Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
Dear all, With Dave kindly offering access to a PowerPC, I was able to fix this bug. I have uploaded a fixed version of Bio/Cluster/clustermodule.c to the Biopython github repository; see https://github.com/biopython/biopython/blob/master/Bio/Cluster/clustermodule.c Can you try this version? This should solve the test failures. Best, -Michiel. On Mon, 8/18/14, Andreas Tille andr...@an3as.eu wrote: Subject: Re: Bug#751277: python-biopython: FTBFS on mips* powerpc s390x To: Michiel de Hoon mjldeh...@yahoo.com, debian-powe...@lists.debian.org, debian-m...@lists.debian.org, debian-s...@lists.debian.org Cc: Peter Cock p.j.a.c...@googlemail.com, Dejan Latinovic dejan.latino...@imgtec.com, Biopython discussion list biopyt...@lists.open-bio.org, 751...@bugs.debian.org 751...@bugs.debian.org, biopython-...@biopython.org biopython-...@biopython.org Date: Monday, August 18, 2014, 5:01 PM Hi porters, could you please be so kind to check this issue? It would be great to find out why the test suite of biopython fails on these architectures. Thanks a lot Andreas. On Mon, Aug 18, 2014 at 12:35:53AM -0700, Michiel de Hoon wrote: Hi Andreas, Without access to powerpc, I have no way to test the code. Can you try recompiling Biopython and checking what exactly happens inside the distance_converter function in Bio/Cluster/clustermodule.c ? For example, I am really wondering what strlen(data) inside this function returns on powerpc. Best, -Michiel. On Sat, 8/16/14, Andreas Tille andr...@an3as.eu wrote: Subject: Re: Bug#751277: python-biopython: FTBFS on mips* powerpc s390x To: Peter Cock p.j.a.c...@googlemail.com Cc: Dejan Latinovic dejan.latino...@imgtec.com, Michiel de Hoon mjldeh...@yahoo.com, Biopython discussion list biopyt...@lists.open-bio.org, 751...@bugs.debian.org 751...@bugs.debian.org, biopython-...@biopython.org biopython-...@biopython.org Date: Saturday, August 16, 2014, 5:37 AM Hi Peter, On Thu, Aug 14, 2014 at 09:52:40AM +0100, Peter Cock wrote: 1. waiting for your confirmation / patch 2. deactivating the specific test 3. exclude mips for biopython 4. ? any better idea ? In the current state all the work we spent in biopython over the last monthes will not migrate to testing for the simple reason that the current package in testing just does not run the test suite at build time and moreover python3 is not supported. Kind regards Andreas. I would suggest (2), deactivate this test (at least for for mips) as the most practical short term solution for the Debian packages. Or if you prefer (3), don't target mips for the Biopython package (yet). Medium term, I hope we can fix the C code to handle either Endian platform - option (1). It seems after having fixed the issue caused by wise we have one remaining problem: On powerpc[1] and s390x[2] test_Cluster fails even with Python 2.7 with: == 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
Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
Hi Michiel, thanks for testing this. Just to let you know: I personally need to admit that I do not feel capable to verify your test for the next couple of weeks. Just from my gut feling I'd say: If you find a workaround here that's probably helpful to run the test suite successfully. Thanks again Andreas. On Sat, Aug 23, 2014 at 06:47:00PM -0700, Michiel de Hoon wrote: Hi Andreas, I was able to replicate this bug on a PowerPC with Python 2.7, but only if I replace the single character into a single unicode character (e.g. in line 212 of test_Cluster.py, if I replace method='a' by method=u'a'). Can you confirm that you get this bug with Python 2.7 even with simple strings rather than unicode? Thanks, -Michiel. On Sat, 8/16/14, Andreas Tille andr...@an3as.eu wrote: Subject: Re: Bug#751277: python-biopython: FTBFS on mips* powerpc s390x To: Peter Cock p.j.a.c...@googlemail.com Cc: Dejan Latinovic dejan.latino...@imgtec.com, Michiel de Hoon mjldeh...@yahoo.com, Biopython discussion list biopyt...@lists.open-bio.org, 751...@bugs.debian.org 751...@bugs.debian.org, biopython-...@biopython.org biopython-...@biopython.org Date: Saturday, August 16, 2014, 5:37 AM Hi Peter, On Thu, Aug 14, 2014 at 09:52:40AM +0100, Peter Cock wrote: 1. waiting for your confirmation / patch 2. deactivating the specific test 3. exclude mips for biopython 4. ? any better idea ? In the current state all the work we spent in biopython over the last monthes will not migrate to testing for the simple reason that the current package in testing just does not run the test suite at build time and moreover python3 is not supported. Kind regards Andreas. I would suggest (2), deactivate this test (at least for for mips) as the most practical short term solution for the Debian packages. Or if you prefer (3), don't target mips for the Biopython package (yet). Medium term, I hope we can fix the C code to handle either Endian platform - option (1). It seems after having fixed the issue caused by wise we have one remaining problem: On powerpc[1] and s390x[2] test_Cluster fails even with Python 2.7 with: == 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 293.712 seconds FAILED (failures = 1) On sparc[3] there is a problem with dialign but sparc is no release architecture and wie might ignore this. It might be a helpful hint anyway. Any hint for the test_Cluster problem? If not I would also consider to hide it cowardly under the carpet for the moment. The new package is so much better tested than the one in the testing distribution which does not even dare about any unit tests and only for this reason reached the testing distribution. What do you think? Kind regards Andreas. scrool these links to the end to see the problem: [1] https
Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
Hi Andreas, I was able to replicate this bug on a PowerPC with Python 2.7, but only if I replace the single character into a single unicode character (e.g. in line 212 of test_Cluster.py, if I replace method='a' by method=u'a'). Can you confirm that you get this bug with Python 2.7 even with simple strings rather than unicode? Thanks, -Michiel. On Sat, 8/16/14, Andreas Tille andr...@an3as.eu wrote: Subject: Re: Bug#751277: python-biopython: FTBFS on mips* powerpc s390x To: Peter Cock p.j.a.c...@googlemail.com Cc: Dejan Latinovic dejan.latino...@imgtec.com, Michiel de Hoon mjldeh...@yahoo.com, Biopython discussion list biopyt...@lists.open-bio.org, 751...@bugs.debian.org 751...@bugs.debian.org, biopython-...@biopython.org biopython-...@biopython.org Date: Saturday, August 16, 2014, 5:37 AM Hi Peter, On Thu, Aug 14, 2014 at 09:52:40AM +0100, Peter Cock wrote: 1. waiting for your confirmation / patch 2. deactivating the specific test 3. exclude mips for biopython 4. ? any better idea ? In the current state all the work we spent in biopython over the last monthes will not migrate to testing for the simple reason that the current package in testing just does not run the test suite at build time and moreover python3 is not supported. Kind regards Andreas. I would suggest (2), deactivate this test (at least for for mips) as the most practical short term solution for the Debian packages. Or if you prefer (3), don't target mips for the Biopython package (yet). Medium term, I hope we can fix the C code to handle either Endian platform - option (1). It seems after having fixed the issue caused by wise we have one remaining problem: On powerpc[1] and s390x[2] test_Cluster fails even with Python 2.7 with: == 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 293.712 seconds FAILED (failures = 1) On sparc[3] there is a problem with dialign but sparc is no release architecture and wie might ignore this. It might be a helpful hint anyway. Any hint for the test_Cluster problem? If not I would also consider to hide it cowardly under the carpet for the moment. The new package is so much better tested than the one in the testing distribution which does not even dare about any unit tests and only for this reason reached the testing distribution. What do you think? Kind regards Andreas. scrool these links to the end to see the problem: [1] https://buildd.debian.org/status/fetch.php?pkg=python-biopythonarch=powerpcver=1.64%2Bdfsg-3stamp=1408116532 [2] https://buildd.debian.org/status/fetch.php?pkg=python-biopythonarch=s390xver=1.64%2Bdfsg-3stamp=1408107524 [3] https://buildd.debian.org/status/fetch.php?pkg=python-biopythonarch=sparcver=1.64%2Bdfsg-3stamp=1408130792 -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
Hi Andreas, Without access to powerpc, I have no way to test the code. Can you try recompiling Biopython and checking what exactly happens inside the distance_converter function in Bio/Cluster/clustermodule.c ? For example, I am really wondering what strlen(data) inside this function returns on powerpc. Best, -Michiel. On Sat, 8/16/14, Andreas Tille andr...@an3as.eu wrote: Subject: Re: Bug#751277: python-biopython: FTBFS on mips* powerpc s390x To: Peter Cock p.j.a.c...@googlemail.com Cc: Dejan Latinovic dejan.latino...@imgtec.com, Michiel de Hoon mjldeh...@yahoo.com, Biopython discussion list biopyt...@lists.open-bio.org, 751...@bugs.debian.org 751...@bugs.debian.org, biopython-...@biopython.org biopython-...@biopython.org Date: Saturday, August 16, 2014, 5:37 AM Hi Peter, On Thu, Aug 14, 2014 at 09:52:40AM +0100, Peter Cock wrote: 1. waiting for your confirmation / patch 2. deactivating the specific test 3. exclude mips for biopython 4. ? any better idea ? In the current state all the work we spent in biopython over the last monthes will not migrate to testing for the simple reason that the current package in testing just does not run the test suite at build time and moreover python3 is not supported. Kind regards Andreas. I would suggest (2), deactivate this test (at least for for mips) as the most practical short term solution for the Debian packages. Or if you prefer (3), don't target mips for the Biopython package (yet). Medium term, I hope we can fix the C code to handle either Endian platform - option (1). It seems after having fixed the issue caused by wise we have one remaining problem: On powerpc[1] and s390x[2] test_Cluster fails even with Python 2.7 with: == 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 293.712 seconds FAILED (failures = 1) On sparc[3] there is a problem with dialign but sparc is no release architecture and wie might ignore this. It might be a helpful hint anyway. Any hint for the test_Cluster problem? If not I would also consider to hide it cowardly under the carpet for the moment. The new package is so much better tested than the one in the testing distribution which does not even dare about any unit tests and only for this reason reached the testing distribution. What do you think? Kind regards Andreas. scrool these links to the end to see the problem: [1] https://buildd.debian.org/status/fetch.php?pkg=python-biopythonarch=powerpcver=1.64%2Bdfsg-3stamp=1408116532 [2] https://buildd.debian.org/status/fetch.php?pkg=python-biopythonarch=s390xver=1.64%2Bdfsg-3stamp=1408107524 [3] https://buildd.debian.org/status/fetch.php?pkg=python-biopythonarch=sparcver=1.64%2Bdfsg-3stamp=1408130792 -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
