[Debian-med-packaging] Bug#917670: python-pbcore: FTBFS: dh_auto_test: pybuild --test --test-nose -i python{version} -p 2.7 returned exit code 13
Lucas Nussbaum
lucas at debian.org
Sat Dec 29 21:44:55 GMT 2018
Source: python-pbcore
Version: 1.5.0+git20180606.43fcd9d+dfsg-2
Severity: serious
Justification: FTBFS on amd64
Tags: buster sid
Usertags: ftbfs-20181229 ftbfs-buster
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> make[1]: Entering directory '/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg'
> PYBUILD_SYSTEM=custom \
> PYBUILD_TEST_ARGS="{interpreter} setup.py test" \
> dh_auto_test
> I: pybuild base:217: python2.7 setup.py test
> running test
> running egg_info
> creating pbcore.egg-info
> writing requirements to pbcore.egg-info/requires.txt
> writing pbcore.egg-info/PKG-INFO
> writing top-level names to pbcore.egg-info/top_level.txt
> writing dependency_links to pbcore.egg-info/dependency_links.txt
> writing entry points to pbcore.egg-info/entry_points.txt
> writing manifest file 'pbcore.egg-info/SOURCES.txt'
> reading manifest file 'pbcore.egg-info/SOURCES.txt'
> reading manifest template 'MANIFEST.in'
> warning: no files found matching '*.conf' under directory 'doc'
> warning: no files found matching '*.jpg' under directory 'doc'
> writing manifest file 'pbcore.egg-info/SOURCES.txt'
> running build_ext
> test_pbcore_data.TestGetCmpH5.test_get_cmp_h5 ... ok
> test_pbcore_data.TestGetCmpH5s.test_get_cmp_h5s ... ok
> test_reverse_complement (test_pbcore_extract_bam_sequence.TestCase) ... ok
> test_pbcore_io_AlnFileReaders.TestBasicBam.testAlignedRead ... ok
> test_pbcore_io_AlnFileReaders.TestBasicBam.testAlignedReference ... ok
> test_pbcore_io_AlnFileReaders.TestBasicBam.testBasicOperations ... ok
> test_pbcore_io_AlnFileReaders.TestBasicBam.testBaxAttaching ... ERROR
> test_pbcore_io_AlnFileReaders.TestBasicBam.testClippedAlignments ... ok
> test_pbcore_io_AlnFileReaders.TestBasicBam.testClippingsVsBaxData ... ERROR
> test_pbcore_io_AlnFileReaders.TestBasicBam.testDeletionQV ... ok
> test_pbcore_io_AlnFileReaders.TestBasicBam.testReadGroupTable ... ok
> test_pbcore_io_AlnFileReaders.TestBasicBam.testReadName ... ok
> test_pbcore_io_AlnFileReaders.TestBasicBam.testReadScore ... ok
> test_pbcore_io_AlnFileReaders.TestBasicBam.testReadsInRange ... ok
> test_pbcore_io_AlnFileReaders.TestBasicBam.testSequencingChemistry ... ok
> test_pbcore_io_AlnFileReaders.TestBasicBam.testSpecVersion ... ok
> test_pbcore_io_AlnFileReaders.TestBasicBam.testStrandOrientation ... ok
> test_pbcore_io_AlnFileReaders.TestBasicBam.testTranscript ... ok
> test_pbcore_io_AlnFileReaders.TestBasicBam.testUnalignedRead ... ok
> test_pbcore_io_AlnFileReaders.TestBasicBam.testUnalignedReference ... ok
> test_pbcore_io_AlnFileReaders.TestCCSBam.testQStartEndUnavailable ... ok
> test_pbcore_io_AlnFileReaders.TestCmpH5.testAlignedRead ... ok
> test_pbcore_io_AlnFileReaders.TestCmpH5.testAlignedReference ... ok
> test_pbcore_io_AlnFileReaders.TestCmpH5.testBasicOperations ... ok
> test_pbcore_io_AlnFileReaders.TestCmpH5.testBaxAttaching ... ERROR
> test_pbcore_io_AlnFileReaders.TestCmpH5.testClippedAlignments ... ok
> test_pbcore_io_AlnFileReaders.TestCmpH5.testClippingsVsBaxData ... ERROR
> test_pbcore_io_AlnFileReaders.TestCmpH5.testDeletionQV ... ok
> test_pbcore_io_AlnFileReaders.TestCmpH5.testErrorCounts ... ok
> test_pbcore_io_AlnFileReaders.TestCmpH5.testHoleNumbers ... ok
> test_pbcore_io_AlnFileReaders.TestCmpH5.testLazyChemistryResolution
> The CmpH5Reader allows reading of files that have missing ... ok
> test_pbcore_io_AlnFileReaders.TestCmpH5.testMapQV ... ok
> test_pbcore_io_AlnFileReaders.TestCmpH5.testReadGroupTable ... ok
> test_pbcore_io_AlnFileReaders.TestCmpH5.testReadName ... ok
> test_pbcore_io_AlnFileReaders.TestCmpH5.testReadsByName ... ok
> test_pbcore_io_AlnFileReaders.TestCmpH5.testReadsInRange ... ok
> test_pbcore_io_AlnFileReaders.TestCmpH5.testSequencingChemistry ... ok
> test_pbcore_io_AlnFileReaders.TestCmpH5.testStrandOrientation ... ok
> test_pbcore_io_AlnFileReaders.TestCmpH5.testTranscript ... ok
> test_pbcore_io_AlnFileReaders.TestCmpH5.testUnalignedRead ... ok
> test_pbcore_io_AlnFileReaders.TestCmpH5.testUnalignedReference ... ok
> test_pbcore_io_AlnFileReaders.TestEmptyBam.test_empty_bam_reads_in_range ... ok
> test_pbcore_io_AlnFileReaders.TestIndexedBam.testAlignedRead ... ok
> test_pbcore_io_AlnFileReaders.TestIndexedBam.testAlignedReference ... ok
> test_pbcore_io_AlnFileReaders.TestIndexedBam.testBasicOperations ... ok
> test_pbcore_io_AlnFileReaders.TestIndexedBam.testBaxAttaching ... ERROR
> test_pbcore_io_AlnFileReaders.TestIndexedBam.testClippedAlignments ... ok
> test_pbcore_io_AlnFileReaders.TestIndexedBam.testClippingsVsBaxData ... ERROR
> test_pbcore_io_AlnFileReaders.TestIndexedBam.testDeletionQV ... ok
> test_pbcore_io_AlnFileReaders.TestIndexedBam.testErrorCounts ... ok
> test_pbcore_io_AlnFileReaders.TestIndexedBam.testHoleNumbers ... ok
> test_pbcore_io_AlnFileReaders.TestIndexedBam.testMapQV ... ok
> test_pbcore_io_AlnFileReaders.TestIndexedBam.testReadGroupTable ... ok
> test_pbcore_io_AlnFileReaders.TestIndexedBam.testReadName ... ok
> test_pbcore_io_AlnFileReaders.TestIndexedBam.testReadsByName ... ok
> test_pbcore_io_AlnFileReaders.TestIndexedBam.testReadsInRange ... ok
> test_pbcore_io_AlnFileReaders.TestIndexedBam.testSequencingChemistry ... ok
> test_pbcore_io_AlnFileReaders.TestIndexedBam.testStrandOrientation ... ok
> test_pbcore_io_AlnFileReaders.TestIndexedBam.testTranscript ... ok
> test_pbcore_io_AlnFileReaders.TestIndexedBam.testUnalignedRead ... ok
> test_pbcore_io_AlnFileReaders.TestIndexedBam.testUnalignedReference ... ok
> test_pbcore_io_AlnFileReaders.TestIndexedBam.test_alignment_identity
> Check that the values of the 'identity' property are consistent ... ok
> test_pbcore_io_AlnFileReaders.TestIndexedBam.test_alignment_identity_unindexed
> Check that the value of the 'identity' property is the same whether ... ok
> test_pbcore_io_AlnFileReaders.TestIndexedBam.test_empty_bam ... ok
> test_pbcore_io_AlnFileReaders.TestMultipleReadGroups.test_retrieve_read_group_properties ... ok
> Failure: SkipTest (Testdata not present) ... SKIP: Testdata not present
> test_pbcore_io_AlnFileReaders.TestUpdatedChemistryMapping.test_load_updated_mapping ... ok
> test_pbcore_io_BarcodeH5Reader.TestBarcodeH5Fofn.test_BasH5Fofn_basicTest
> Test that BcH5Fofn correctly sets movie name, barcode labels, and hole numbers ... ok
> test_pbcore_io_BarcodeH5Reader.TestBarcodeH5Fofn.test_BcH5Fofn_indexing
> Test that BcH5Fofn's indexing correctly slices and returns its contents ... ok
> test_pbcore_io_BarcodeH5Reader.TestBarcodeH5Fofn.test_BcH5Fofn_iterator
> Test that BcH5Fofn correctly iterates over it's labeled ZMWs ... ok
> test_pbcore_io_BarcodeH5Reader.TestBarcodeH5Reader.test_BarcodeH5Reader_basicTest
> Test that BcH5Reader correctly sets movie name, barcode labels, and hole numbers ... ok
> test_pbcore_io_BarcodeH5Reader.TestBarcodeH5Reader.test_BarcodeH5Reader_iterator
> Test that BcH5Reader correctly iterates over it's labeled ZMWs ... ok
> test_pbcore_io_BasH5Collection.test ... ERROR
> test_pbcore_io_BasH5Collection.test_read_iterators ... ERROR
> Failure: TypeError (dtype of to_begin must be compatible with input ary) ... ERROR
> Failure: TypeError (dtype of to_begin must be compatible with input ary) ... ERROR
> Failure: TypeError (dtype of to_begin must be compatible with input ary) ... ERROR
> Failure: TypeError (dtype of to_begin must be compatible with input ary) ... ERROR
> Failure: TypeError (dtype of to_begin must be compatible with input ary) ... ERROR
> Failure: TypeError (dtype of to_begin must be compatible with input ary) ... ERROR
> Failure: TypeError (dtype of to_begin must be compatible with input ary) ... ERROR
> Failure: TypeError (dtype of to_begin must be compatible with input ary) ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_20.test_20_constructor_bash5 ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_20.test_20_constructor_baxh5 ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_20.test_20_missing_chemistry
> Tests that we raise an exception when we can't find chemistry information ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_20.test_all_fields_accessible ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_20.test_multipart_constructor_bash5 ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_20.test_multipart_hole_lookup ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_20.test_multippart_constructor_baxh5 ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_20.test_productivity
> Test that productivities are set correctly for the ZMW objects. ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_20.test_read_iterators ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_20.test_zmw_multipart_regions ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_20.test_zmw_region_table ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_21.test_21_bad_external_region_baxh5
> Tests that we raise an exception when incorrect region file given ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_21.test_21_constructor_bash5 ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_21.test_21_constructor_baxh5 ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_21.test_21_external_region_baxh5
