[Debian-med-packaging] Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
Andreas Tille
andreas at an3as.eu
Fri Jun 13 12:55:06 UTC 2014
Hi BioPython developers,
I have updated the Debian package to version 1.64 (BTW, it is fine to
ping debian-med at lists.debian.org about new upstream versions - we might
become more quick in packaging new versions). Thanks for adopting the
patches we sended to you.
Since the Debian package is built on different hardware architectures,
we were facing different problems in the test suite. Here you have an
overview about all build logs:
https://buildd.debian.org/status/package.php?p=python-biopython&suite=unstable
Jakub Wilk was kind enough to point to the real problems of the tests
which can be read below (since the end of the build log does not say
a lot).
It would be great if you give some advise how to deal with these
problems.
Kind regards
Andreas.
On Fri, Jun 13, 2014 at 02:18:48PM +0200, Jakub Wilk wrote:
> ... 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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