------------------------------------------
| Traceback (most recent call last):
| File "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_3.4/build/Tests/test_Cluster.py", line 212, in test_clusterdistance
| method='a', transpose=0)
| ValueError: method should be a single character
|
| ======================================================================
| ERROR: test_kcluster (test_Cluster.TestCluster)
| ----------------------------------------------------------------------
| Traceback (most recent call last):
| File "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_3.4/build/Tests/test_Cluster.py", line 141, in test_kcluster
| method='a', dist='e')
| ValueError: method should be a single character
|
| ======================================================================
| ERROR: test_somcluster (test_Cluster.TestCluster)
| ----------------------------------------------------------------------
| Traceback (most recent call last):
| File "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_3.4/build/Tests/test_Cluster.py", line 557, in test_somcluster
| inittau=0.02, niter=100, dist='e')
| ValueError: distance should be a single character
|
| ======================================================================
| ERROR: test_treecluster (test_Cluster.TestCluster)
| ----------------------------------------------------------------------
| Traceback (most recent call last):
| File "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_3.4/build/Tests/test_Cluster.py", line 290, in test_treecluster
| transpose=0, method='a', dist='e')
| ValueError: method should be a single character
|
| ----------------------------------------------------------------------
| Ran 210 tests in 337.138 seconds
|
| FAILED (failures = 1)
| Skipping any tests requiring internet access
| Python version: 3.4.1 (default, Jun 7 2014, 17:37:50)
On sparc (not a release architecture, but mentioning for completeness):
| ======================================================================
| ERROR: test_Dialign_complex_command_line (test_Dialign_tool.DialignApplication)
| Round-trip through app with complex command line.
| ----------------------------------------------------------------------
| Traceback (most recent call last):
| File "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/test_Dialign_tool.py", line 107, in test_Dialign_complex_command_line
| stdout, stderr = cmdline()
| File "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Application/__init__.py", line 513, in __call__
| stdout_str, stderr_str)
| ApplicationError: Non-zero return code 148 from 'dialign2-2 -cs -mask -nt -ow -stars 9 -thr 4 Fasta/f002'
|
| ======================================================================
| ERROR: test_Dialign_simple (test_Dialign_tool.DialignApplication)
| Simple round-trip through app with infile.
| ----------------------------------------------------------------------
| Traceback (most recent call last):
| File "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/test_Dialign_tool.py", line 62, in test_Dialign_simple
| stdout, stderr = cmdline()
| File "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Application/__init__.py", line 513, in __call__
| stdout_str, stderr_str)
| ApplicationError: Non-zero return code 212 from 'dialign2-2 Fasta/f002
|
| ======================================================================
| ERROR: test_Dialign_simple_with_MSF_output (test_Dialign_tool.DialignApplication)
| Simple round-trip through app with infile, output MSF
| ----------------------------------------------------------------------
| Traceback (most recent call last):
| File "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/test_Dialign_tool.py", line 89, in test_Dialign_simple_with_MSF_output
| stdout, stderr = cmdline()
| File "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Application/__init__.py", line 513, in __call__
| stdout_str, stderr_str)
| ApplicationError: Non-zero return code 212 from 'dialign2-2 -msf Fasta/f002'
|
| ======================================================================
| ERROR: test_Dialign_simple_with_options (test_Dialign_tool.DialignApplication)
| Simple round-trip through app with infile and options
| ----------------------------------------------------------------------
| Traceback (most recent call last):
| File "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/test_Dialign_tool.py", line 76, in test_Dialign_simple_with_options
| stdout, stderr = cmdline()
| File "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Application/__init__.py", line 513, in __call__
| stdout_str, stderr_str)
| ApplicationError: Non-zero return code 180 from 'dialign2-2 -max_link -stars 4 Fasta/f002'
|
| ======================================================================
| ERROR: test_align (test_Wise.TestWise)
| Call dnal with optional arguments, and do a trivial check on the output.
| ----------------------------------------------------------------------
| Traceback (most recent call last):
| File "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/test_Wise.py", line 45, in test_align
| temp_file = Wise.align(["dnal"], ("Wise/human_114_g01_exons.fna_01", "Wise/human_114_g02_exons.fna_01"), kbyte=100000, force_type="DNA", quiet=True)
| File "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Wise/__init__.py", line 111, in align
| return align(cmdline, pair, 0, force_type, dry_run, quiet, debug)
| File "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Wise/__init__.py", line 113, in align
| raise OSError("%s returned %s" % (" ".join(cmdline), status))
| OSError: dnal returned 80
|
| ----------------------------------------------------------------------
| Ran 211 tests in 1636.716 seconds
|
| FAILED (failures = 2)
| Skipping any tests requiring internet access
| Python version: 2.7.7 (default, Jun 3 2014, 08:24:14)
--
Jakub Wilk
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