> Test the optional region file override ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_21.test_21_missing_chemistry
> Tests that we raise an exception when we can't find chemistry information ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_21.test_all_fields_accessible ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_21.test_multipart_constructor_bash5 ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_21.test_multipart_hole_lookup ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_21.test_multippart_constructor_baxh5 ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_21.test_read_iterators ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_21.test_zmw_multipart_regions ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_21.test_zmw_region_table ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_23.test_23_constructor_bash5 ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_23.test_23_constructor_baxh5 ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_23.test_all_fields_accessible ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_23.test_multipart_constructor_bash5 ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_23.test_multipart_hole_lookup ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_23.test_multippart_constructor_baxh5 ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_23.test_read_iterators ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_23.test_zmw_multipart_regions ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_23.test_zmw_region_table ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_CCS.test_ccs_zmw ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_CCS.test_constructor_ccsh5 ... ERROR
> test_pbcore_io_BasH5Reader.TestBasH5Reader_CCS.test_read_iterators ... ERROR
> test_pbcore_io_BlasrIO.test_m4 ... ok
> test_pbcore_io_BlasrIO.test_m5 ... ok
> test_pbcore_io_FastaIO.TestFastaReader.test_dosLineEndingsFasta ... ok
> test_pbcore_io_FastaIO.TestFastaReader.test_readFasta ... ok
> test_pbcore_io_FastaIO.TestFastaRecord.test__init__ ... ok
> test_pbcore_io_FastaIO.TestFastaRecord.test__str__ ... ok
> test_pbcore_io_FastaIO.TestFastaRecord.test_eq ... ok
> test_pbcore_io_FastaIO.TestFastaRecord.test_fromString ... ok
> test_pbcore_io_FastaIO.TestFastaRecord.test_len ... ok
> test_pbcore_io_FastaIO.TestFastaRecord.test_not_equal ... ok
> test_pbcore_io_FastaIO.TestFastaRecord.test_reverse_complement1 ... ok
> test_pbcore_io_FastaIO.TestFastaRecord.test_reverse_complement2 ... ok
> test_pbcore_io_FastaIO.TestFastaWriter.test_writeFasta1 ... ok
> test_pbcore_io_FastaIO.TestFastaWriter.test_writeFasta2 ... ok
> test_pbcore_io_FastaTable.TestIndexedFastaReader.testAccessById ... ok
> test_pbcore_io_FastaTable.TestIndexedFastaReader.testAccessByName ... ok
> test_pbcore_io_FastaTable.TestIndexedFastaReader.testAccessByPosition ... ok
> test_pbcore_io_FastaTable.TestIndexedFastaReader.testIteration ... ok
> test_pbcore_io_FastaTable.TestIndexedFastaReader.testSlice ... ok
> test_pbcore_io_FastaTable.TestIndexedFastaReader.test_dosLineEndingsFasta ... ok
> test_pbcore_io_FastaTable.TestIndexedFastaReader.test_readWeirdFastaIndex ... ok
> test_pbcore_io_FastqIO.TestFastqReader.test_readFastq1 ... ok
> test_pbcore_io_FastqIO.TestFastqReader.test_readFastq2 ... ok
> test_pbcore_io_FastqIO.TestFastqRecord.test__init__ ... ok
> test_pbcore_io_FastqIO.TestFastqRecord.test__str__ ... ok
> test_pbcore_io_FastqIO.TestFastqRecord.test_eq ... ok
> test_pbcore_io_FastqIO.TestFastqRecord.test_fromString ... ok
> test_pbcore_io_FastqIO.TestFastqRecord.test_len ... ok
> test_pbcore_io_FastqIO.TestFastqRecord.test_not_equal ... ok
> test_pbcore_io_FastqIO.TestFastqRecord.test_reverse_complement1 ... ok
> test_pbcore_io_FastqIO.TestFastqRecord.test_reverse_complement2 ... ok
> test_pbcore_io_FastqIO.TestFastqWriter.test_writeFastq1 ... ok
> test_pbcore_io_FastqIO.TestFastqWriter.test_writeFastq2 ... ok
> test_pbcore_io_FastqIO.TestFastqWriter.test_writeFastq3 ... ok
> test_pbcore_io_FastqIO.TestQvConversion.testAsciiFromQvs ... ok
> test_pbcore_io_FastqIO.TestQvConversion.testQvsFromAscii ... ok
> test_pbcore_io_FofnIO.test_simple ... ok
> test_pbcore_io_FofnIO.test_empty_lines ... ok
> test_pbcore_io_FofnIO.test_absolutifying ... ok
> test_pbcore_io_GffIO.TestGff3Record.test_fromString ... ok
> test_pbcore_io_GffIO.TestGff3Record.test_get
> Verify field access behavior ... ok
> test_pbcore_io_GffIO.TestGff3Record.test_modification ... ok
> test_pbcore_io_GffIO.TestGff3Record.test_str ... ok
> test_pbcore_io_GffIO.TestGffReader.test__iter__ ... ok
> test_pbcore_io_GffIO.TestGffReader.test_headers ... ok
> test_empty_file (test_pbcore_io_GffIO.TestGffSorting) ... ok
> test_merge_gffs (test_pbcore_io_GffIO.TestGffSorting) ... ok
> test_merge_gffs_sorted (test_pbcore_io_GffIO.TestGffSorting) ... ok
> test_sort_gff (test_pbcore_io_GffIO.TestGffSorting) ... ok
> test_pbcore_io_GffIO.TestGffWriter.test_writeHeader ... ok
> test_pbcore_io_GffIO.TestGffWriter.test_writeRecord ... ok
> test_merge_vcfs_sorted (test_pbcore_io_VcfIO.TestVcfSorting) ... ok
> test_pbcore_io_bgzf.TestBgzf.test_partial_reads ... ok
> test_pbcore_io_bgzf.TestBgzf.test_small_data ... ok
> test_pbcore_io_rangeQueries.TestGetReadsInRange.test_coverage_in_range2 ... ok
> test_pbcore_io_rangeQueries.TestGetReadsInRange.test_get_coverage_in_range ... ok
> test_pbcore_io_rangeQueries.TestGetReadsInRange.test_get_reads_in_range ... ok
> test_pbcore_io_rangeQueries.TestGetReadsInRange.test_reads_in_range2 ... ok
> test_pbcore_io_rangeQueries.TestProjectIntoRange.test_project_into_range ... ok
> Failure: TypeError (dtype of to_begin must be compatible with input ary) ... ERROR
> Failure: TypeError (dtype of to_begin must be compatible with input ary) ... ERROR
> Failure: TypeError (dtype of to_begin must be compatible with input ary) ... ERROR
> Failure: TypeError (dtype of to_begin must be compatible with input ary) ... ERROR
> Failure: TypeError (dtype of to_begin must be compatible with input ary) ... ERROR
> Failure: TypeError (dtype of to_begin must be compatible with input ary) ... ERROR
> test_pbcore_util_sequences.TestReverseComplement.test_complement ... ok
> test_pbcore_util_sequences.TestReverseComplement.test_complement_error ... ok
> test_pbcore_util_sequences.TestReverseComplement.test_iupac ... ok
> test_pbcore_util_sequences.TestReverseComplement.test_reverse ... ok
> test_pbcore_util_sequences.TestReverseComplement.test_reverseComplement ... ok
> test_pbcore_util_sequences.TestReverseComplement.test_reverse_complement_error ... ok
> test_addExternalResources (test_pbdataset.TestDataSet) ... ok
> test_addMetadata (test_pbdataset.TestDataSet) ... ok
> test_attributes (test_pbdataset.TestDataSet) ... ok
> test_bad_xml_extension (test_pbdataset.TestDataSet) ... ok
> test_barcode_accession (test_pbdataset.TestDataSet) ... SKIP: Missing testadata directory
> test_build (test_pbdataset.TestDataSet) ... ok
> test_chunk_list (test_pbdataset.TestDataSet) ... ok
> test_copy (test_pbdataset.TestDataSet) ... ok
> test_copyTo (test_pbdataset.TestDataSet) ... ok
> test_copyTo_same_base_names (test_pbdataset.TestDataSet) ... SKIP: Internal data not available
> test_createdAt (test_pbdataset.TestDataSet) ... ok
> test_distribution_accessors (test_pbdataset.TestDataSet) ... ok
> test_distribution_name_accessor (test_pbdataset.TestDataSet) ... ok
> test_empty_aligned_bam_index_dtype (test_pbdataset.TestDataSet) ... ok
> test_empty_bam_index_dtype (test_pbdataset.TestDataSet) ... ok
> test_empty_file_counts (test_pbdataset.TestDataSet) ... SKIP: bamtools or pbindex not found, skipping
> test_empty_metatype (test_pbdataset.TestDataSet) ... ok
> test_exceptions (test_pbdataset.TestDataSet) ... ok
> test_factory_function (test_pbdataset.TestDataSet) ... ok
> test_fixed_bin_sts (test_pbdataset.TestDataSet) ... SKIP: Internal data not available
> test_get_item (test_pbdataset.TestDataSet) ... ok
> test_induce_indices (test_pbdataset.TestDataSet) ... SKIP: bamtools or pbindex not found, skipping
> test_intervalContour (test_pbdataset.TestDataSet) ... ok
> test_large_pbi (test_pbdataset.TestDataSet) ... SKIP: Too expensive
> test_load_sts_from_extres (test_pbdataset.TestDataSet) ... SKIP: Internal data not available
> test_loading_reference (test_pbdataset.TestDataSet) ... ok
> test_merge (test_pbdataset.TestDataSet) ... ok
> test_merge_subdatasets (test_pbdataset.TestDataSet) ... [E::hts_open_format] Failed to open file /blah.bam
> [E::hts_open_format] Failed to open file /blah.bam
> ok
> test_merge_uuid (test_pbdataset.TestDataSet) ... ok
> test_merged_CreatedAt (test_pbdataset.TestDataSet) ... ok
> test_merged_Name (test_pbdataset.TestDataSet) ... ok
> test_merged_Tags (test_pbdataset.TestDataSet) ... ok
> test_merged_cmp (test_pbdataset.TestDataSet) ... SKIP: Internal data not available
> test_missing_extres (test_pbdataset.TestDataSet) ... SKIP: Internal data not available
> test_missing_file (test_pbdataset.TestDataSet) ... ok
> test_multi_channel_dists (test_pbdataset.TestDataSet) ... ok
> test_multi_movie_readsByName (test_pbdataset.TestDataSet) ... SKIP: Missing testadata directory
> test_newUuid (test_pbdataset.TestDataSet) ... ok
> test_newUuid_copy (test_pbdataset.TestDataSet) ... ok
