Summary

Bugs of task bio-dev

Total bugs: 174

Open bugs: 136

Fixed bugs: 38

Links to other tasks

Tasks overview

Biology 287 (2532)

Biology development 136 (1184)

Next generation sequencing 8 (87)

Phylogeny 7 (54)

Cloud 46 (504)

Content management 0 (0)

Covid-19 180 (1800)

Medical data 2 (10)

Dental 2 (12)

Epidemiology 11 (102)

Hospital information systems 1 (9)

Imaging 198 (826)

Imaging development 79 (576)

Laboratory 1 (9)

Oncology 1 (3)

Pharmacology 1 (9)

Physics 27 (192)

Practice 8 (51)

Psychology 12 (121)

Rehabilitation 0 (0)

Research 0 (0)

Statistics 4 (16)

Tools 39 (240)

Typesetting 68 (543)

Legend

Severity	Dependent	Suggested
critical	0	0
grave	0	1
serious	9	14
important	17	3
normal	45	6
minor	22	5
wishlist	12	2

Summary bugs page of task Biology development

Immediately looking into bugs of the dependencies of this task is advised (1184)^*

Open bugs in dependent packages

9 serious, 17 important, 45 normal, 22 minor, 12 wishlist

bamtools (1) Homepage: https://github.com/pezmaster31/bamtools/wiki Vcs Debian Med Packaging Team
865130	reapr FTBFS on big endian: Error sampling from files '00.Sample/fragCov.gz', '00.assembly.fa.gc.gz'	ftbfs, upstream
bioperl-run (1) Homepage: https://metacpan.org/release/BioPerl-Run Vcs Debian Med Packaging Team
1077454	bioperl-run: FTBFS: dh_auto_test: error: /usr/bin/perl Build test --verbose 1 returned exit code 255	confirmed, ftbfs, sid, trixie, upstream
cdk (1) Homepage: https://cdk.github.io/ Vcs Debian Java Maintainers
1081606	cdk: run upstream tests during build	help
cwltool (1) Homepage: https://cwltool.readthedocs.io/ Vcs Debian Med Packaging Team
1083349	cwltool: (build-)depends on deprecated module python3-pkg-resources	sid, trixie
fermi-lite (2) Homepage: https://github.com/lh3/fermi-lite Vcs Debian Med Packaging Team
1044647	fermi-lite: Fails to build source after successful build	ftbfs, sid, trixie
1049564	fermi-lite: Fails to build binary packages again after successful build	ftbfs, sid, trixie
gatb-core (2) Homepage: https://github.com/GATB/gatb-core Vcs Debian Med Packaging Team
929564	gatb-core-testdata: broken symlink: /usr/share/doc/gatb-core/test/gatb-core-cppunit -> ../../../../lib/gatb-core/gatb-core-cppunit
983926	gatb-core: ftbfs with -march=x86-64-v2
hdf5 (23) Homepage: http://hdfgroup.org/HDF5/ Vcs Gilles Filippini
638753	libhdf5-serial-1.8.7: threadsafe memory leaks	moreinfo
715959	[Mayhem] Bug report on hdf5-tools: gif2h5 crashes with exit status 139
716008	[Mayhem] Bug report on hdf5-tools: h5copy crashes with exit status 139
716010	[Mayhem] Bug report on hdf5-tools: h5diff crashes with exit status 139
716011	[Mayhem] Bug report on hdf5-tools: h5dump crashes with exit status 139
716012	[Mayhem] Bug report on hdf5-tools: h5import crashes with exit status 139
740613	libhdf5-7: Please include support for compression with libaec
748587	Duplicate and conflicting definitions of variable FILENAME	upstream
839784	libhdf5-dev: pkg-config file references ONLY the C library
915807	hdf5: CVE-2017-17507	security, upstream
958174	hdf5: please add the hdf5plugins
968559	libhdf5-openmpi-dev: hdf5-mpi.pc alternative sometimes goes missing	moreinfo
1023446	libhdf5-openmpi-dev: h5pcc configured as static build
1023820	hdf5: Dependencies not tight enough