Hi porters, could you please be so kind to check this issue? It would be great to find out why the test suite of biopython fails on these architectures. Thanks a lot Andreas. On Mon, Aug 18, 2014 at 12:35:53AM -0700, Michiel de Hoon wrote: Hi Andreas, Without access to powerpc, I have no way to test the code. Can you try recompiling Biopython and checking what exactly happens inside the distance_converter function in Bio/Cluster/clustermodule.c ? For example, I am really wondering what strlen(data) inside this function returns on powerpc. Best, -Michiel. On Sat, 8/16/14, Andreas Tille andr...@an3as.eu wrote: Subject: Re: Bug#751277: python-biopython: FTBFS on mips* powerpc s390x To: Peter Cock p.j.a.c...@googlemail.com Cc: Dejan Latinovic dejan.latino...@imgtec.com, Michiel de Hoon mjldeh...@yahoo.com, Biopython discussion list biopyt...@lists.open-bio.org, 751...@bugs.debian.org 751...@bugs.debian.org, biopython-...@biopython.org biopython-...@biopython.org Date: Saturday, August 16, 2014, 5:37 AM Hi Peter, On Thu, Aug 14, 2014 at 09:52:40AM +0100, Peter Cock wrote: 1. waiting for your confirmation / patch 2. deactivating the specific test 3. exclude mips for biopython 4. ? any better idea ? In the current state all the work we spent in biopython over the last monthes will not migrate to testing for the simple reason that the current package in testing just does not run the test suite at build time and moreover python3 is not supported. Kind regards Andreas. I would suggest (2), deactivate this test (at least for for mips) as the most practical short term solution for the Debian packages. Or if you prefer (3), don't target mips for the Biopython package (yet). Medium term, I hope we can fix the C code to handle either Endian platform - option (1). It seems after having fixed the issue caused by wise we have one remaining problem: On powerpc[1] and s390x[2] test_Cluster fails even with Python 2.7 with: == 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 293.712 seconds FAILED (failures = 1) On sparc[3] there is a problem with dialign but sparc is no release architecture and wie might ignore this. It might be a helpful hint anyway. Any hint for the test_Cluster problem? If not I would also consider to hide it cowardly under the carpet for the moment. The new package is so much better tested than the one in the testing distribution which does not even dare about any unit tests and only for this reason reached the testing distribution. What do you think? Kind regards Andreas. scrool these links to the end to see the problem: [1] https://buildd.debian.org/status/fetch.php?pkg=python-biopythonarch=powerpcver=1.64%2Bdfsg-3stamp=1408116532 [2] https://buildd.debian.org/status/fetch.php?pkg=python
Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
I can provide SSH access to a PowerMac G5 running 7.6 if you'd like to test this. On Aug 18, 2014, at 4:01, Andreas Tille andr...@an3as.eu wrote: Hi porters, could you please be so kind to check this issue? It would be great to find out why the test suite of biopython fails on these architectures. Thanks a lot Andreas. On Mon, Aug 18, 2014 at 12:35:53AM -0700, Michiel de Hoon wrote: Hi Andreas, Without access to powerpc, I have no way to test the code. Can you try recompiling Biopython and checking what exactly happens inside the distance_converter function in Bio/Cluster/clustermodule.c ? For example, I am really wondering what strlen(data) inside this function returns on powerpc. Best, -Michiel. On Sat, 8/16/14, Andreas Tille andr...@an3as.eu wrote: Subject: Re: Bug#751277: python-biopython: FTBFS on mips* powerpc s390x To: Peter Cock p.j.a.c...@googlemail.com Cc: Dejan Latinovic dejan.latino...@imgtec.com, Michiel de Hoon mjldeh...@yahoo.com, Biopython discussion list biopyt...@lists.open-bio.org, 751...@bugs.debian.org 751...@bugs.debian.org, biopython-...@biopython.org biopython-...@biopython.org Date: Saturday, August 16, 2014, 5:37 AM Hi Peter, On Thu, Aug 14, 2014 at 09:52:40AM +0100, Peter Cock wrote: 1. waiting for your confirmation / patch 2. deactivating the specific test 3. exclude mips for biopython 4. ? any better idea ? In the current state all the work we spent in biopython over the last monthes will not migrate to testing for the simple reason that the current package in testing just does not run the test suite at build time and moreover python3 is not supported. Kind regards Andreas. I would suggest (2), deactivate this test (at least for for mips) as the most practical short term solution for the Debian packages. Or if you prefer (3), don't target mips for the Biopython package (yet). Medium term, I hope we can fix the C code to handle either Endian platform - option (1). It seems after having fixed the issue caused by