Debian Med Project
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Summary
Bugs of task bio-ngs
Total bugs: 8
Open bugs: 3
Fixed bugs: 5
Links to other tasks
Tasks overview
Biology 206 (1968)
Phylogeny 11 (150)
Cloud 39 (422)
Covid-19 175 (1770)
Medical data 0 (0)
Dental 2 (18)
Epidemiology 16 (193)
Imaging 201 (936)
Laboratory 0 (0)
Oncology 0 (0)
Pharmacology 1 (30)
Physics 26 (180)
Practice 8 (60)
Psychology 17 (153)
Research 0 (0)
Statistics 8 (12)
Tools 34 (227)
Typesetting 72 (621)
Legend
SeverityDependentSuggested
critical 0 0
grave 0 0
serious 1 0
important 1 0
normal 1 0
minor 0 0
wishlist 0 0

Summary bugs page of task Next generation sequencing

Looking into bugs of this task is recommended*

Open bugs in dependent packages

1 serious, 1 important, 1 normal
bcftools (1) Homepage: https://samtools.github.io/bcftools/ Vcs Debian Med Packaging Team
1144268 Remove depends on sse2-support (baseline now)
htslib (1) Homepage: https://github.com/samtools/htslib Vcs Debian Med Packaging Team
1131493 htslib: CVE-2026-31962 CVE-2026-31963 CVE-2026-31964 CVE-2026-31965 CVE-2026-31966 CVE-2026-31967 CVE-2026-31968 CVE-2026-31969 CVE-2026-31970 CVE-2026-31971 security, upstream
sra-sdk (1) Homepage: https://github.com/ncbi/sra-tools/ Vcs Debian Med Packaging Team
1144917 sra-sdk: autopkgtest regression: Segmentation fault

Open bugs in suggested packages

Done bugs

bedtools (1) Homepage: https://github.com/arq5x/bedtools2 Vcs Debian Med Packaging Team
1105730 bedtools: FTBFS with make --shuffle=random: src/utils/version/version.cpp:2:10: fatal error: version_git.h: No such file or directory ftbfs, sid, trixie, forky
last-align (1) Homepage: https://gitlab.com/mcfrith/last Vcs Debian Med Packaging Team
1048396 last-align: Fails to build source after successful build trixie, forky, sid, ftbfs
picard-tools (1) Homepage: https://broadinstitute.github.io/picard/ Vcs Debian Med Packaging Team
1139484 picard-tools: FTBFS: Test: Test method testCleanSam[1](simple_overhang.sam, 99M1S)(picard.sam.CleanSamTest) produced standard out/err: Ignoring SAM validation error: ERROR::CIGAR_MAPS_OFF_REFERENCE:Read name simple_overhang, Read CIGAR M operator maps off end of reference forky, ftbfs, sid
rna-star (1) Homepage: https://github.com/alexdobin/STAR/ Vcs Debian Med Packaging Team
1143695 rna-star: FTBFS: readLoad.cpp:19:14: error: no match for 'operator>>' (operand types are 'std::istringstream' {aka 'std::__cxx11::basic_istringstream<char>'} and 'char*') forky, ftbfs, sid
velvet (1) Homepage: https://github.com/dzerbino/velvet Vcs Debian Med Packaging Team
1105569 velvet: FTBFS with make --shuffle=reverse: Fatal error: can't create obj/autoOpen.o: No such file or directory sid, trixie, ftbfs, forky
*To estimate the overall status of the packages in the dependencies of a metapackage a weighted severity is calculated. Done bugs are ignored and bugs in dependent and recommended packages are weighted by factor three compared to suggested packages. Release critical bugs have a much larger weight than important, while the contribution of normal bugs is even smaller and minor bugs have a very small weight. Wishlist bugs are ignored in this calculation. The resulting sum is compared to some boundaries to find a verbal form. The actual numbers need some adjustment to make real sense - this evaluation method is in testing phase.
The severities of bugs are weighted as follows:
critical10
grave10
serious10
important5
normal3
minor1
wishlist0
Last update: Wed, 02 Sep 2026 04:37:45 -0000