1031726	hdf5: CVE-2022-26061 CVE-2022-25972 CVE-2022-25942	security, upstream
1034807	hdf5: CVE-2018-11205	security, upstream
1034838	hdf5: CVE-2019-8396 CVE-2019-8398	security
1040862	hdf5: S3 VFD pulls in networking dependencies (libcurl), please package it as a VFD plugin
1052250	pkg-config file incorrect for static linking
1063856	hdf5: new upstream release
1067758	Please provide a nojava build profile
1067789	hdf5: diff for NMU version 1.10.10+repack-3.2	patch, pending
1067950	hdf5: diff for NMU version 1.10.10+repack-3.3	patch, pending
htseq (1) Homepage: https://www-huber.embl.de/users/anders/HTSeq/doc/overview.html Vcs Debian Med Packaging Team
1085638	htseq: Python SyntaxWarning
kmer (1) Homepage: http://kmer.sourceforge.net Vcs Debian Med Packaging Team
1081273	meryl: Meryl should be packaged separately from new upstream location
libai-fann-perl (1) Homepage: https://metacpan.org/release/AI-FANN Vcs Debian Perl Group
948463	libai-fann-perl: Integer overflow leading to heap buffer overflow
libbio-das-lite-perl (1) Homepage: http://biodas.org/ Vcs Debian Med Packaging Team
1081376	libbio-das-lite-perl: homepage defunct
libbio-scf-perl (1) Homepage: https://metacpan.org/release/Bio-SCF Vcs Debian Perl Group
599961	libbio-scf-perl: FTBFS: Neither BIG nor LITTLE endian defined
libchado-perl (3) Homepage: http://gmod.org/wiki/Chado Vcs Debian Med Packaging Team
1039562	libchado-perl: fails to access database during installation	wontfix
1047661	libchado-perl: Fails to build source after successful build	ftbfs, sid, trixie
1049705	libchado-perl: Fails to build binary packages again after successful build	ftbfs, sid, trixie
libcifpp (1) Homepage: https://github.com/PDB-REDO/libcifpp Vcs Debian Med Packaging Team
1048817	libcifpp: Fails to build source after successful build	ftbfs, sid, trixie
libnhgri-blastall-perl (1) Homepage: ftp://ftp.nhgri.nih.gov/pub/software/blastall/ Vcs Debian Perl Group
1081295	libnhgri-blastall-perl: homepage defunct
libpwiz (1) Homepage: http://proteowizard.sourceforge.net/downloads.shtml Vcs The Debichem Group
1075199	libpwiz: ftbfs with GCC-14	ftbfs, sid, trixie
librcsb-core-wrapper (1) Homepage: https://sw-tools.rcsb.org/apps/CORE-WRAPPER/index.html Vcs Debian Med Packaging Team
1046372	librcsb-core-wrapper: Fails to build source after successful build	ftbfs, sid, trixie
librostlab (1) Homepage: https://rostlab.org/ Vcs Debian Med Packaging Team
1047025	librostlab: Fails to build source after successful build	ftbfs, sid, trixie
libsbml (1) Homepage: http://www.sbml.org/ Vcs Debian Med Packaging Team
1079883	libsbml: please drop mono support
libslow5lib (3) Homepage: https://github.com/hasindu2008/slow5lib Vcs Debian Med Packaging Team
1048497	libslow5lib: Fails to build source after successful build	ftbfs, sid, trixie
1049769	libslow5lib: Fails to build binary packages again after successful build	ftbfs, sid, trixie
1069771	libslow5lib FTBFS on big endian architectures	ftbfs
libvcflib (2) Homepage: https://github.com/vcflib/vcflib Vcs Debian Med Packaging Team
1073098	math-numeric-tower-clojure: build-depends on markdown	pending
1074044	libvcflib: Improve support for loongarch64	patch, pending
libzerg-perl (1) Homepage: https://tracker.debian.org/libzerg-perl Vcs Debian Med Packaging Team
