[Debian-med-packaging] Bug#1120205: python-pysam: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.13 returned exit code 13
Santiago Vila
sanvila at debian.org
Thu Nov 6 12:00:11 GMT 2025
Package: src:python-pysam
Version: 0.23.0+ds-1
Severity: serious
Tags: ftbfs forky sid
Dear maintainer:
During a rebuild of all packages in unstable, this package failed to build.
Below you will find the last part of the build log (probably the most
relevant part, but not necessarily). If required, the full build log
is available here:
https://people.debian.org/~sanvila/build-logs/202511/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you cannot reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:python-pysam, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
debian/rules clean
cd tests/pysam_data && /usr/bin/make clean
make[1]: Entering directory '/<<PKGBUILDDIR>>/tests/pysam_data'
rm -fr *.bai *.csi *.fai *.gzi *.pileup* [A-Za-z]*.cram *.crai \
all.lock all.stamp *~ calDepth *.dSYM pysam_*.sam \
ex2.sam ex2.sam.gz ex1.sam ex1.fa.gz \
with_md.sam.gz \
*.fq.gz
make[1]: Leaving directory '/<<PKGBUILDDIR>>/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make clean
make[1]: Entering directory '/<<PKGBUILDDIR>>/tests/cbcf_data'
rm -rf all.lock all.stamp *.gz *.tbi *.csi *.bcf
make[1]: Leaving directory '/<<PKGBUILDDIR>>/tests/cbcf_data'
find . -name "*.pyc" -delete
find . -name "*.pyxbldc" -delete
[... snipped ...]
[bam_fillmd1] different NM for read 'EAS114_30:6:238:803:383': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_105:3:232:364:583': 0 -> 3
[bam_fillmd1] different NM for read 'B7_595:2:29:729:70': 3 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:6:220:809:850': 4 -> 6
[bam_fillmd1] different NM for read 'EAS54_65:2:264:157:150': 3 -> 5
[bam_fillmd1] different NM for read 'B7_595:8:26:242:35': 2 -> 1
[bam_fillmd1] different NM for read 'B7_610:7:34:144:868': 4 -> 5
[bam_fillmd1] different NM for read 'B7_597:8:147:360:141': 1 -> 2
[bam_fillmd1] different NM for read 'EAS139_19:2:82:154:1333': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_63:3:41:468:459': 0 -> 3
[bam_fillmd1] different NM for read 'EAS1_97:4:274:287:423': 0 -> 1
[bam_fillmd1] different NM for read 'EAS114_30:2:303:428:326': 0 -> 1
[bam_fillmd1] different NM for read 'EAS54_71:8:105:854:975': 0 -> 3
gunzip < with_md.sam.gz > with_md.sam
samtools view --no-PG -bo with_md.bam with_md.sam
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
samtools index with_md.bam
samtools view --no-PG -bu -o uncompressed.bam ex2.sam
samtools view --no-PG -bo MM-chebi.bam MM-chebi.sam
samtools view --no-PG -bo MM-double.bam MM-double.sam
samtools view --no-PG -bo MM-explicit.bam MM-explicit.sam
samtools view --no-PG -bo MM-multi.bam MM-multi.sam
samtools view --no-PG -bo MM-orient.bam MM-orient.sam
samtools view --no-PG -bo ex10.bam ex10.sam
samtools view --no-PG -bo ex3.bam ex3.sam
samtools view --no-PG -bo ex4.bam ex4.sam
samtools view --no-PG -bo ex5.bam ex5.sam
samtools view --no-PG -bo ex6.bam ex6.sam
samtools view --no-PG -bo ex8.bam ex8.sam
samtools view --no-PG -bo ex9_fail.bam ex9_fail.sam
samtools view --no-PG -bo ex9_nofail.bam ex9_nofail.sam
samtools view --no-PG -bo ex_spliced.bam ex_spliced.sam
samtools view --no-PG -bo example_aligned_pairs.bam example_aligned_pairs.sam
samtools view --no-PG -bo example_btag.bam example_btag.sam
samtools view --no-PG -bo example_dash_in_chr.bam example_dash_in_chr.sam
samtools view --no-PG -bo example_empty_header.bam example_empty_header.sam
samtools view --no-PG -bo example_empty_with_header.bam example_empty_with_header.sam
samtools view --no-PG -bo example_reverse_complement.bam example_reverse_complement.sam
touch tmp.list
samtools view --no-PG -bo example_unmapped_reads_no_sq.bam -t tmp.list example_unmapped_reads_no_sq.sam
rm -f tmp.list
samtools view --no-PG -bo issue100.bam issue100.sam
samtools view --no-PG -bo rg_with_tab.bam rg_with_tab.sam