wise we have one remaining problem: On powerpc[1] and s390x[2] test_Cluster fails even with Python 2.7 with: == 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 293.712 seconds FAILED (failures = 1) On sparc[3] there is a problem with dialign but sparc is no release architecture and wie might ignore this. It might be a helpful hint anyway. Any hint for the test_Cluster problem? If not I would also consider to hide it cowardly under the carpet for the moment. The new package is so much better tested than the one in the testing distribution which does not even dare about any unit tests and only for this reason reached the testing distribution. What do you think? Kind regards Andreas. scrool these links to the end to see the problem: [1] https://buildd.debian.org/status/fetch.php?pkg=python-biopythonarch=powerpcver=1.64%2Bdfsg-3stamp=1408116532 [2] https://buildd.debian.org/status/fetch.php?pkg=python-biopythonarch=s390xver
Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
I can provide SSH access to a PowerMac G5 running 7.6 if you'd like to test this. That would be great. Then I can test it. Best, -Michiel. On Mon, 8/18/14, David Gosselin d...@appleside.org wrote: Subject: Re: Bug#751277: python-biopython: FTBFS on mips* powerpc s390x To: Andreas Tille andr...@an3as.eu Cc: Michiel de Hoon mjldeh...@yahoo.com, debian-powe...@lists.debian.org debian-powe...@lists.debian.org, debian-m...@lists.debian.org debian-m...@lists.debian.org, debian-s...@lists.debian.org debian-s...@lists.debian.org, Peter Cock p.j.a.c...@googlemail.com, Dejan Latinovic dejan.latino...@imgtec.com, Biopython discussion list biopyt...@lists.open-bio.org, 751...@bugs.debian.org 751...@bugs.debian.org, biopython-...@biopython.org biopython-...@biopython.org Date: Monday, August 18, 2014, 8:43 PM I can provide SSH access to a PowerMac G5 running 7.6 if you'd like to test this. On Aug 18, 2014, at 4:01, Andreas Tille andr...@an3as.eu wrote: Hi porters, could you please be so kind to check this issue? It would be great to find out why the test suite of biopython fails on these architectures. Thanks a lot Andreas. On Mon, Aug 18, 2014 at 12:35:53AM -0700, Michiel de Hoon wrote: Hi Andreas, Without access to powerpc, I have no way to test the code. Can you try recompiling Biopython and checking what exactly happens inside the distance_converter function in Bio/Cluster/clustermodule.c ? For example, I am really wondering what strlen(data) inside this function returns on powerpc. Best, -Michiel. On Sat, 8/16/14, Andreas Tille andr...@an3as.eu wrote: Subject: Re: Bug#751277: python-biopython: FTBFS on mips* powerpc s390x To: Peter Cock p.j.a.c...@googlemail.com Cc: Dejan Latinovic dejan.latino...@imgtec.com, Michiel de Hoon mjldeh...@yahoo.com, Biopython discussion list biopyt...@lists.open-bio.org, 751...@bugs.debian.org 751...@bugs.debian.org, biopython-...@biopython.org biopython-...@biopython.org Date: Saturday, August 16, 2014, 5:37 AM Hi Peter, On Thu, Aug 14, 2014 at 09:52:40AM +0100, Peter Cock wrote: 1. waiting for your confirmation / patch 2. deactivating the specific test 3. exclude mips for biopython 4. ? any better idea ? In the current state all the work we spent in biopython over the last monthes will not migrate to testing for the simple reason that the current package in testing just does not run the test suite at build time and moreover python3 is not supported. Kind regards Andreas. I would suggest (2), deactivate this test (at least for for mips) as the most practical short term solution for the Debian packages. Or if you prefer (3), don't target mips for the Biopython package (yet). Medium term, I hope we can fix the C code to handle either Endian platform - option (1). It seems after having fixed the issue caused by wise we have one remaining problem: On powerpc[1] and s390x[2] test_Cluster fails even with Python 2.7 with: == 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
Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
Hi Peter, On Thu, Aug 14, 2014 at 09:52:40AM +0100, Peter Cock wrote: 1. waiting for your confirmation / patch 2. deactivating the specific test 3. exclude mips for biopython 4. ? any better idea ? In the current state all the work we spent in biopython over the last monthes will not migrate to testing for the simple reason that the current package in testing just does not run the test suite at build time and moreover python3 is not supported. Kind regards Andreas. I would suggest (2), deactivate this test (at least for for mips) as the most practical short term solution for the Debian packages. Or if you prefer (3), don't target mips for the Biopython package (yet). Medium term, I hope we can fix the C code to handle either Endian platform - option (1). It seems after having fixed the issue caused by wise we have one remaining problem: On powerpc[1] and s390x[2] test_Cluster fails even with Python 2.7 with: == 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 293.712 seconds FAILED (failures = 1) On sparc[3] there is a problem with dialign but sparc is no release architecture and wie might ignore this. It might be a helpful hint anyway. Any hint for the test_Cluster problem? If not I would also consider to hide it cowardly under the carpet for the moment. The new package is so much better tested than the one in the testing distribution which does not even dare about any unit tests and only for this reason reached the testing distribution. What do you think? Kind regards Andreas. scrool these links to the end to see the problem: [1] https://buildd.debian.org/status/fetch.php?pkg=python-biopythonarch=powerpcver=1.64%2Bdfsg-3stamp=1408116532 [2] https://buildd.debian.org/status/fetch.php?pkg=python-biopythonarch=s390xver=1.64%2Bdfsg-3stamp=1408107524 [3] https://buildd.debian.org/status/fetch.php?pkg=python-biopythonarch=sparcver=1.64%2Bdfsg-3stamp=1408130792 -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