> test_newUuid_random (test_pbdataset.TestDataSet) ... ok
> test_newUuid_repeat (test_pbdataset.TestDataSet) ... ok
> test_new_distribution (test_pbdataset.TestDataSet) ... ok
> test_nonempty_metatype (test_pbdataset.TestDataSet) ... ok
> test_openDataSet_unicode (test_pbdataset.TestDataSet) ... ok
> test_opening (test_pbdataset.TestDataSet)
> Test whether relativizing paths is working. If your subdataset ... ok
> test_read_ranges (test_pbdataset.TestDataSet) ... ok
> test_reads_in_contig (test_pbdataset.TestDataSet) ... ok
> test_reads_in_range (test_pbdataset.TestDataSet) ... ok
> test_reads_in_range_indices (test_pbdataset.TestDataSet) ... ok
> test_reads_in_range_order (test_pbdataset.TestDataSet) ... SKIP: Missing testadata directory
> test_reads_in_range_order_large (test_pbdataset.TestDataSet) ... SKIP: Missing testadata directory
> test_reads_in_reference (test_pbdataset.TestDataSet) ... ok
> test_records (test_pbdataset.TestDataSet) ... ok
> test_reduced_sts_merging (test_pbdataset.TestDataSet) ... SKIP: Internal data not available
> test_refLengths (test_pbdataset.TestDataSet) ... ok
> test_ref_names (test_pbdataset.TestDataSet) ... ok
> test_referenceInfo (test_pbdataset.TestDataSet) ... ok
> test_referenceInfoTableMerging (test_pbdataset.TestDataSet) ... SKIP: Internal data not available
> test_repr (test_pbdataset.TestDataSet) ... ok
> test_resourceReaders (test_pbdataset.TestDataSet) ... ok
> test_scraps_detection (test_pbdataset.TestDataSet) ... SKIP: Internal data not available
> test_space_in_filename (test_pbdataset.TestDataSet) ... ok
> test_staggered_reads_in_range (test_pbdataset.TestDataSet) ... ok
> test_stats_metadata (test_pbdataset.TestDataSet) ... ok
> test_stats_metadata_zero_binwidth (test_pbdataset.TestDataSet) ... ok
> test_subreadset_get_movie_sample_names (test_pbdataset.TestDataSet) ... SKIP: PacBioTestData not installed
> test_toExternalFiles (test_pbdataset.TestDataSet) ... ok
> test_toFofn (test_pbdataset.TestDataSet) ... ok
> test_two_bam (test_pbdataset.TestDataSet) ... SKIP: Internal data not available
> test_two_cmpH5 (test_pbdataset.TestDataSet) ... SKIP: Internal data not available
> test_two_ref_bam (test_pbdataset.TestDataSet) ... SKIP: Internal data not available
> test_two_ref_cmpH5 (test_pbdataset.TestDataSet) ... SKIP: Internal data not available
> test_two_ref_three_bam (test_pbdataset.TestDataSet) ... SKIP: Internal data not available
> test_two_xml (test_pbdataset.TestDataSet) ... SKIP: Internal data not available
> test_type_checking (test_pbdataset.TestDataSet) ... ERROR
> test_updateCounts (test_pbdataset.TestDataSet) ... ok
> test_updateCounts_without_pbi (test_pbdataset.TestDataSet) ... ok
> test_write (test_pbdataset.TestDataSet) ... ok
> test_accuracy_filter (test_pbdataset_filters.TestDataSetFilters) ... ok
> test_addFilters (test_pbdataset_filters.TestDataSetFilters) ... ok
> test_add_double_bound_filters (test_pbdataset_filters.TestDataSetFilters) ... ok
> test_broadcastFilters (test_pbdataset_filters.TestDataSetFilters) ... ok
> test_cmp_alignmentset_filters (test_pbdataset_filters.TestDataSetFilters) ... ok
> test_context_filters (test_pbdataset_filters.TestDataSetFilters) ... ok
> test_contigset_filter (test_pbdataset_filters.TestDataSetFilters) ... ok
> test_file_arg (test_pbdataset_filters.TestDataSetFilters) ... ok
> test_filter (test_pbdataset_filters.TestDataSetFilters) ... ok
> test_filter_reference_contigs (test_pbdataset_filters.TestDataSetFilters) ... ok
> test_mapqv_filter (test_pbdataset_filters.TestDataSetFilters) ... ok
> test_membership_filter (test_pbdataset_filters.TestDataSetFilters) ... ok
> test_membership_filter_with_equal_operator (test_pbdataset_filters.TestDataSetFilters) ... ok
> test_movie_filter (test_pbdataset_filters.TestDataSetFilters) ... SKIP: Internal data not available
> test_n_subreads_filter (test_pbdataset_filters.TestDataSetFilters) ... ok
> test_not_in_filter (test_pbdataset_filters.TestDataSetFilters) ... ok
> test_qname_css (test_pbdataset_filters.TestDataSetFilters) ... SKIP: Internal data not available
> test_qname_filter_scaling (test_pbdataset_filters.TestDataSetFilters) ... SKIP: Internal data not available
> test_setFilters (test_pbdataset_filters.TestDataSetFilters) ... ok
> test_de_novo (test_pbdataset_metadata.TestDataSet) ... ok
> test_existing (test_pbdataset_metadata.TestDataSet) ... ok
> test_loadMetadata (test_pbdataset_metadata.TestDataSet) ... SKIP: Internal data not available
> test_uuid (test_pbdataset_metadata.TestDataSet) ... ok
> test_barcode_split_cornercases (test_pbdataset_split.TestDataSetSplit) ... SKIP: Missing internal testadata directory
> test_barcode_split_maxChunks (test_pbdataset_split.TestDataSetSplit) ... SKIP: Missing internal testadata directory
> test_contigset_split (test_pbdataset_split.TestDataSetSplit) ... ok
> test_huge_zmw_split (test_pbdataset_split.TestDataSetSplit) ... SKIP: Too expensive
> test_isBarcoded (test_pbdataset_split.TestDataSetSplit) ... SKIP: Internal data or binaries not found, skipping
> test_large_split_zmws (test_pbdataset_split.TestDataSetSplit) ... SKIP: Too expensive
> test_movie_split (test_pbdataset_split.TestDataSetSplit) ... SKIP: Missing internal testadata directory
> test_multi_movie_split_zmws (test_pbdataset_split.TestDataSetSplit) ... SKIP: Missing internal testadata directory
> test_multi_movie_split_zmws_existing_filters (test_pbdataset_split.TestDataSetSplit) ... SKIP: Missing internal testadata directory
> test_multi_movie_split_zmws_existing_simple_filters (test_pbdataset_split.TestDataSetSplit) ... SKIP: Missing internal testadata directory
> test_multi_movie_split_zmws_with_existing_movie_filter (test_pbdataset_split.TestDataSetSplit) ... SKIP: Missing internal testadata directory
> test_refWindows (test_pbdataset_split.TestDataSetSplit) ... ok
> test_split (test_pbdataset_split.TestDataSetSplit) ... ok
> test_split_by_contigs_with_split (test_pbdataset_split.TestDataSetSplit) ... ok
> test_split_by_contigs_with_split_and_maxChunks (test_pbdataset_split.TestDataSetSplit) ... ok
> test_split_hdfsubreadset (test_pbdataset_split.TestDataSetSplit) ... ERROR
> test_split_references (test_pbdataset_split.TestDataSetSplit) ... SKIP: Missing internal testadata directory
> test_split_zmws (test_pbdataset_split.TestDataSetSplit) ... ok
> test_split_zmws_targetsize (test_pbdataset_split.TestDataSetSplit) ... ok
> test_subreadset_split_metadata_element_name (test_pbdataset_split.TestDataSetSplit) ... ok
> test_adapters_resource (test_pbdataset_subtypes.TestDataSet) ... SKIP: Internal data not found, skipping
> test_alignment_reference (test_pbdataset_subtypes.TestDataSet) ... ok
> test_alignmentset_consolidate (test_pbdataset_subtypes.TestDataSet) ... SKIP: bamtools or pbindex not found, skipping
> test_alignmentset_index (test_pbdataset_subtypes.TestDataSet) ... ok
> test_alignmentset_partial_consolidate (test_pbdataset_subtypes.TestDataSet) ... SKIP: bamtools, pbindex or data not found, skipping
> test_autofilled_metatypes (test_pbdataset_subtypes.TestDataSet) ... ok
> test_barcodeset (test_pbdataset_subtypes.TestDataSet) ... ok
> test_ccsalignment_build (test_pbdataset_subtypes.TestDataSet) ... [E::hts_open_format] Failed to open file /mnt/path/to/ccsreads0.bam
> ok
> test_ccsread_build (test_pbdataset_subtypes.TestDataSet) ... [E::hts_open_format] Failed to open file /mnt/path/to/ccsreads0.bam
> [E::hts_open_format] Failed to open file /mnt/path/to/ccsreads0.bam
> ok
> test_ccsset_from_bam (test_pbdataset_subtypes.TestDataSet) ... ok
> test_contigset_build (test_pbdataset_subtypes.TestDataSet) ... ok
> test_contigset_consolidate (test_pbdataset_subtypes.TestDataSet) ... ok
> test_contigset_consolidate_genomic_consensus (test_pbdataset_subtypes.TestDataSet)
> Verify that the contigs output by GenomicConsensus (e.g. quiver) can ... ok
> test_contigset_consolidate_int_names (test_pbdataset_subtypes.TestDataSet) ... ok
> test_contigset_empty (test_pbdataset_subtypes.TestDataSet) ... ok
> test_contigset_index (test_pbdataset_subtypes.TestDataSet) ... ok
> test_contigset_len (test_pbdataset_subtypes.TestDataSet) ... ok
> test_contigset_write (test_pbdataset_subtypes.TestDataSet) ... ok
> test_empty_fastq_consolidate (test_pbdataset_subtypes.TestDataSet) ... SKIP: Internal data not found, skipping
> test_fastq_consolidate (test_pbdataset_subtypes.TestDataSet) ... SKIP: Internal data not found, skipping
> test_file_factory (test_pbdataset_subtypes.TestDataSet) ... ERROR
> test_file_factory_css (test_pbdataset_subtypes.TestDataSet) ... SKIP: Missing testadata directory
> test_file_factory_fofn (test_pbdataset_subtypes.TestDataSet) ... ok
> test_getitem (test_pbdataset_subtypes.TestDataSet) ... ok
> test_gmapreferenceset_len (test_pbdataset_subtypes.TestDataSet) ... SKIP: Internal data not found, skipping
> test_incorrect_len_getitem (test_pbdataset_subtypes.TestDataSet) ... ERROR
> test_len (test_pbdataset_subtypes.TestDataSet) ... ERROR
> test_len_fastq (test_pbdataset_subtypes.TestDataSet) ... SKIP: Internal data not found, skipping
> test_merged_contigset (test_pbdataset_subtypes.TestDataSet) ... ok
> test_missing_fai_error_message (test_pbdataset_subtypes.TestDataSet) ... ok
> test_nested_external_resources (test_pbdataset_subtypes.TestDataSet) ... ok
