[Debian-med-packaging] Bug#1026580: svim: FTBFS: ModuleNotFoundError: No module named 'pysam.libchtslib'
Lucas Nussbaum
lucas at debian.org
Tue Dec 20 17:12:31 GMT 2022
Source: svim
Version: 2.0.0-2
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20221220 ftbfs-bookworm
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_test -- --system=custom --test-args="PYTHONPATH={build_dir} {interpreter} -m unittest discover -v src/tests"
> I: pybuild base:240: PYTHONPATH=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build python3.11 -m unittest discover -v src/tests
> test_Collect (unittest.loader._FailedTest.test_Collect) ... ERROR
> test_downstream_distance_to (test_SVCandidate.DeletionCandidateTestCase.test_downstream_distance_to) ... ok
> test_get_key (test_SVCandidate.DeletionCandidateTestCase.test_get_key) ... ok
> test_get_source (test_SVCandidate.DeletionCandidateTestCase.test_get_source) ... ok
> test_get_std_pos (test_SVCandidate.DeletionCandidateTestCase.test_get_std_pos) ... ok
> test_get_std_span (test_SVCandidate.DeletionCandidateTestCase.test_get_std_span) ... ok
> test_get_vcf_entry (test_SVCandidate.DeletionCandidateTestCase.test_get_vcf_entry) ... ok
> test_accessors (test_Signature.TestSVSignature.test_accessors) ... ok
> test_as_string (test_Signature.TestSVSignature.test_as_string) ... ok
> test_downstream_distance_to (test_Signature.TestSVSignature.test_downstream_distance_to) ... ok
> test_clustering (unittest.loader._FailedTest.test_clustering) ... ERROR
> test_consensus (unittest.loader._FailedTest.test_consensus) ... ERROR
> test_guess_file_type (test_input_parsing.TestInputParsing.test_guess_file_type) ... ok
> test_inter (unittest.loader._FailedTest.test_inter) ... ERROR
> test_analyze_cigar_indel (test_intra.TestSVIMIntra.test_analyze_cigar_indel) ... ok
> test_satag (unittest.loader._FailedTest.test_satag) ... ERROR
>
> ======================================================================
> ERROR: test_Collect (unittest.loader._FailedTest.test_Collect)
> ----------------------------------------------------------------------
> ImportError: Failed to import test module: test_Collect
> Traceback (most recent call last):
> File "/usr/lib/python3.11/unittest/loader.py", line 407, in _find_test_path
> module = self._get_module_from_name(name)
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> File "/usr/lib/python3.11/unittest/loader.py", line 350, in _get_module_from_name
> __import__(name)
> File "/<<PKGBUILDDIR>>/src/tests/test_Collect.py", line 2, in <module>
> import pysam
> File "/usr/lib/python3/dist-packages/pysam/__init__.py", line 4, in <module>
> from pysam.libchtslib import *
> ModuleNotFoundError: No module named 'pysam.libchtslib'
>
>
> ======================================================================
> ERROR: test_clustering (unittest.loader._FailedTest.test_clustering)
> ----------------------------------------------------------------------
> ImportError: Failed to import test module: test_clustering
> Traceback (most recent call last):
> File "/usr/lib/python3.11/unittest/loader.py", line 407, in _find_test_path
> module = self._get_module_from_name(name)
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> File "/usr/lib/python3.11/unittest/loader.py", line 350, in _get_module_from_name
> __import__(name)
> File "/<<PKGBUILDDIR>>/src/tests/test_clustering.py", line 6, in <module>
> from svim.SVIM_clustering import form_partitions, partition_and_cluster
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/svim/SVIM_clustering.py", line 11, in <module>
> from pysam import FastaFile
> File "/usr/lib/python3/dist-packages/pysam/__init__.py", line 4, in <module>
> from pysam.libchtslib import *
> ModuleNotFoundError: No module named 'pysam.libchtslib'
>
>
> ======================================================================
> ERROR: test_consensus (unittest.loader._FailedTest.test_consensus)
> ----------------------------------------------------------------------
> ImportError: Failed to import test module: test_consensus
> Traceback (most recent call last):
> File "/usr/lib/python3.11/unittest/loader.py", line 407, in _find_test_path
> module = self._get_module_from_name(name)
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> File "/usr/lib/python3.11/unittest/loader.py", line 350, in _get_module_from_name
> __import__(name)
> File "/<<PKGBUILDDIR>>/src/tests/test_consensus.py", line 5, in <module>
> from svim.SVIM_COMBINE import generate_insertion_consensus
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/svim/SVIM_COMBINE.py", line 9, in <module>
> from pysam import FastaFile
> File "/usr/lib/python3/dist-packages/pysam/__init__.py", line 4, in <module>
> from pysam.libchtslib import *
> ModuleNotFoundError: No module named 'pysam.libchtslib'
>
>
