Bug#900485: [Debian-med-packaging] Bug#900485: python-pbcore: FTBFS and Debci failure with NumPy 1.14
On June 26, 2018 3:45:49 AM EDT, Andreas Tille wrote: >On Mon, Jun 25, 2018 at 09:52:50AM -0400, Afif Elghraoui wrote: >> I think we can give 1.5.0 a try, but it might have the same problem. > >Since it builds successfully I've just uploaded. > Ok >> > (And what do you think about watch mode=git?) >> >> I don't know much about it, but I don't have any strong preference >here. > >It might serve as a sensible solution for all upstreams using Git >without proper release tagging. I guess the pbcore example will >explain >what to do. > >BTW, I remembered to late that you are not happy about the cme >formatting. I just fired up cme for Vcs-fields, Standards-Version etc. >I hope you don't mind - feel free to revert to your prefered formatting >and I hope I will not forget if I touch some of your packages in >future. > Don't worry about this. > >PS: I'm currently checking pbseqlib since now upstream has tagged a >release but there are some hdf5 issues which prevent me from >uploading. Please let me know if you want me to revert the cme >formatting to its previous shape. > No need to revert anything. regards Afif
Bug#900485: [Debian-med-packaging] Bug#900485: python-pbcore: FTBFS and Debci failure with NumPy 1.14
On Mon, Jun 25, 2018 at 09:52:50AM -0400, Afif Elghraoui wrote: > I think we can give 1.5.0 a try, but it might have the same problem. Since it builds successfully I've just uploaded. > > (And what do you think about watch mode=git?) > > I don't know much about it, but I don't have any strong preference here. It might serve as a sensible solution for all upstreams using Git without proper release tagging. I guess the pbcore example will explain what to do. BTW, I remembered to late that you are not happy about the cme formatting. I just fired up cme for Vcs-fields, Standards-Version etc. I hope you don't mind - feel free to revert to your prefered formatting and I hope I will not forget if I touch some of your packages in future. Kind regards Andreas. PS: I'm currently checking pbseqlib since now upstream has tagged a release but there are some hdf5 issues which prevent me from uploading. Please let me know if you want me to revert the cme formatting to its previous shape. -- http://fam-tille.de
Bug#900485: [Debian-med-packaging] Bug#900485: python-pbcore: FTBFS and Debci failure with NumPy 1.14
On June 25, 2018 5:07:48 AM EDT, Andreas Tille wrote: >Hi Afif, > >On Mon, Jun 25, 2018 at 03:41:11AM -0400, Afif Elghraoui wrote: >> >pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: >> >/tmp/tmpveTAsa.subreadset.xml >> > >> >Before I start diving into this: Afif, upstream seems to have >released >> >1.5.0 which might be worth a try. While I asked for creating >according >> >release tags[2] I remember you said that upstream does not care much >> >about this metadata. I wonder whether we should possibly use >mode=git >> >inside the watch file, inject version 1.5.0 into packaging Git, >cross >> >fingers that the issue might be fixed and if not report the issue >> >upstream. >> > >> >> I believe that error had to do with the package requiring an older >version of some dependency. At least, the error I was seeing at the >time was for that reason, which prevented me from uploading. > >So we can either skip those tests (no idea how important is this for >general functionality) or give 1.5.0 a try. What do you think is >the better strategy? I think we can give 1.5.0 a try, but it might have the same problem. > (And what do you think about watch mode=git?) > I don't know much about it, but I don't have any strong preference here. regards Afif
Bug#900485: [Debian-med-packaging] Bug#900485: python-pbcore: FTBFS and Debci failure with NumPy 1.14
Hi Afif, On Mon, Jun 25, 2018 at 03:41:11AM -0400, Afif Elghraoui wrote: > >pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: > >/tmp/tmpveTAsa.subreadset.xml > > > >Before I start diving into this: Afif, upstream seems to have released > >1.5.0 which might be worth a try. While I asked for creating according > >release tags[2] I remember you said that upstream does not care much > >about this metadata. I wonder whether we should possibly use mode=git > >inside the watch file, inject version 1.5.0 into packaging Git, cross > >fingers that the issue might be fixed and if not report the issue > >upstream. > > > > I believe that error had to do with the package requiring an older version of > some dependency. At least, the error I was seeing at the time was for that > reason, which prevented me from uploading. So we can either skip those tests (no idea how important is this for general functionality) or give 1.5.0 a try. What do you think is the better strategy? (And what do you think about watch mode=git?) Kind regards Andreas. -- http://fam-tille.de