> test_pbmerge (test_pbdataset_subtypes.TestDataSet) ... SKIP: bamtools or pbindex not found, skipping
> test_pbmerge_indexing (test_pbdataset_subtypes.TestDataSet) ... SKIP: bamtools or pbindex not found, skipping
> test_provenance_record_ordering (test_pbdataset_subtypes.TestDataSet) ... SKIP: PacBioTestData not found, skipping
> test_referenceset_contigs (test_pbdataset_subtypes.TestDataSet) ... ok
> test_subread_build (test_pbdataset_subtypes.TestDataSet) ... ok
> test_subreads_parent_dataset (test_pbdataset_subtypes.TestDataSet) ... [E::hts_open_format] Failed to open file /mnt/path/to/subreads0.bam
> [E::hts_open_format] Failed to open file /mnt/path/to/subreads0.bam
> ok
> test_subreadset_consolidate (test_pbdataset_subtypes.TestDataSet) ... SKIP: bamtools or pbindex not found, skipping
> test_subreadset_from_bam (test_pbdataset_subtypes.TestDataSet) ... ok
> test_subreadset_metadata_element_name (test_pbdataset_subtypes.TestDataSet) ... ok
> test_transcriptset (test_pbdataset_subtypes.TestDataSet) ... SKIP: Internal data not found, skipping
> test_valid_hdfsubreadsets (test_pbdataset_subtypes.TestDataSet) ... ok
> test_valid_referencesets (test_pbdataset_subtypes.TestDataSet) ... ok
> test_divideKeys_keysToRanges (test_pbdataset_utils.TestDataSetUtils) ... ok
> test_dsIdToSuffix (test_pbdataset_utils.TestDataSetUtils) ... ok
> test_get_dataset_metatype (test_pbdataset_utils.TestDataSetUtils) ... ok
> test_get_dataset_uuid (test_pbdataset_utils.TestDataSetUtils) ... ok
>
> ======================================================================
> ERROR: test_pbcore_io_AlnFileReaders.TestBasicBam.testBaxAttaching
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_AlnFileReaders.py", line 293, in testBaxAttaching
> self.f.attach(self.BAX_FILE)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/align/_AlignmentMixin.py", line 22, in attach
> self.basH5Collection = BasH5Collection(fofnFilename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 817, in __init__
> for k, v in groupby(movieNamesAndFiles, lambda t: t[0]) ])
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 661, in __init__
> self._parts = [ BaxH5Reader(self.filename) ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_AlnFileReaders.TestBasicBam.testClippingsVsBaxData
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_AlnFileReaders.py", line 308, in testClippingsVsBaxData
> self.f.attach(self.BAX_FILE)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/align/_AlignmentMixin.py", line 22, in attach
> self.basH5Collection = BasH5Collection(fofnFilename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 817, in __init__
> for k, v in groupby(movieNamesAndFiles, lambda t: t[0]) ])
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 661, in __init__
> self._parts = [ BaxH5Reader(self.filename) ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_AlnFileReaders.TestCmpH5.testBaxAttaching
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_AlnFileReaders.py", line 293, in testBaxAttaching
> self.f.attach(self.BAX_FILE)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/align/_AlignmentMixin.py", line 22, in attach
> self.basH5Collection = BasH5Collection(fofnFilename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 817, in __init__
> for k, v in groupby(movieNamesAndFiles, lambda t: t[0]) ])
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 661, in __init__
> self._parts = [ BaxH5Reader(self.filename) ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_AlnFileReaders.TestCmpH5.testClippingsVsBaxData
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_AlnFileReaders.py", line 308, in testClippingsVsBaxData
> self.f.attach(self.BAX_FILE)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/align/_AlignmentMixin.py", line 22, in attach
> self.basH5Collection = BasH5Collection(fofnFilename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 817, in __init__
> for k, v in groupby(movieNamesAndFiles, lambda t: t[0]) ])
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 661, in __init__
> self._parts = [ BaxH5Reader(self.filename) ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_AlnFileReaders.TestIndexedBam.testBaxAttaching
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_AlnFileReaders.py", line 293, in testBaxAttaching
> self.f.attach(self.BAX_FILE)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/align/_AlignmentMixin.py", line 22, in attach
> self.basH5Collection = BasH5Collection(fofnFilename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 817, in __init__
> for k, v in groupby(movieNamesAndFiles, lambda t: t[0]) ])
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 661, in __init__
> self._parts = [ BaxH5Reader(self.filename) ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_AlnFileReaders.TestIndexedBam.testClippingsVsBaxData
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_AlnFileReaders.py", line 308, in testClippingsVsBaxData
> self.f.attach(self.BAX_FILE)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/align/_AlignmentMixin.py", line 22, in attach
> self.basH5Collection = BasH5Collection(fofnFilename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 817, in __init__
> for k, v in groupby(movieNamesAndFiles, lambda t: t[0]) ])
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 661, in __init__
> self._parts = [ BaxH5Reader(self.filename) ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Collection.test
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Collection.py", line 13, in test
> bc = BasH5Collection(fofn)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 817, in __init__
> for k, v in groupby(movieNamesAndFiles, lambda t: t[0]) ])
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 661, in __init__
> self._parts = [ BaxH5Reader(self.filename) ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Collection.test_read_iterators
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Collection.py", line 23, in test_read_iterators
> bc = BasH5Collection(fofn)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 817, in __init__
> for k, v in groupby(movieNamesAndFiles, lambda t: t[0]) ])
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 661, in __init__
> self._parts = [ BaxH5Reader(self.filename) ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: Failure: TypeError (dtype of to_begin must be compatible with input ary)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 523, in makeTest
> return self._makeTest(obj, parent)
> File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 582, in _makeTest
> return MethodTestCase(obj)
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 345, in __init__
> self.inst = self.cls()
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 22, in __init__
> self.bas1, self.bas2 = map(pbcore.io.BasH5Reader, basFiles)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 661, in __init__
> self._parts = [ BaxH5Reader(self.filename) ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: Failure: TypeError (dtype of to_begin must be compatible with input ary)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 523, in makeTest
> return self._makeTest(obj, parent)
> File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 582, in _makeTest
> return MethodTestCase(obj)
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 345, in __init__
> self.inst = self.cls()
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 22, in __init__
> self.bas1, self.bas2 = map(pbcore.io.BasH5Reader, basFiles)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 661, in __init__
> self._parts = [ BaxH5Reader(self.filename) ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: Failure: TypeError (dtype of to_begin must be compatible with input ary)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 523, in makeTest
> return self._makeTest(obj, parent)
> File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 582, in _makeTest
> return MethodTestCase(obj)
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 345, in __init__
> self.inst = self.cls()
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 22, in __init__
> self.bas1, self.bas2 = map(pbcore.io.BasH5Reader, basFiles)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 661, in __init__
> self._parts = [ BaxH5Reader(self.filename) ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: Failure: TypeError (dtype of to_begin must be compatible with input ary)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 523, in makeTest
> return self._makeTest(obj, parent)
> File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 582, in _makeTest
> return MethodTestCase(obj)
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 345, in __init__
> self.inst = self.cls()
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 22, in __init__
> self.bas1, self.bas2 = map(pbcore.io.BasH5Reader, basFiles)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 661, in __init__
> self._parts = [ BaxH5Reader(self.filename) ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: Failure: TypeError (dtype of to_begin must be compatible with input ary)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 523, in makeTest
> return self._makeTest(obj, parent)
> File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 582, in _makeTest