Hi, On Tue, Aug 05, 2014 Peter Cock wrote Unfortunately, on mips (BE) test test_Cluster.py failed under Python 3.4. Any progress on this issue? No. See discussion on https://github.com/biopython/biopython/pull/340 Do you have any suggestion what to do regarding the Debian package? I see the following options: 1. waiting for your confirmation / patch 2. deactivating the specific test 3. exclude mips for biopython 4. ? any better idea ? In the current state all the work we spent in biopython over the last monthes will not migrate to testing for the simple reason that the current package in testing just does not run the test suite at build time and moreover python3 is not supported. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
On Thu, Aug 14, 2014 at 9:38 AM, Andreas Tille andr...@an3as.eu wrote: Hi, On Tue, Aug 05, 2014 Peter Cock wrote Unfortunately, on mips (BE) test test_Cluster.py failed under Python 3.4. Any progress on this issue? No. See discussion on https://github.com/biopython/biopython/pull/340 Do you have any suggestion what to do regarding the Debian package? I see the following options: 1. waiting for your confirmation / patch 2. deactivating the specific test 3. exclude mips for biopython 4. ? any better idea ? In the current state all the work we spent in biopython over the last monthes will not migrate to testing for the simple reason that the current package in testing just does not run the test suite at build time and moreover python3 is not supported. Kind regards Andreas. I would suggest (2), deactivate this test (at least for for mips) as the most practical short term solution for the Debian packages. Or if you prefer (3), don't target mips for the Biopython package (yet). Medium term, I hope we can fix the C code to handle either Endian platform - option (1). Peter -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
Hi Dejan, thanks for the hint. I'll apply your patch which looks promising. When checking the wise package I detected some other issues when trying to run wise's own test suite which I need to fix before an upload. Once this is done I'll upload biopython with a versioned Build-Depends. This would leave us only with the mips Python 3.4 issue. I wonder whether I should cheat and skip this test for the moment to let the package migrate to testing with this known minor issue. Kind regards Andreas. On Mon, Aug 04, 2014 at 05:10:38PM +, Dejan Latinovic wrote: Hello, I took a look at test failures on mips/mipsel. Test that fails is based on a result of dnal tool. dnal is part of a debian package wise. In file: Bio/Wise/__init__.py, an error was raised because the return value from dnal is greater than 1. If you look at dnal.c: alb = make_align_dnaalign(one,two,mat,dse,-gap,-ext,-gap,-ext,dpri); printf(Score %d\n,alb-score); if( alb == NULL ) fatal(Could not build alignment!); if( show_pretty == TRUE ) write_pretty_seq_align(alb,one,two,12,60,stdout); if( show_alb == TRUE ) dump_ascii_AlnBlock(alb,stdout); } you can see that there is no return statement. In this case the return value of dnal usually will be the return value of last used function. This behavior is mutable. It can not be guaranteed on all architectures, or if different optimization flags are used. Further, using dnal with different options, last used function could be changed. Adding return 0; at the end of main function in dnal.c, test_align (test_Wise.TestWise) successfully passes on mips/mipsel. With this fix, package python-biopython successfully builds for mipsel. Patch that includes this fix is attached. Unfortunately, on mips (BE) test test_Cluster.py failed under Python 3.4. Any progress on this issue? Best Regards, Dejan --- wise-2.4.1.orig/src/models/dnal.c 2004-11-24 16:26:11.0 + +++ wise-2.4.1/src/models/dnal.c 2014-07-31 14:53:54.0 + @@ -75,6 +75,8 @@ if( show_alb == TRUE ) dump_ascii_AlnBlock(alb,stdout); + + return 0; } -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
Hello, I took a look at test failures on mips/mipsel. Test that fails is based on a result of dnal tool. dnal is part of a debian package wise. In file: Bio/Wise/__init__.py, an error was raised because the return value from dnal is greater than 1. If you look at dnal.c: alb = make_align_dnaalign(one,two,mat,dse,-gap,-ext,-gap,-ext,dpri); printf(Score %d\n,alb-score); if( alb == NULL ) fatal(Could not build alignment!); if( show_pretty == TRUE ) write_pretty_seq_align(alb,one,two,12,60,stdout); if( show_alb == TRUE ) dump_ascii_AlnBlock(alb,stdout); } you can see that there is no return statement. In this case the return value of dnal usually will be the return value of last used function. This behavior is mutable. It can not be guaranteed on all architectures, or if different optimization flags are used. Further, using dnal with different options, last used function could be changed. Adding return 0; at the end of main function in dnal.c, test_align (test_Wise.TestWise) successfully passes on mips/mipsel. With this fix, package python-biopython successfully builds for mipsel. Patch that includes this fix is attached. Unfortunately, on mips (BE) test test_Cluster.py failed under Python 3.4. Any progress on this issue? Best Regards, Dejan --- wise-2.4.1.orig/src/models/dnal.c 2004-11-24 16:26:11.0 + +++ wise-2.4.1/src/models/dnal.c 2014-07-31 14:53:54.0 + @@ -75,6 +75,8 @@ if( show_alb == TRUE ) dump_ascii_AlnBlock(alb,stdout); + + return 0; }
Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
On Mon, Aug 4, 2014 at 6:10 PM, Dejan Latinovic dejan.latino...@imgtec.com wrote: Hello, I took a look at test failures on mips/mipsel. Test that fails is based on a result of dnal tool. dnal is part of a debian package wise. ... With this fix, package python-biopython successfully builds for mipsel. Patch that includes this fix is attached. That sounds useful for the wise package :) Unfortunately, on mips (BE) test test_Cluster.py failed under Python 3.4. Any progress on this issue? No. See discussion on https://github.com/biopython/biopython/pull/340 Peter -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
On Mon, Jun 16, 2014 at 5:31 AM, Michiel de Hoon mjldeh...@yahoo.com wrote: This commit verifies the errors are thrown (and they are not under Python 3 on the Mac): https://github.com/peterjc/biopython/commit/5b99854a82f08321ad78feaf0b362002d2d1fd2b I'm going to have to pass this one to Michiel to look at... but it looks like a glitch in the bytes vs unicode handling, which for some reason mostly works - but breaks under some unusual platforms? Was there a bug report filed for this issue? Then I can have a look at it. Best, -Michiel There is now, https://github.com/biopython/biopython/pull/340 Peter P.S. A replacement mail server is being setup for lists.open-bio.org, waiting DNS propagation etc. -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
This commit verifies the errors are thrown (and they are not under Python 3 on the Mac): https://github.com/peterjc/biopython/commit/5b99854a82f08321ad78feaf0b362002d2d1fd2b I'm going to have to pass this one to Michiel to look at... but it looks like a glitch in the bytes vs unicode handling, which for some reason mostly works - but breaks under some unusual platforms? Was there a bug report filed for this issue? Then I can have a look at it. Best, -Michiel -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
On Fri, Jun 13, 2014 at 11:05 PM, Andreas Tille andr...@an3as.eu wrote: Hi Peter, thanks for your quick response. On Fri, Jun 13, 2014 at 02:57:37PM +0100, Peter Cock wrote: I have updated the Debian package to version 1.64 (BTW, it is fine to ping debian-...@lists.debian.org about new upstream versions - we might become more quick in packaging new versions). Good point. I used to email the Phillipe Charles when there was a change I anticipated might cause trouble. Should we just email debian-...@lists.debian.org after each new Biopython release? Yes, that's perfectly OK. It might happen that certain persons might be busy with other things. I also see no point to waste the chance to make new versions of BioPython even more popular - so let readers of the Debian Med list know about what you are doing. If so we can add that to our build process: http://biopython.org/wiki/Building_a_release +1 Done. We can add other Linux etc packaging contacts too... 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. Most of these are tests where we call an external command line tool (i.e. muscle, dnal, dialign2-2). The purpose of the tests is in part to check our command line wrappers are current (and catch any API changes), but also in many cases to check we can parse the current output (to catch any format changes). I would *guess* that some of these platforms have problems in these underlying tools - or a very different version is being tested? i.e. Older than the mainstream platforms. Usually all these tools are in sync. However, not all of these are tested since most are missing unit tests - so BioPython is a great test for these tools. Indirectly yes :) -- The final category of failures was from test_Cluster.py under powerpc and s390x, under Python 3.4, which suggests it could be something in the C code for Bio.Cluster - probably Python 3 specific. From line 138-141, clusterid, error, nfound = kcluster(data, nclusters=nclusters, mask=mask, weight=weight, transpose=0, npass=100, method='a', dist='e') Line 210-212, distance = clusterdistance(data, mask=mask, weight=weight, index1=c1, index2=c2, dist='e', method='a', transpose=0) Line 289-290, tree = treecluster(data=data1, mask=mask1, weight=weight1, transpose=0, method='a', dist='e') Line 555-557, clusterid, celldata = somcluster(data=data, mask=mask, weight=weight, transpose=0, nxgrid=10, nygrid=10, inittau=0.02, niter=100, dist='e') This all give the following error via C function distance_converter in Bio/Cluster/clustermodule.c ValueError: distance should be a single character Yet in all those examples, dist='e' which is a single character... The good news is I can reproduce a related problem on Mac OS X under