Bug#900485: [Debian-med-packaging] Bug#900485: python-pbcore: FTBFS and Debci failure with NumPy 1.14
Hi, Andreas On June 25, 2018 3:32:00 AM EDT, Andreas Tille wrote: >Hi Graham, > >On Sun, Jun 24, 2018 at 08:48:32PM +0200, Graham Inggs wrote: >> Control: tags -1 + patch > >thanks for the patch. Since we are targeting in Git at version 1.4.2 I >adapted the patch to this version and it works for this. I also fixed >another issue in the test suite[1]. Unfortunately there are remaining >errors in the test suite which are all connected to a possible issue >with >XML files: > >$ grep "ERROR: Invalid file produced" >python-pbcore_1.4.2+dfsg-1_amd64.build >pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: >/tmp/tmpiOHCZI.alignmentset.xml.disabled >pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: >/tmp/tmplAqR2T.alignmentset.xml >pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: >/tmp/tmpMyWNXh.subreadset.xml >pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: >/tmp/tmps4GD0E.subreadset.xml >pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: >/tmp/tmp71IS22dataset-unittest/test.alignmentset.xml >pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: >/tmp/tmpUn37tBdataset unittest/spaced.subreadset.xml >pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: >/tmp/tmpMouabqdataset-unittest/tempfile.xml >pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: >/tmp/tmpN0pUz2alignmentset.xml >pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: >/tmp/tmpeQ4v3jalignmentset.xml >pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: >/tmp/tmp0Kb6RWdataset-doctest/tempfile.xml >pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: >/tmp/tmpj20209.subreadset.xml >pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: >/tmp/tmp2XGDAY.barcodeset.xml >pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: >/tmp/tmpXtaXG3.consensusreadset.xml >pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: >/tmp/tmpJlLjAA.contigset.xml >pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: >/tmp/tmpDKGXFh.contigset.xml >pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: >/tmp/tmptZ4Kro.xml >pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: >/tmp/tmp6ySKmX.contigset.xml >pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: >/tmp/tmpvYTcX1.subreadset.xml >pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: >/tmp/tmpiXc1ez.subreadset.xml >pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: >/tmp/tmpdiSRmI.subreadset.xml >pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: >/tmp/tmpveTAsa.subreadset.xml > > >Before I start diving into this: Afif, upstream seems to have released >1.5.0 which might be worth a try. While I asked for creating according >release tags[2] I remember you said that upstream does not care much >about this metadata. I wonder whether we should possibly use mode=git >inside the watch file, inject version 1.5.0 into packaging Git, cross >fingers that the issue might be fixed and if not report the issue >upstream. > I believe that error had to do with the package requiring an older version of some dependency. At least, the error I was seeing at the time was for that reason, which prevented me from uploading. regards Afif . > >[1] >https://salsa.debian.org/med-team/python-pbcore/blob/master/debian/patches/relax_test_constraint.patch >[2] https://github.com/PacificBiosciences/pbcore/issues/116 > >-- >http://fam-tille.de > >___ >Debian-med-packaging mailing list >debian-med-packag...@alioth-lists.debian.net >https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging
Bug#900485: python-pbcore: FTBFS and Debci failure with NumPy 1.14