> return MethodTestCase(obj)
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 345, in __init__
> self.inst = self.cls()
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 22, in __init__
> self.bas1, self.bas2 = map(pbcore.io.BasH5Reader, basFiles)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 661, in __init__
> self._parts = [ BaxH5Reader(self.filename) ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: Failure: TypeError (dtype of to_begin must be compatible with input ary)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 523, in makeTest
> return self._makeTest(obj, parent)
> File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 582, in _makeTest
> return MethodTestCase(obj)
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 345, in __init__
> self.inst = self.cls()
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 22, in __init__
> self.bas1, self.bas2 = map(pbcore.io.BasH5Reader, basFiles)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 661, in __init__
> self._parts = [ BaxH5Reader(self.filename) ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: Failure: TypeError (dtype of to_begin must be compatible with input ary)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 523, in makeTest
> return self._makeTest(obj, parent)
> File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 582, in _makeTest
> return MethodTestCase(obj)
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 345, in __init__
> self.inst = self.cls()
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 22, in __init__
> self.bas1, self.bas2 = map(pbcore.io.BasH5Reader, basFiles)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 661, in __init__
> self._parts = [ BaxH5Reader(self.filename) ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: Failure: TypeError (dtype of to_begin must be compatible with input ary)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 523, in makeTest
> return self._makeTest(obj, parent)
> File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 582, in _makeTest
> return MethodTestCase(obj)
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 345, in __init__
> self.inst = self.cls()
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 22, in __init__
> self.bas1, self.bas2 = map(pbcore.io.BasH5Reader, basFiles)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 661, in __init__
> self._parts = [ BaxH5Reader(self.filename) ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_20.test_20_constructor_bash5
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 326, in test_20_constructor_bash5
> reader = pbcore.io.BasH5Reader(self.bash5_filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 656, in __init__
> for fn in self.file["/MultiPart/Parts"] ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_20.test_20_constructor_baxh5
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 335, in test_20_constructor_baxh5
> reader = pbcore.io.BasH5Reader(filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 661, in __init__
> self._parts = [ BaxH5Reader(self.filename) ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_20.test_20_missing_chemistry
> Tests that we raise an exception when we can't find chemistry information
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/usr/lib/python2.7/dist-packages/nose/tools/nontrivial.py", line 60, in newfunc
> func(*arg, **kw)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 343, in test_20_missing_chemistry
> reader = pbcore.io.BasH5Reader(self.bash5_filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 656, in __init__
> for fn in self.file["/MultiPart/Parts"] ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_20.test_all_fields_accessible
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 133, in test_all_fields_accessible
> reader = pbcore.io.BasH5Reader(self.bash5_filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 656, in __init__
> for fn in self.file["/MultiPart/Parts"] ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_20.test_multipart_constructor_bash5
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 196, in test_multipart_constructor_bash5
> reader = pbcore.io.BasH5Reader(self.bash5_filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 656, in __init__
> for fn in self.file["/MultiPart/Parts"] ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_20.test_multipart_hole_lookup
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 245, in test_multipart_hole_lookup
> reader = pbcore.io.BasH5Reader(self.bash5_filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 656, in __init__
> for fn in self.file["/MultiPart/Parts"] ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_20.test_multippart_constructor_baxh5
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 221, in test_multippart_constructor_baxh5
> reader = pbcore.io.BasH5Reader(filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 661, in __init__
> self._parts = [ BaxH5Reader(self.filename) ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_20.test_productivity
> Test that productivities are set correctly for the ZMW objects.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 356, in test_productivity
> reader = pbcore.io.BasH5Reader(self.bash5_filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 656, in __init__
> for fn in self.file["/MultiPart/Parts"] ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_20.test_read_iterators
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 169, in test_read_iterators
> reader = pbcore.io.BasH5Reader(self.bash5_filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 656, in __init__
> for fn in self.file["/MultiPart/Parts"] ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_20.test_zmw_multipart_regions
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 274, in test_zmw_multipart_regions
> reader = pbcore.io.BasH5Reader(self.bash5_filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 656, in __init__
> for fn in self.file["/MultiPart/Parts"] ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_20.test_zmw_region_table
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 145, in test_zmw_region_table
> reader = pbcore.io.BasH5Reader(self.bash5_filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 656, in __init__
> for fn in self.file["/MultiPart/Parts"] ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_21.test_21_bad_external_region_baxh5
> Tests that we raise an exception when incorrect region file given
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/usr/lib/python2.7/dist-packages/nose/tools/nontrivial.py", line 60, in newfunc
> func(*arg, **kw)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 415, in test_21_bad_external_region_baxh5
> pbcore.io.BaxH5Reader(baxfile, regionH5Filename=rgnfile)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 331, in __init__
> self.loadExternalRegions(regionH5Filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 400, in loadExternalRegions
> self._loadRegions(fh)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_21.test_21_constructor_bash5
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 375, in test_21_constructor_bash5
> reader = pbcore.io.BasH5Reader(self.bash5_filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 656, in __init__
> for fn in self.file["/MultiPart/Parts"] ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_21.test_21_constructor_baxh5
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 384, in test_21_constructor_baxh5
> reader = pbcore.io.BasH5Reader(filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 661, in __init__
> self._parts = [ BaxH5Reader(self.filename) ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_21.test_21_external_region_baxh5
> Test the optional region file override
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 393, in test_21_external_region_baxh5
> reader = pbcore.io.BaxH5Reader(baxfile)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_21.test_21_missing_chemistry
> Tests that we raise an exception when we can't find chemistry information
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/usr/lib/python2.7/dist-packages/nose/tools/nontrivial.py", line 60, in newfunc
> func(*arg, **kw)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 406, in test_21_missing_chemistry
> reader = pbcore.io.BasH5Reader(self.bash5_filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 656, in __init__
> for fn in self.file["/MultiPart/Parts"] ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_21.test_all_fields_accessible
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 133, in test_all_fields_accessible
> reader = pbcore.io.BasH5Reader(self.bash5_filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 656, in __init__
> for fn in self.file["/MultiPart/Parts"] ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_21.test_multipart_constructor_bash5
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 196, in test_multipart_constructor_bash5
> reader = pbcore.io.BasH5Reader(self.bash5_filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 656, in __init__
> for fn in self.file["/MultiPart/Parts"] ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_21.test_multipart_hole_lookup
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 245, in test_multipart_hole_lookup
