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 --------------------------------------------------------------------------------