Python 3.3 and 3.4 where this error is not raised: Test branch: https://github.com/peterjc/biopython/tree/cluster_single_char This commit makes the error messages more explicit: https://github.com/peterjc/biopython/commit/fa597040cfb7e5f18d55257367397e88274563b8 This commit verifies the errors are thrown (and they are not under Python 3 on the Mac): https://github.com/peterjc/biopython/commit/5b99854a82f08321ad78feaf0b362002d2d1fd2b I'm going to have to pass this one to Michiel to look at... but it looks like a glitch in the bytes vs unicode handling, which for some reason mostly works - but breaks under some unusual platforms? I'll try to ask porters to check this patch on the different architectures. I think Jakub is correct that the original problem is a big-endian issue, but it appears to have helped me spot a Python 3 specific problem in our error handling as well (the work on that branch). Thanks, Peter P.S. There is a problem with our mail server, which is being looked, at but some of these messages may have been lost and never appear on the Biopython archives :( -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
* Scott Kitterman deb...@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=10, 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=10, 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
|
|
Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
Hi BioPython developers, I have updated the Debian package to version 1.64 (BTW, it is fine to ping debian-...@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-biopythonsuite=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=10, 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=10, 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 |
Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
Hi Andreas, Jakub, On Fri, Jun 13, 2014 at 1:55 PM, Andreas Tille andr...@an3as.eu wrote: Hi BioPython developers, I have updated the Debian package to version 1.64 (BTW, it is fine to ping debian-...@lists.debian.org about new upstream versions - we might become more quick in packaging new versions). Good point. I used to email the Phillipe Charles when there was a change I anticipated might cause trouble. Should we just email debian-...@lists.debian.org after each new Biopython release? If so we can add that to our build process: http://biopython.org/wiki/Building_a_release Thanks for adopting the patches we sended to you. No problem - while some of your tweaks are Debian specific, where it makes sense to incorporate fixes into Biopython we try to do that. 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-biopythonsuite=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. Most of these are tests where we call an external command line tool (i.e. muscle, dnal, dialign2-2). The purpose of the tests is in part to check our command line wrappers are current (and catch any API changes), but also in many cases to check we can parse the current output (to catch any format changes). I would *guess* that some of these platforms have problems in these underlying tools - or a very different version is being tested? i.e. Older than the mainstream platforms. -- The final category of failures was from test_Cluster.py under powerpc and s390x, under Python 3.4, which suggests it could be something in the C code for Bio.Cluster - probably Python 3 specific. From line 138-141, clusterid, error, nfound = kcluster(data, nclusters=nclusters, mask=mask, weight=weight, transpose=0, npass=100, method='a', dist='e') Line 210-212, distance = clusterdistance(data, mask=mask, weight=weight, index1=c1, index2=c2, dist='e', method='a', transpose=0) Line 289-290, tree = treecluster(data=data1, mask=mask1, weight=weight1, transpose=0, method='a', dist='e') Line 555-557, clusterid, celldata = somcluster(data=data, mask=mask, weight=weight, transpose=0, nxgrid=10, nygrid=10, inittau=0.02, niter=100, dist='e') This all give the following error via C function distance_converter in Bio/Cluster/clustermodule.c ValueError: distance should be a single character Yet in all those examples, dist='e' which is a single character... The good news is I can reproduce a related problem on Mac OS X under Python 3.3 and 3.4 where this error is not raised: Test branch: https://github.com/peterjc/biopython/tree/cluster_single_char This commit makes the error messages more explicit: https://github.com/peterjc/biopython/commit/fa597040cfb7e5f18d55257367397e88274563b8 This commit verifies the errors are thrown (and they are not under Python 3 on the Mac): https://github.com/peterjc/biopython/commit/5b99854a82f08321ad78feaf0b362002d2d1fd2b I'm going to have to pass this one to Michiel to look at... but it looks like a glitch in the bytes vs unicode handling, which for some reason mostly works - but breaks under some unusual platforms? Thanks, Peter -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
* Peter Cock p.j.a.c...@googlemail.com, 2014-06-13, 14:57:
Line 555-557,
clusterid, celldata = somcluster(data=data, mask=mask, weight=weight,
transpose=0, nxgrid=10, nygrid=10,
inittau=0.02, niter=100, dist='e')
This all give the following error via C function distance_converter in
Bio/Cluster/clustermodule.c
ValueError: distance should be a single character
Yet in all those examples, dist='e' which is a single character...