> reader = pbcore.io.BasH5Reader(self.bash5_filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 656, in __init__
> for fn in self.file["/MultiPart/Parts"] ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_21.test_multippart_constructor_baxh5
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 221, in test_multippart_constructor_baxh5
> reader = pbcore.io.BasH5Reader(filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 661, in __init__
> self._parts = [ BaxH5Reader(self.filename) ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_21.test_read_iterators
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 169, in test_read_iterators
> reader = pbcore.io.BasH5Reader(self.bash5_filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 656, in __init__
> for fn in self.file["/MultiPart/Parts"] ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_21.test_zmw_multipart_regions
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 274, in test_zmw_multipart_regions
> reader = pbcore.io.BasH5Reader(self.bash5_filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 656, in __init__
> for fn in self.file["/MultiPart/Parts"] ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_21.test_zmw_region_table
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 145, in test_zmw_region_table
> reader = pbcore.io.BasH5Reader(self.bash5_filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 656, in __init__
> for fn in self.file["/MultiPart/Parts"] ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_23.test_23_constructor_bash5
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 430, in test_23_constructor_bash5
> reader = pbcore.io.BasH5Reader(self.bash5_filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 656, in __init__
> for fn in self.file["/MultiPart/Parts"] ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_23.test_23_constructor_baxh5
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 440, in test_23_constructor_baxh5
> reader = pbcore.io.BasH5Reader(filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 661, in __init__
> self._parts = [ BaxH5Reader(self.filename) ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_23.test_all_fields_accessible
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 133, in test_all_fields_accessible
> reader = pbcore.io.BasH5Reader(self.bash5_filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 656, in __init__
> for fn in self.file["/MultiPart/Parts"] ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_23.test_multipart_constructor_bash5
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 196, in test_multipart_constructor_bash5
> reader = pbcore.io.BasH5Reader(self.bash5_filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 656, in __init__
> for fn in self.file["/MultiPart/Parts"] ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_23.test_multipart_hole_lookup
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 245, in test_multipart_hole_lookup
> reader = pbcore.io.BasH5Reader(self.bash5_filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 656, in __init__
> for fn in self.file["/MultiPart/Parts"] ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_23.test_multippart_constructor_baxh5
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 221, in test_multippart_constructor_baxh5
> reader = pbcore.io.BasH5Reader(filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 661, in __init__
> self._parts = [ BaxH5Reader(self.filename) ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_23.test_read_iterators
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 169, in test_read_iterators
> reader = pbcore.io.BasH5Reader(self.bash5_filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 656, in __init__
> for fn in self.file["/MultiPart/Parts"] ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_23.test_zmw_multipart_regions
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 274, in test_zmw_multipart_regions
> reader = pbcore.io.BasH5Reader(self.bash5_filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 656, in __init__
> for fn in self.file["/MultiPart/Parts"] ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_23.test_zmw_region_table
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 145, in test_zmw_region_table
> reader = pbcore.io.BasH5Reader(self.bash5_filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 656, in __init__
> for fn in self.file["/MultiPart/Parts"] ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_CCS.test_ccs_zmw
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 476, in test_ccs_zmw
> reader = pbcore.io.BasH5Reader(self.bash5_filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 661, in __init__
> self._parts = [ BaxH5Reader(self.filename) ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_CCS.test_constructor_ccsh5
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 456, in test_constructor_ccsh5
> reader = pbcore.io.BasH5Reader(self.bash5_filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 661, in __init__
> self._parts = [ BaxH5Reader(self.filename) ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_pbcore_io_BasH5Reader.TestBasH5Reader_CCS.test_read_iterators
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_BasH5Reader.py", line 169, in test_read_iterators
> reader = pbcore.io.BasH5Reader(self.bash5_filename)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 661, in __init__
> self._parts = [ BaxH5Reader(self.filename) ]
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: Failure: TypeError (dtype of to_begin must be compatible with input ary)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 523, in makeTest
> return self._makeTest(obj, parent)
> File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 582, in _makeTest
> return MethodTestCase(obj)
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 345, in __init__
> self.inst = self.cls()
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_unaligned_bam.py", line 23, in __init__
> self.bax = BaxH5Reader(data.getBaxForBam())
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: Failure: TypeError (dtype of to_begin must be compatible with input ary)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 523, in makeTest
> return self._makeTest(obj, parent)
> File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 582, in _makeTest
> return MethodTestCase(obj)
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 345, in __init__
> self.inst = self.cls()
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_unaligned_bam.py", line 23, in __init__
> self.bax = BaxH5Reader(data.getBaxForBam())
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: Failure: TypeError (dtype of to_begin must be compatible with input ary)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 523, in makeTest
> return self._makeTest(obj, parent)
> File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 582, in _makeTest
> return MethodTestCase(obj)
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 345, in __init__
> self.inst = self.cls()
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_unaligned_bam.py", line 23, in __init__
> self.bax = BaxH5Reader(data.getBaxForBam())
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: Failure: TypeError (dtype of to_begin must be compatible with input ary)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 523, in makeTest
> return self._makeTest(obj, parent)
> File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 582, in _makeTest
> return MethodTestCase(obj)
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 345, in __init__
> self.inst = self.cls()
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_unaligned_bam.py", line 23, in __init__
> self.bax = BaxH5Reader(data.getBaxForBam())
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: Failure: TypeError (dtype of to_begin must be compatible with input ary)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 523, in makeTest
> return self._makeTest(obj, parent)
> File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 582, in _makeTest
> return MethodTestCase(obj)
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 345, in __init__
> self.inst = self.cls()
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_unaligned_bam.py", line 23, in __init__
> self.bax = BaxH5Reader(data.getBaxForBam())
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: Failure: TypeError (dtype of to_begin must be compatible with input ary)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 523, in makeTest
> return self._makeTest(obj, parent)
> File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 582, in _makeTest
> return MethodTestCase(obj)
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 345, in __init__
> self.inst = self.cls()
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbcore_io_unaligned_bam.py", line 23, in __init__
> self.bax = BaxH5Reader(data.getBaxForBam())
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
>
> ======================================================================
> ERROR: test_type_checking (test_pbdataset.TestDataSet)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbdataset.py", line 768, in test_type_checking
> HdfSubreadSet(bax, strict=True)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 2534, in __init__