samtools view --no-PG -bo softclip.bam softclip.sam
samtools view --no-PG -bo tag_bug.bam tag_bug.sam
samtools view --no-PG -bo test_mapped_unmapped.bam test_mapped_unmapped.sam
samtools view --no-PG -bo test_query_position.bam test_query_position.sam
samtools view --no-PG -bo test_unaligned.bam test_unaligned.sam
samtools index MM-chebi.bam
samtools index MM-double.bam
samtools index MM-explicit.bam
samtools index MM-multi.bam
samtools index MM-orient.bam
samtools index ex10.bam
samtools index ex3.bam
samtools index ex4.bam
samtools index ex5.bam
samtools index ex6.bam
samtools index ex8.bam
samtools index ex9_fail.bam
samtools index ex9_nofail.bam
samtools index ex_spliced.bam
samtools index example_aligned_pairs.bam
samtools index example_btag.bam
samtools index example_dash_in_chr.bam
samtools index example_empty_header.bam
samtools index example_empty_with_header.bam
samtools index example_reverse_complement.bam
samtools index example_unmapped_reads_no_sq.bam
samtools index issue100.bam
samtools index rg_with_tab.bam
samtools index softclip.bam
samtools index tag_bug.bam
samtools index test_mapped_unmapped.bam
samtools index test_query_position.bam
samtools index test_unaligned.bam
samtools view --no-PG -Co ex1.cram -T ex1.fa ex1.sam
samtools view --no-PG -Co ex2.cram -T ex1.fa ex2.sam
samtools view --no-PG -Co ex3.cram -T ex1.fa ex3.sam
samtools index ex1.cram
samtools index ex2.cram
samtools index ex3.cram
cp ex1.bam example_bai.bam
samtools index example_bai.bam
mv example_bai.bam.bai example_bai.bai
dd if=ex2.bam of=ex2_truncated.bam bs=$((`wc -c < ex2.bam`-512)) count=1
1+0 records in
1+0 records out
122288 bytes (122 kB, 119 KiB) copied, 0.00014754 s, 829 MB/s
(bgzip -d < ex2.bam; printf '\37\0\0\0\1\0\0\0') | bgzip > ex2_corrupt.bam
grep "^@" ex2.sam | samtools view --no-PG -bo empty.bam -
samtools index empty.bam
cp ex1.bam explicit_index.bam
cp ex1.cram explicit_index.cram
gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz
bgzip < ex1.fa > ex1.fa.gz
samtools faidx ex1.fa.gz
cp ex1.bam ex1_csi.bam
samtools index -c ex1_csi.bam
touch all.stamp
rm with_md.sam
make[2]: Leaving directory '/<<PKGBUILDDIR>>/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make all
make[2]: Entering directory '/<<PKGBUILDDIR>>/tests/cbcf_data'
bgzip < example_vcf40.vcf > example_vcf40.vcf.gz
tabix -f -p vcf example_vcf40.vcf.gz # create tbi index
bcftools index -f example_vcf40.vcf.gz # create csi index
bgzip < example_vcf42.vcf > example_vcf42.vcf.gz
tabix -f -p vcf example_vcf42.vcf.gz # create tbi index
bcftools index -f example_vcf42.vcf.gz # create csi index
bgzip < example_vcf42_only_header.vcf > example_vcf42_only_header.vcf.gz
tabix -f -p vcf example_vcf42_only_header.vcf.gz # create tbi index
bcftools index -f example_vcf42_only_header.vcf.gz # create csi index
bgzip < example_vcf42_withcontigs.vcf > example_vcf42_withcontigs.vcf.gz
tabix -f -p vcf example_vcf42_withcontigs.vcf.gz # create tbi index
bcftools index -f example_vcf42_withcontigs.vcf.gz # create csi index
bgzip < example_vcf43.vcf > example_vcf43.vcf.gz
tabix -f -p vcf example_vcf43.vcf.gz # create tbi index
bcftools index -f example_vcf43.vcf.gz # create csi index
bgzip < example_vcf43_with_utf8.vcf > example_vcf43_with_utf8.vcf.gz
tabix -f -p vcf example_vcf43_with_utf8.vcf.gz # create tbi index
bcftools index -f example_vcf43_with_utf8.vcf.gz # create csi index
bgzip < gnomad.vcf > gnomad.vcf.gz
tabix -f -p vcf gnomad.vcf.gz # create tbi index
bcftools index -f gnomad.vcf.gz # create csi index
bgzip < gnomad_fixed.vcf > gnomad_fixed.vcf.gz
tabix -f -p vcf gnomad_fixed.vcf.gz # create tbi index
bcftools index -f gnomad_fixed.vcf.gz # create csi index
bgzip < missing_genotypes.vcf > missing_genotypes.vcf.gz
tabix -f -p vcf missing_genotypes.vcf.gz # create tbi index
bcftools index -f missing_genotypes.vcf.gz # create csi index
bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf
bcftools index -f example_vcf40.bcf
bcftools view -O b example_vcf42.vcf.gz -o example_vcf42.bcf
bcftools index -f example_vcf42.bcf
bcftools view -O b example_vcf42_only_header.vcf.gz -o example_vcf42_only_header.bcf
bcftools index -f example_vcf42_only_header.bcf
bcftools view -O b example_vcf42_withcontigs.vcf.gz -o example_vcf42_withcontigs.bcf
bcftools index -f example_vcf42_withcontigs.bcf
bcftools view -O b example_vcf43.vcf.gz -o example_vcf43.bcf
bcftools index -f example_vcf43.bcf
bcftools view -O b example_vcf43_with_utf8.vcf.gz -o example_vcf43_with_utf8.bcf
bcftools index -f example_vcf43_with_utf8.bcf
bcftools view -O b gnomad.vcf.gz -o gnomad.bcf
bcftools index -f gnomad.bcf
bcftools view -O b gnomad_fixed.vcf.gz -o gnomad_fixed.bcf
[W::bcf_hdr_check_sanity] PL should be declared as Number=G
bcftools index -f gnomad_fixed.bcf
[W::bcf_hdr_check_sanity] PL should be declared as Number=G
bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf
bcftools index -f missing_genotypes.bcf
touch all.stamp
make[2]: Leaving directory '/<<PKGBUILDDIR>>/tests/cbcf_data'
dh_auto_test
I: pybuild base:311: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pysam/build; python3.13 -m pytest tests
============================= test session starts ==============================
platform linux -- Python 3.13.9, pytest-8.4.2, pluggy-1.6.0 -- /usr/bin/python3.13
cachedir: .pytest_cache
rootdir: /<<PKGBUILDDIR>>
configfile: setup.cfg
plugins: typeguard-4.4.4
collecting ... collected 0 items / 15 errors
==================================== ERRORS ====================================
_ ERROR collecting .pybuild/cpython3_3.13_pysam/build/tests/AlignedSegment_test.py _
tests/AlignedSegment_test.py:2: in <module>
import pysam
pysam/__init__.py:21: in <module>
from pysam.libcalignedsegment import *
E AttributeError: module 'pysam.libcalignedsegment' has no attribute 'CMATCH'
_ ERROR collecting .pybuild/cpython3_3.13_pysam/build/tests/AlignmentFileHeader_test.py _
tests/AlignmentFileHeader_test.py:13: in <module>
import pysam
pysam/__init__.py:21: in <module>
from pysam.libcalignedsegment import *
E AttributeError: module 'pysam.libcalignedsegment' has no attribute 'CMATCH'
_ ERROR collecting .pybuild/cpython3_3.13_pysam/build/tests/AlignmentFilePileup_test.py _
tests/AlignmentFilePileup_test.py:3: in <module>
import pysam
pysam/__init__.py:21: in <module>
from pysam.libcalignedsegment import *
E AttributeError: module 'pysam.libcalignedsegment' has no attribute 'CMATCH'
_ ERROR collecting .pybuild/cpython3_3.13_pysam/build/tests/AlignmentFile_test.py _
tests/AlignmentFile_test.py:20: in <module>
import pysam
pysam/__init__.py:21: in <module>
from pysam.libcalignedsegment import *
E AttributeError: module 'pysam.libcalignedsegment' has no attribute 'CMATCH'
_ ERROR collecting .pybuild/cpython3_3.13_pysam/build/tests/StreamFiledescriptors_test.py _
tests/StreamFiledescriptors_test.py:6: in <module>
from pysam import AlignmentFile
pysam/__init__.py:21: in <module>
from pysam.libcalignedsegment import *
E AttributeError: module 'pysam.libcalignedsegment' has no attribute 'CMATCH'
_ ERROR collecting .pybuild/cpython3_3.13_pysam/build/tests/VariantFile_test.py _
tests/VariantFile_test.py:6: in <module>
import pysam
pysam/__init__.py:21: in <module>
from pysam.libcalignedsegment import *
E AttributeError: module 'pysam.libcalignedsegment' has no attribute 'CMATCH'
_ ERROR collecting .pybuild/cpython3_3.13_pysam/build/tests/VariantRecord_test.py _
tests/VariantRecord_test.py:1: in <module>
import pysam
pysam/__init__.py:21: in <module>
from pysam.libcalignedsegment import *
E AttributeError: module 'pysam.libcalignedsegment' has no attribute 'CMATCH'
__ ERROR collecting .pybuild/cpython3_3.13_pysam/build/tests/compile_test.py ___
tests/compile_test.py:12: in <module>
import pysam
pysam/__init__.py:21: in <module>
from pysam.libcalignedsegment import *
E AttributeError: module 'pysam.libcalignedsegment' has no attribute 'CMATCH'