I had a quick looks at the code:
if (PyUnicode_Check(object))
data = PyUnicode_AS_DATA(object);
# ...
if (strlen(data)!=1)
{ PyErr_Format(PyExc_ValueError, method should be a single character (not
'%s'), data);
return 0;
}
But PyUnicode_AS_DATA() returns a pointer to UTF-32 data. On big-endian
architectures (such as powerpc or s390x), the first byte is always 0, so
strlen() returns 0.
--
Jakub Wilk
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Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
Hi Peter, thanks for your quick response. On Fri, Jun 13, 2014 at 02:57:37PM +0100, Peter Cock wrote: I have updated the Debian package to version 1.64 (BTW, it is fine to ping debian-...@lists.debian.org about new upstream versions - we might become more quick in packaging new versions). Good point. I used to email the Phillipe Charles when there was a change I anticipated might cause trouble. Should we just email debian-...@lists.debian.org after each new Biopython release? Yes, that's perfectly OK. It might happen that certain persons might be busy with other things. I also see no point to waste the chance to make new versions of BioPython even more popular - so let readers of the Debian Med list know about what you are doing. If so we can add that to our build process: http://biopython.org/wiki/Building_a_release +1 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. Most of these are tests where we call an external command line tool (i.e. muscle, dnal, dialign2-2). The purpose of the tests is in part to check our command line wrappers are current (and catch any API changes), but also in many cases to check we can parse the current output (to catch any format changes). I would *guess* that some of these platforms have problems in these underlying tools - or a very different version is being tested? i.e. Older than the mainstream platforms. Usually all these tools are in sync. However, not all of these are tested since most are missing unit tests - so BioPython is a great test for these tools. -- The final category of failures was from test_Cluster.py under powerpc and s390x, under Python 3.4, which suggests it could be something in the C code for Bio.Cluster - probably Python 3 specific. From line 138-141, clusterid, error, nfound = kcluster(data, nclusters=nclusters, mask=mask, weight=weight, transpose=0, npass=100, method='a', dist='e') Line 210-212, distance = clusterdistance(data, mask=mask, weight=weight, index1=c1, index2=c2, dist='e', method='a', transpose=0) Line 289-290, tree = treecluster(data=data1, mask=mask1, weight=weight1, transpose=0, method='a', dist='e') Line 555-557, clusterid, celldata = somcluster(data=data, mask=mask, weight=weight, transpose=0, nxgrid=10, nygrid=10, inittau=0.02, niter=100, dist='e') This all give the following error via C function distance_converter in Bio/Cluster/clustermodule.c ValueError: distance should be a single character Yet in all those examples, dist='e' which is a single character... The good news is I can reproduce a related problem on Mac OS X under Python 3.3 and 3.4 where this error is not raised: Test branch: https://github.com/peterjc/biopython/tree/cluster_single_char This commit makes the error messages more explicit: https://github.com/peterjc/biopython/commit/fa597040cfb7e5f18d55257367397e88274563b8 This commit verifies the errors are thrown (and they are not under Python 3 on the Mac): https://github.com/peterjc/biopython/commit/5b99854a82f08321ad78feaf0b362002d2d1fd2b I'm going to have to pass this one to Michiel to look at... but it looks like a glitch in the bytes vs unicode handling, which for some reason mostly works - but breaks under some unusual platforms? I'll try to ask porters to check this patch on the different architectures. Thanks again Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
Source: python-biopython
Version: 1.64+dfsg-1
Severity: serious
Justification: fails to build from source (but built successfully in the past)
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
debian/rules:56: recipe for target 'override_dh_auto_test' failed
make[1]: Leaving directory '/«BUILDDIR»/python-biopython-1.64+dfsg'
make: *** [build-arch] Error 2
debian/rules:48: recipe for target 'build-arch' failed
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