> super(HdfSubreadSet, self).__init__(*files, **kwargs)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 1960, in __init__
> super(ReadSet, self).__init__(*files, **kwargs)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 450, in __init__
> self.updateCounts()
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 2585, in updateCounts
> numRecords, totalLength = self._length
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 2570, in _length
> for rec in self.records:
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 148, in wrapper
> for read in generator(dset, *args, **kwargs):
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 1521, in records
> for resource in self.resourceReaders():
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 2419, in resourceReaders
> self._openFiles()
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 2559, in _openFiles
> resource = BaxH5Reader(location)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
> -------------------- >> begin captured logging << --------------------
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Making paths absolute...
> pbcore.io.dataset.DataSetIO: DEBUG: Unable to assume path is already absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Unable to assume path is already absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Done making paths absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Making paths absolute...
> pbcore.io.dataset.DataSetIO: DEBUG: Unable to assume path is already absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Unable to assume path is already absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Done making paths absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> 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
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Opening ReferenceSet resources
> pbcore.io.dataset.DataSetIO: DEBUG: Done opening ReferenceSet resources
> pbcore.io.dataset.DataSetIO: DEBUG: Updating counts
> pbcore.io.dataset.DataSetIO: DEBUG: Populating index
> pbcore.io.dataset.DataSetIO: DEBUG: Done populating index
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Updating counts
> pbcore.io.dataset.DataSetIO: DEBUG: Opening resources
> --------------------- >> end captured logging << ---------------------
>
> ======================================================================
> ERROR: test_split_hdfsubreadset (test_pbdataset_split.TestDataSetSplit)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbdataset_split.py", line 722, in test_split_hdfsubreadset
> hdfds = HdfSubreadSet(*upstreamdata.getBaxH5_v23())
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 2534, in __init__
> super(HdfSubreadSet, self).__init__(*files, **kwargs)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 1960, in __init__
> super(ReadSet, self).__init__(*files, **kwargs)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 450, in __init__
> self.updateCounts()
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 2585, in updateCounts
> numRecords, totalLength = self._length
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 2570, in _length
> for rec in self.records:
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 148, in wrapper
> for read in generator(dset, *args, **kwargs):
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 1521, in records
> for resource in self.resourceReaders():
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 2419, in resourceReaders
> self._openFiles()
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 2559, in _openFiles
> resource = BaxH5Reader(location)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
> -------------------- >> begin captured logging << --------------------
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Updating counts
> pbcore.io.dataset.DataSetIO: DEBUG: Opening resources
> --------------------- >> end captured logging << ---------------------
>
> ======================================================================
> ERROR: test_file_factory (test_pbdataset_subtypes.TestDataSet)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbdataset_subtypes.py", line 260, in test_file_factory
> mystery = openDataFile(ds.toExternalFiles()[0])
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 114, in openDataFile
> return options[0](*origFiles, **kwargs)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 2534, in __init__
> super(HdfSubreadSet, self).__init__(*files, **kwargs)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 1960, in __init__
> super(ReadSet, self).__init__(*files, **kwargs)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 450, in __init__
> self.updateCounts()
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 2585, in updateCounts
> numRecords, totalLength = self._length
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 2570, in _length
> for rec in self.records:
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 148, in wrapper
> for read in generator(dset, *args, **kwargs):
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 1521, in records
> for resource in self.resourceReaders():
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 2419, in resourceReaders
> self._openFiles()
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 2559, in _openFiles
> resource = BaxH5Reader(location)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
> -------------------- >> begin captured logging << --------------------
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Making paths absolute...
> pbcore.io.dataset.DataSetIO: DEBUG: Unable to assume path is already absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Unable to assume path is already absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Unable to assume path is already absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Done making paths absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Making paths absolute...
> pbcore.io.dataset.DataSetIO: DEBUG: Unable to assume path is already absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Unable to assume path is already absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Done making paths absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Making paths absolute...
> pbcore.io.dataset.DataSetIO: DEBUG: Unable to assume path is already absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Done making paths absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> 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: Done populating index
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Making paths absolute...
> pbcore.io.dataset.DataSetIO: DEBUG: Unable to assume path is already absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Unable to assume path is already absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Done making paths absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> 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
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Opening ReferenceSet resources
> pbcore.io.dataset.DataSetIO: DEBUG: Done opening ReferenceSet resources
> pbcore.io.dataset.DataSetIO: DEBUG: Updating counts
> pbcore.io.dataset.DataSetIO: DEBUG: Populating index
> pbcore.io.dataset.DataSetIO: DEBUG: Done populating index
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> 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: Done populating index
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Updating counts
> pbcore.io.dataset.DataSetIO: DEBUG: Opening resources
> --------------------- >> end captured logging << ---------------------
>
> ======================================================================
> ERROR: test_incorrect_len_getitem (test_pbdataset_subtypes.TestDataSet)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbdataset_subtypes.py", line 1074, in test_incorrect_len_getitem
> with openDataFile(ds.toExternalFiles()[0]) as mystery:
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 114, in openDataFile
> return options[0](*origFiles, **kwargs)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 2534, in __init__
> super(HdfSubreadSet, self).__init__(*files, **kwargs)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 1960, in __init__
> super(ReadSet, self).__init__(*files, **kwargs)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 450, in __init__
> self.updateCounts()
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 2585, in updateCounts
> numRecords, totalLength = self._length
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 2570, in _length
> for rec in self.records:
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 148, in wrapper
> for read in generator(dset, *args, **kwargs):
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 1521, in records
> for resource in self.resourceReaders():
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 2419, in resourceReaders
> self._openFiles()
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 2559, in _openFiles
> resource = BaxH5Reader(location)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
> -------------------- >> begin captured logging << --------------------
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Making paths absolute...