___ ERROR collecting .pybuild/cpython3_3.13_pysam/build/tests/faidx_test.py ____
tests/faidx_test.py:1: in <module>
import pysam
pysam/__init__.py:21: in <module>
from pysam.libcalignedsegment import *
E AttributeError: module 'pysam.libcalignedsegment' has no attribute 'CMATCH'
__ ERROR collecting .pybuild/cpython3_3.13_pysam/build/tests/linking_test.py ___
tests/linking_test.py:7: in <module>
import pysam
pysam/__init__.py:21: in <module>
from pysam.libcalignedsegment import *
E AttributeError: module 'pysam.libcalignedsegment' has no attribute 'CMATCH'
__ ERROR collecting .pybuild/cpython3_3.13_pysam/build/tests/samtools_test.py __
tests/samtools_test.py:16: in <module>
import pysam
pysam/__init__.py:21: in <module>
from pysam.libcalignedsegment import *
E AttributeError: module 'pysam.libcalignedsegment' has no attribute 'CMATCH'
___ ERROR collecting .pybuild/cpython3_3.13_pysam/build/tests/tabix_test.py ____
tests/tabix_test.py:11: in <module>
import pysam
pysam/__init__.py:21: in <module>
from pysam.libcalignedsegment import *
E AttributeError: module 'pysam.libcalignedsegment' has no attribute 'CMATCH'
_ ERROR collecting .pybuild/cpython3_3.13_pysam/build/tests/tabixproxies_test.py _
tests/tabixproxies_test.py:2: in <module>
import pysam
pysam/__init__.py:21: in <module>
from pysam.libcalignedsegment import *
E AttributeError: module 'pysam.libcalignedsegment' has no attribute 'CMATCH'
_ ERROR collecting .pybuild/cpython3_3.13_pysam/build/tests/test_samtools_python.py _
tests/test_samtools_python.py:1: in <module>
import pysam
pysam/__init__.py:21: in <module>
from pysam.libcalignedsegment import *
E AttributeError: module 'pysam.libcalignedsegment' has no attribute 'CMATCH'
_ ERROR collecting .pybuild/cpython3_3.13_pysam/build/tests/typechecking_test.py _
tests/typechecking_test.py:7: in <module>
import pysam
pysam/__init__.py:21: in <module>
from pysam.libcalignedsegment import *
E AttributeError: module 'pysam.libcalignedsegment' has no attribute 'CMATCH'
=========================== short test summary info ============================
ERROR tests/AlignedSegment_test.py - AttributeError: module 'pysam.libcaligne...
ERROR tests/AlignmentFileHeader_test.py - AttributeError: module 'pysam.libca...
ERROR tests/AlignmentFilePileup_test.py - AttributeError: module 'pysam.libca...
ERROR tests/AlignmentFile_test.py - AttributeError: module 'pysam.libcaligned...
ERROR tests/StreamFiledescriptors_test.py - AttributeError: module 'pysam.lib...
ERROR tests/VariantFile_test.py - AttributeError: module 'pysam.libcalignedse...
ERROR tests/VariantRecord_test.py - AttributeError: module 'pysam.libcaligned...
ERROR tests/compile_test.py - AttributeError: module 'pysam.libcalignedsegmen...
ERROR tests/faidx_test.py - AttributeError: module 'pysam.libcalignedsegment'...
ERROR tests/linking_test.py - AttributeError: module 'pysam.libcalignedsegmen...
ERROR tests/samtools_test.py - AttributeError: module 'pysam.libcalignedsegme...
ERROR tests/tabix_test.py - AttributeError: module 'pysam.libcalignedsegment'...
ERROR tests/tabixproxies_test.py - AttributeError: module 'pysam.libcaligneds...
ERROR tests/test_samtools_python.py - AttributeError: module 'pysam.libcalign...
ERROR tests/typechecking_test.py - AttributeError: module 'pysam.libcaligneds...
!!!!!!!!!!!!!!!!!!! Interrupted: 15 errors during collection !!!!!!!!!!!!!!!!!!!
============================== 15 errors in 0.26s ==============================
E: pybuild pybuild:389: test: plugin distutils failed with: exit code=2: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pysam/build; python3.13 -m pytest tests
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.13 returned exit code 13
make[1]: *** [debian/rules:31: override_dh_auto_test] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:22: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
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