Your message dated Tue, 20 Dec 2022 21:27:12 +0000
with message-id <e1p7k8m-005fvs...@fasolo.debian.org>
and subject line Bug#1026580: fixed in svim 2.0.0-3
has caused the Debian Bug report #1026580,
regarding svim: FTBFS: ModuleNotFoundError: No module named 'pysam.libchtslib'
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
1026580: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1026580
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: svim
Version: 2.0.0-2
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lu...@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=lu...@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20221220&fusertaguser=lu...@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.
--- End Message ---
--- Begin Message ---
Source: svim
Source-Version: 2.0.0-3
Done: Nilesh Patra <nil...@debian.org>
We believe that the bug you reported is fixed in the latest version of
svim, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1026...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Nilesh Patra <nil...@debian.org> (supplier of updated svim package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Wed, 21 Dec 2022 02:30:09 +0530
Source: svim
Architecture: source
Version: 2.0.0-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Nilesh Patra <nil...@debian.org>
Closes: 1026580
Changes:
svim (2.0.0-3) unstable; urgency=medium
.
[ Andreas Tille ]
* Revert "Add missing build dependency on dh addon."
.
[ Nilesh Patra ]
* B-D and test dep on default python3 version as pysam
is not compatible with python3.11 yet (Closes: #1026580)
* Bump Standards-Version to 4.6.1 (no changes needed)
Checksums-Sha1:
ab6a02751ba0b2ecb749326c3888951fec14807c 1467 svim_2.0.0-3.dsc
4477c1dae1d39fd18dc042a22fcbd48ac144af41 4216 svim_2.0.0-3.debian.tar.xz
22be3b6b1a733a2dd496fe5fb5ad9e4167e9b7a7 9526 svim_2.0.0-3_amd64.buildinfo
Checksums-Sha256:
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svim_2.0.0-3.dsc
f9bf14f85fd88844703c2b6ac62340d0263455f46404885e1f371fdd4d7b61cf 4216
svim_2.0.0-3.debian.tar.xz
fd3eb6a8737294be861f153857201dc882241de02a170b5107acad4dec369e95 9526
svim_2.0.0-3_amd64.buildinfo
Files:
9d79e8f231a0b01c91fbb6b69f6cacd1 1467 science optional svim_2.0.0-3.dsc
d7bc9aa97b06e6c1bac859826de67ada 4216 science optional
svim_2.0.0-3.debian.tar.xz
897e7c746413f180a3a54e09c54edcc5 9526 science optional
svim_2.0.0-3_amd64.buildinfo
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--- End Message ---