> pbcore.io.dataset.DataSetIO: DEBUG: Unable to assume path is already absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Unable to assume path is already absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Unable to assume path is already absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Done making paths absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Making paths absolute...
> pbcore.io.dataset.DataSetIO: DEBUG: Unable to assume path is already absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Unable to assume path is already absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Done making paths absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Making paths absolute...
> pbcore.io.dataset.DataSetIO: DEBUG: Unable to assume path is already absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Done making paths absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> 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: Done populating index
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Making paths absolute...
> pbcore.io.dataset.DataSetIO: DEBUG: Unable to assume path is already absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Unable to assume path is already absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Done making paths absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> 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
> pbcore.io.dataset.DataSetIO: DEBUG: Writing DataSet...
> pbcore.io.dataset.DataSetIO: DEBUG: Serializing XML...
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Done serializing XML
> pbcore.io.dataset.DataSetIO: DEBUG: Making pretty...
> pbcore.io.dataset.DataSetIO: DEBUG: Done making pretty...
> pbcore.io.dataset.DataSetIO: DEBUG: Validating...
> pbcore.io.dataset.DataSetValidator: DEBUG: Validating with PyXb
> pbcore.io.dataset.DataSetIO: DEBUG: Done validating
> pbcore.io.dataset.DataSetIO: DEBUG: Writing...
> pbcore.io.dataset.DataSetIO: DEBUG: Done writing
> pbcore.io.dataset.DataSetIO: DEBUG: Done writing DataSet
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Making paths absolute...
> pbcore.io.dataset.DataSetIO: DEBUG: Done making paths absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> 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
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Opening ReferenceSet resources
> pbcore.io.dataset.DataSetIO: DEBUG: Done opening ReferenceSet resources
> pbcore.io.dataset.DataSetIO: DEBUG: Updating counts
> pbcore.io.dataset.DataSetIO: DEBUG: Populating index
> pbcore.io.dataset.DataSetIO: DEBUG: Done populating index
> pbcore.io.dataset.DataSetIO: DEBUG: Writing DataSet...
> pbcore.io.dataset.DataSetIO: DEBUG: Serializing XML...
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Done serializing XML
> pbcore.io.dataset.DataSetIO: DEBUG: Making pretty...
> pbcore.io.dataset.DataSetIO: DEBUG: Done making pretty...
> pbcore.io.dataset.DataSetIO: DEBUG: Validating...
> pbcore.io.dataset.DataSetValidator: DEBUG: Validating with PyXb
> pbcore.io.dataset.DataSetIO: DEBUG: Done validating
> pbcore.io.dataset.DataSetIO: DEBUG: Writing...
> pbcore.io.dataset.DataSetIO: DEBUG: Done writing
> pbcore.io.dataset.DataSetIO: DEBUG: Done writing DataSet
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Making paths absolute...
> pbcore.io.dataset.DataSetIO: DEBUG: Done making paths absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetIO: DEBUG: Opening ReferenceSet resources
> pbcore.io.dataset.DataSetIO: DEBUG: Done opening ReferenceSet resources
> pbcore.io.dataset.DataSetIO: DEBUG: Updating counts
> pbcore.io.dataset.DataSetIO: DEBUG: Populating index
> pbcore.io.dataset.DataSetIO: DEBUG: Done populating index
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> 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: Done populating index
> pbcore.io.dataset.DataSetIO: DEBUG: Writing DataSet...
> pbcore.io.dataset.DataSetIO: DEBUG: Serializing XML...
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Done serializing XML
> pbcore.io.dataset.DataSetIO: DEBUG: Making pretty...
> pbcore.io.dataset.DataSetIO: DEBUG: Done making pretty...
> pbcore.io.dataset.DataSetIO: DEBUG: Validating...
> pbcore.io.dataset.DataSetValidator: DEBUG: Validating with PyXb
> pbcore.io.dataset.DataSetIO: DEBUG: Done validating
> pbcore.io.dataset.DataSetIO: DEBUG: Writing...
> pbcore.io.dataset.DataSetIO: DEBUG: Done writing
> pbcore.io.dataset.DataSetIO: DEBUG: Done writing DataSet
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Making paths absolute...
> pbcore.io.dataset.DataSetIO: DEBUG: Done making paths absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> 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: Done populating index
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Updating counts
> pbcore.io.dataset.DataSetIO: DEBUG: Opening resources
> --------------------- >> end captured logging << ---------------------
>
> ======================================================================
> ERROR: test_len (test_pbdataset_subtypes.TestDataSet)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/tests/test_pbdataset_subtypes.py", line 834, in test_len
> self.assertEqual(len(sset), 9)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 682, in __len__
> self.updateCounts()
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 2585, in updateCounts
> numRecords, totalLength = self._length
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 2570, in _length
> for rec in self.records:
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 148, in wrapper
> for read in generator(dset, *args, **kwargs):
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 1521, in records
> for resource in self.resourceReaders():
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 2419, in resourceReaders
> self._openFiles()
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/dataset/DataSetIO.py", line 2559, in _openFiles
> resource = BaxH5Reader(location)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 328, in __init__
> self._loadRegions(self.file)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 355, in _loadRegions
> self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber)
> File "/<<BUILDDIR>>/python-pbcore-1.5.0+git20180606.43fcd9d+dfsg/pbcore/io/BasH5IO.py", line 284, in _makeRegionTableIndex
> to_begin=[1], to_end=[1])
> File "/usr/lib/python2.7/dist-packages/numpy/lib/arraysetops.py", line 111, in ediff1d
> raise TypeError("dtype of to_begin must be compatible "
> TypeError: dtype of to_begin must be compatible with input ary
> -------------------- >> begin captured logging << --------------------
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Making paths absolute...
> pbcore.io.dataset.DataSetIO: DEBUG: Unable to assume path is already absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Unable to assume path is already absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Unable to assume path is already absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Done making paths absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> 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
> pbcore.io.dataset.DataSetIO: DEBUG: Updating counts
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Making paths absolute...
> pbcore.io.dataset.DataSetIO: DEBUG: Unable to assume path is already absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Unable to assume path is already absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Unable to assume path is already absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Done making paths absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> 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
> pbcore.io.dataset.DataSetIO: DEBUG: Updating counts
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> 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
> pbcore.io.dataset.DataSetIO: DEBUG: Updating counts
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Making paths absolute...
> pbcore.io.dataset.DataSetIO: DEBUG: Unable to assume path is already absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Done making paths absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> 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: Done populating index
> pbcore.io.dataset.DataSetIO: DEBUG: Updating counts
> pbcore.io.dataset.DataSetWriter: DEBUG: Making elementtree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done making ElementTree...
> pbcore.io.dataset.DataSetWriter: DEBUG: Converting ElementTree to string...
> pbcore.io.dataset.DataSetWriter: DEBUG: Done converting ElementTree to string
> pbcore.io.dataset.DataSetIO: DEBUG: Making paths absolute...
> pbcore.io.dataset.DataSetIO: DEBUG: Unable to assume path is already absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Done making paths absolute
> pbcore.io.dataset.DataSetIO: DEBUG: Updating metatypes...
> pbcore.io.dataset.DataSetIO: DEBUG: Done updating metatypes
> pbcore.io.dataset.DataSetIO: DEBUG: Checking that the files exist...
> pbcore.io.dataset.DataSetIO: DEBUG: Done checking that the files exist
> pbcore.io.dataset.DataSetIO: DEBUG: Updating counts
> pbcore.io.dataset.DataSetIO: DEBUG: Opening resources
> --------------------- >> end captured logging << ---------------------
>
> ----------------------------------------------------------------------
> Ran 356 tests in 11.958s
>
> FAILED (errors=62, skipped=51)
> Test failed: <unittest.runner.TextTestResult run=356 errors=62 failures=0>
> error: Test failed: <unittest.runner.TextTestResult run=356 errors=62 failures=0>
> E: pybuild pybuild:338: test: plugin custom failed with: exit code=1: python2.7 setup.py test
> dh_auto_test: pybuild --test --test-nose -i python{version} -p 2.7 returned exit code 13
The full build log is available from:
http://aws-logs.debian.net/2018/12/29/python-pbcore_1.5.0+git20180606.43fcd9d+dfsg-2_unstable.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.
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