Hi Graham, On Sun, Jun 24, 2018 at 08:48:32PM +0200, Graham Inggs wrote: > Control: tags -1 + patch thanks for the patch. Since we are targeting in Git at version 1.4.2 I adapted the patch to this version and it works for this. I also fixed another issue in the test suite[1]. Unfortunately there are remaining errors in the test suite which are all connected to a possible issue with XML files: $ grep "ERROR: Invalid file produced" python-pbcore_1.4.2+dfsg-1_amd64.build pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: /tmp/tmpiOHCZI.alignmentset.xml.disabled pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: /tmp/tmplAqR2T.alignmentset.xml pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: /tmp/tmpMyWNXh.subreadset.xml pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: /tmp/tmps4GD0E.subreadset.xml pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: /tmp/tmp71IS22dataset-unittest/test.alignmentset.xml pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: /tmp/tmpUn37tBdataset unittest/spaced.subreadset.xml pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: /tmp/tmpMouabqdataset-unittest/tempfile.xml pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: /tmp/tmpN0pUz2alignmentset.xml pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: /tmp/tmpeQ4v3jalignmentset.xml pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: /tmp/tmp0Kb6RWdataset-doctest/tempfile.xml pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: /tmp/tmpj20209.subreadset.xml pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: /tmp/tmp2XGDAY.barcodeset.xml pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: /tmp/tmpXtaXG3.consensusreadset.xml pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: /tmp/tmpJlLjAA.contigset.xml pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: /tmp/tmpDKGXFh.contigset.xml pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: /tmp/tmptZ4Kro.xml pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: /tmp/tmp6ySKmX.contigset.xml pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: /tmp/tmpvYTcX1.subreadset.xml pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: /tmp/tmpiXc1ez.subreadset.xml pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: /tmp/tmpdiSRmI.subreadset.xml pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: /tmp/tmpveTAsa.subreadset.xml Before I start diving into this: Afif, upstream seems to have released 1.5.0 which might be worth a try. While I asked for creating according release tags[2] I remember you said that upstream does not care much about this metadata. I wonder whether we should possibly use mode=git inside the watch file, inject version 1.5.0 into packaging Git, cross fingers that the issue might be fixed and if not report the issue upstream. Kind regards Andreas. [1] https://salsa.debian.org/med-team/python-pbcore/blob/master/debian/patches/relax_test_constraint.patch [2] https://github.com/PacificBiosciences/pbcore/issues/116 -- http://fam-tille.de
Bug#900485: python-pbcore: FTBFS and Debci failure with NumPy 1.14
> Do you have any suggestions on how to deal with this? i think you can either add the explicit versioned depends in debian/control or instruct dh_python2 to add such a dependency. -- Sandro "morph" Tosi My website: http://sandrotosi.me/ Me at Debian: http://wiki.debian.org/SandroTosi G+: https://plus.google.com/u/0/+SandroTosi
Bug#900485: python-pbcore: FTBFS and Debci failure with NumPy 1.14
Control: tags -1 + patch
Hi Sandro
I have cherry-picked the attached patch from pbcore upstream which
fixes the problems with NumPy 1.14.
However, with this patch in place, pbcore will need a build-dependency
on python-numpy (>= 1:1.14~) and its autopkgtests will fail with NumPy
1.13.
I thought the latter could be dealt with by dh_numpy, but after
reading /usr/share/doc/python-numpy/README.DebianMaints, it seems it
is only useful for arch:any packages, and python-pbcore is arch:all.
Did I miss something? Do you have any suggestions on how to deal with
this? python-pydap is similarly affected (#900486)
Regards
Graham
Description: Fix FTBFS with NumPy 1.14
Bug-Debian: https://bugs.debian.org/900485
Origin: upstream, https://github.com/PacificBiosciences/pbcore/commit/b7ef4238b6388f984a264b8a912450b652177dbf
Author: David Seifert
Last-Update: 2018-01-10
--- a/tests/test_pbdataset.py
+++ b/tests/test_pbdataset.py
@@ -1405,7 +1405,7 @@
self.assertEqual(
str(readers[0].referenceInfo('E.faecalis.1')),
"(27, 27, 'E.faecalis.1', 'E.faecalis.1', 1482, "
-"'a1a59c267ac1341e5a12bce7a7d37bcb', 0L, 0L)")
+"'a1a59c267ac1341e5a12bce7a7d37bcb', 0, 0)")
# TODO: add a bam with a different referenceInfoTable to check merging
# and id remapping:
#self.assertEqual(
@@ -1748,7 +1748,7 @@
self.assertEqual(
str(aln.referenceInfoTable),