> ======================================================================
> ERROR: test_inter (unittest.loader._FailedTest.test_inter)
> ----------------------------------------------------------------------
> ImportError: Failed to import test module: test_inter
> Traceback (most recent call last):
> File "/usr/lib/python3.11/unittest/loader.py", line 407, in _find_test_path
> module = self._get_module_from_name(name)
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> File "/usr/lib/python3.11/unittest/loader.py", line 350, in _get_module_from_name
> __import__(name)
> File "/<<PKGBUILDDIR>>/src/tests/test_inter.py", line 3, in <module>
> from svim.SVIM_inter import is_similar
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/svim/SVIM_inter.py", line 8, in <module>
> from svim.SVIM_clustering import consolidate_clusters_bilocal, clusters_from_partitions
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/svim/SVIM_clustering.py", line 11, in <module>
> from pysam import FastaFile
> File "/usr/lib/python3/dist-packages/pysam/__init__.py", line 4, in <module>
> from pysam.libchtslib import *
> ModuleNotFoundError: No module named 'pysam.libchtslib'
>
>
> ======================================================================
> ERROR: test_satag (unittest.loader._FailedTest.test_satag)
> ----------------------------------------------------------------------
> ImportError: Failed to import test module: test_satag
> Traceback (most recent call last):
> File "/usr/lib/python3.11/unittest/loader.py", line 407, in _find_test_path
> module = self._get_module_from_name(name)
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> File "/usr/lib/python3.11/unittest/loader.py", line 350, in _get_module_from_name
> __import__(name)
> File "/<<PKGBUILDDIR>>/src/tests/test_satag.py", line 2, in <module>
> import pysam
> File "/usr/lib/python3/dist-packages/pysam/__init__.py", line 4, in <module>
> from pysam.libchtslib import *
> ModuleNotFoundError: No module named 'pysam.libchtslib'
>
>
> ----------------------------------------------------------------------
> Ran 16 tests in 0.003s
>
> FAILED (errors=5)
> E: pybuild pybuild:386: test: plugin custom failed with: exit code=1: PYTHONPATH=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build python3.11 -m unittest discover -v src/tests
> I: pybuild base:240: PYTHONPATH=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build python3.10 -m unittest discover -v src/tests
> test_analyze_alignment_file_querysorted (test_Collect.TestCollect) ... ok
> test_bam_iterator (test_Collect.TestCollect) ... ok
> test_retrieve_primary_alignment_from_supplementary (test_Collect.TestCollect) ... ok
> test_retrieve_supplementary_alignment_from_primary (test_Collect.TestCollect) ... ok
> test_downstream_distance_to (test_SVCandidate.DeletionCandidateTestCase) ... ok
> test_get_key (test_SVCandidate.DeletionCandidateTestCase) ... ok
> test_get_source (test_SVCandidate.DeletionCandidateTestCase) ... ok
> test_get_std_pos (test_SVCandidate.DeletionCandidateTestCase) ... ok
> test_get_std_span (test_SVCandidate.DeletionCandidateTestCase) ... ok
> test_get_vcf_entry (test_SVCandidate.DeletionCandidateTestCase) ... ok
> test_accessors (test_Signature.TestSVSignature) ... ok
> test_as_string (test_Signature.TestSVSignature) ... ok
> test_downstream_distance_to (test_Signature.TestSVSignature) ... ok
> test_clustering (test_clustering.TestSVIMClustering) ... ok
> test_partitioning (test_clustering.TestSVIMClustering) ... ok
> test_partitioning_large_distance (test_clustering.TestSVIMClustering) ... ok
> test_scores (test_clustering.TestSVIMClustering) ... ok
> test_simple (test_consensus.TestSVIMConsensus) ... ok
> test_skipping (test_consensus.TestSVIMConsensus) ... ok
> test_guess_file_type (test_input_parsing.TestInputParsing) ... ok
> test_is_similar (test_inter.TestSVIMInter) ... ok
> test_analyze_cigar_indel (test_intra.TestSVIMIntra) ... ok
> test_fetch (test_satag.TestSAExtraction) ... ok
> test_satag_extraction_complete (test_satag.TestSAExtraction) ... ok
> test_satag_length (test_satag.TestSAExtraction) ... ok
>
> ----------------------------------------------------------------------
> Ran 25 tests in 0.707s
>
> OK
> dh_auto_test: error: pybuild --test -i python{version} -p "3.11 3.10" --system=custom "--test-args=PYTHONPATH={build_dir} {interpreter} -m unittest discover -v src/tests" returned exit code 13
The full build log is available from:
http://qa-logs.debian.net/2022/12/20/svim_2.0.0-2_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20221220;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20221220&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
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!
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
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