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 <dseif...@pacificbiosciences.com> 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))