("[ (1, 1, 'lambda_NEB3011', 'lambda_NEB3011', "
- "48502, 'a1319ff90e994c8190a4fe6569d0822a', 0L, 338113L)]"))
+ "48502, 'a1319ff90e994c8190a4fe6569d0822a', 0, 338113)]"))
self.assertEqual(set(aln.tId), {1})
# + 1, because bounds are inclusive, rather than exclusive
self.assertEqual(len3, (aln.referenceInfoTable[0].EndRow -
@@ -1775,9 +1775,9 @@
self.assertEqual(
str(aln.referenceInfoTable),
("[ (0, 0, 'ecoliK12_pbi_March2013', 'ecoliK12_pbi_March2013', "
- "4642522, '52cd7c5fa92877152fa487906ae484c5', 0L, 57034L)\n"
+ "4642522, '52cd7c5fa92877152fa487906ae484c5', 0, 57034)\n"
" (1, 1, 'lambda_NEB3011', 'lambda_NEB3011', 48502, "
- "'a1319ff90e994c8190a4fe6569d0822a', 57035L, 57146L)]"))
+ "'a1319ff90e994c8190a4fe6569d0822a', 57035, 57146)]"))
self.assertEqual(set(aln.tId), {0, 1})
# + 1, because bounds are inclusive, rather than exclusive
self.assertEqual(len1, (aln.referenceInfoTable[1].EndRow -
@@ -1810,7 +1810,7 @@
self.assertEqual(
str(aln.referenceInfoTable),
("[ (0, 0, 'ecoliK12_pbi_March2013', 'ecoliK12_pbi_March2013', "
- "4642522, '52cd7c5fa92877152fa487906ae484c5', 0L, 0L)]"))
+ "4642522, '52cd7c5fa92877152fa487906ae484c5', 0, 0)]"))
self.assertEqual(set(aln.tId), {0})
self.assertEqual(aln.referenceInfo('ecoliK12_pbi_March2013'),
aln.referenceInfo(0))
@@ -1835,7 +1835,7 @@
self.assertEqual(
str(aln.referenceInfoTable),
("[ (0, 0, 'ecoliK12_pbi_March2013', 'ecoliK12_pbi_March2013', "
- "4642522, '52cd7c5fa92877152fa487906ae484c5', 0L, 0L)]"))
+ "4642522, '52cd7c5fa92877152fa487906ae484c5', 0, 0)]"))
self.assertEqual(set(aln.tId), {0})
self.assertEqual(aln.referenceInfo('ecoliK12_pbi_March2013'),
aln.referenceInfo(0))
@@ -1860,9 +1860,9 @@
self.assertEqual(
str(aln.referenceInfoTable),
("[ (0, 0, 'ecoliK12_pbi_March2013', 'ecoliK12_pbi_March2013', "
- "4642522, '52cd7c5fa92877152fa487906ae484c5', 0L, 0L)\n"
+ "4642522, '52cd7c5fa92877152fa487906ae484c5', 0, 0)\n"
" (1, 1, 'lambda_NEB3011', 'lambda_NEB3011', 48502, "
- "'a1319ff90e994c8190a4fe6569d0822a', 0L, 0L)]"))
+ "'a1319ff90e994c8190a4fe6569d0822a', 0, 0)]"))
self.assertEqual(set(aln.tId), {0, 1})
self.assertEqual(aln.referenceInfo('ecoliK12_pbi_March2013'),
aln.referenceInfo(0))
@@ -1894,9 +1894,9 @@
self.assertEqual(
str(aln.referenceInfoTable),
("[ (0, 0, 'ecoliK12_pbi_March2013', 'ecoliK12_pbi_March2013', "
- "4642522, '52cd7c5fa92877152fa487906ae484c5', 0L, 0L)\n"
+ "4642522, '52cd7c5fa92877152fa487906ae484c5', 0, 0)\n"
" (1, 1, 'lambda_NEB3011', 'lambda_NEB3011', 48502, "
- "'a1319ff90e994c8190a4fe6569d0822a', 0L, 0L)]"))
+ "'a1319ff90e994c8190a4fe6569d0822a', 0, 0)]"))
self.assertEqual(set(aln.tId), {0, 1})
self.assertEqual(aln.referenceInfo('ecoliK12_pbi_March2013'),
aln.referenceInfo(0))
Bug#900485: python-pbcore: FTBFS and Debci failure with NumPy 1.14
Control: forwarded -1 https://github.com/PacificBiosciences/pbcore/issues/115 Control: tags -1 upstream Control: tags -1 help Thanks for this bug report. I've forwarded the issue upsteam, Andreas. -- http://fam-tille.de
Bug#900485: python-pbcore: FTBFS and Debci failure with NumPy 1.14
Source: python-pbcore Version: 1.2.11+dfsg-1 Severity: serious User: debian...@lists.debian.org Usertags: needs-update Hi Maintainer Since the recent upload of python-numpy on 2018-05-05, python-pbcore has been failing its autopkgtests [1] and has now also started to FTBFS in unstable [2] with several errors similar to the following: FAIL: test_referenceInfo (test_pbdataset.TestDataSet) -- Traceback (most recent call last): File "/build/1st/python-pbcore-1.2.11+dfsg/tests/test_pbdataset.py", line 1407, in test_referenceInfo "(27, 27, 'E.faecalis.1', 'E.faecalis.1', 1482, " AssertionError: "(27, 27, 'E.faecalis.1', 'E.faecalis.1', 1482, 'a1a59c267ac1341e5a12bce7a7d37bcb', 0, 0)" != "(27, 27, 'E.faecalis.1', 'E.faecalis.1', 1482, 'a1a59c267ac1341e5a12bce7a7d37bcb', 0L, 0L)" >> begin captured logging << pbcore.io.dataset.DataSetIO: DEBUG: Opening ReadSet resources pbcore.io.dataset.DataSetIO: DEBUG: Done opening resources pbcore.io.dataset.DataSetIO: DEBUG: Updating counts pbcore.io.dataset.DataSetIO: DEBUG: Populating index pbcore.io.dataset.DataSetIO: DEBUG: Processing resource indices pbcore.io.dataset.DataSetIO: DEBUG: Filtering reference entries pbcore.io.dataset.DataSetIO: DEBUG: Done populating index Regards Graham [1] https://ci.debian.net/packages/p/python-pbcore/unstable/amd64/ [2] https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/python-pbcore.html