1081848	libzerg-perl: homepage defunct
macromoleculebuilder (1) Homepage: https://simtk.org/projects/rnatoolbox Vcs Debichem Team
1086362	macromoleculebuilder: FTBFS: /usr/bin/ld: libMMB.so.4.0: undefined reference to `gzerror'	ftbfs
mcl (1) Homepage: https://micans.org/mcl/ Vcs Debian Med Packaging Team
1046152	mcl: Fails to build source after successful build	ftbfs, sid, trixie
mirtop (1) Homepage: https://github.com/miRTop/mirtop Vcs Debian Med Packaging Team
1085726	mirtop: Python SyntaxWarning
ncbi-tools6 (1) Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/ Vcs Debian Med Packaging Team
225651	ncbi-tools-x11: want Cn3D++
nim-hts (3) Homepage: https://github.com/brentp/hts-nim Vcs Debian Med Packaging Team
1046095	nim-hts: Fails to build source after successful build	ftbfs, sid, trixie
1049588	nim-hts: Fails to build binary packages again after successful build	ftbfs, sid, trixie
1081123	nim-hts: FTBFS with gcc-14	ftbfs, sid, trixie
openmm (2) Homepage: https://simtk.org/projects/openmm Vcs Debichem Team
1080690	Missing Build-Depends on python3-setuptools	sid, trixie
1085752	openmm: Python SyntaxWarning
openms (1) Homepage: http://www.openms.de Vcs The Debichem Group
1068052	openms: FTBFS on armel,armhf (error: âQOpenGLFunctions_2_0â does not name a type)	ftbfs
presto (1) Homepage: https://presto.readthedocs.io Vcs Debian Med Packaging Team
1085789	presto: Python SyntaxWarning
pyfai (3) Homepage: https://github.com/silx-kit/pyFAI Vcs Debian PaN Maintainers
1077400	pyfai: FTBFS: src/pyFAI/ext/sparse_utils.cpython-312-x86_64-linux-gnu.so.p/src/pyFAI/ext/sparse_utils.pyx.c:45695:17: error: assignment to âstruct __pyx_obj_5pyFAI_3ext_12sparse_utils_Vector â from incompatible pointer type âPyObject â {aka âstruct _object *â} [-Wincompatible-pointer-types]	ftbfs, sid, trixie
1078268	pyfai: please make the package build reproducible
1085805	pyfai: Python SyntaxWarning
python-airr (1) Homepage: https://docs.airr-community.org/en/latest/packages/airr-python/overview.html Vcs Debian Python Team
1083596	python-airr: (build-)depends on deprecated module python3-pkg-resources	sid, trixie
python-anndata (1) Homepage: https://github.com/theislab/anndata Vcs Debian Med Packaging Team
1075928	python-anndata: tests fail with scipy 1.13
python-cgecore (2) Homepage: https://bitbucket.org/genomicepidemiology/cge_core_module/ Vcs Debian Med Packaging Team
1084632	python-cgecore: removal of Python standard libraries in Python 3.13
1085895	python-cgecore: Python SyntaxWarning
python-cogent (1) Homepage: https://github.com/cogent3/cogent3 Vcs Debian Med Packaging Team
1058479	python-cogent: please (temporarily) drop python3-numba dependencies	wontfix
python-csb (1) Homepage: https://github.com/csb-toolbox/CSB Vcs Debian Med Packaging Team
1085900	python-csb: Python SyntaxWarning
python-dendropy (1) Homepage: https://dendropy.org/ Vcs Debian Med Packaging Team
1083625	python-dendropy: (build-)depends on deprecated module python3-pkg-resources	sid, trixie
python-loompy (3) Homepage: https://github.com/linnarsson-lab/loompy Vcs Debian Med Packaging Team
1058482	python-loompy: please (temporarily) drop python3-numba dependencies
1083659	python-loompy: (build-)depends on deprecated module python3-pkg-resources	sid, trixie
1085932	python-loompy: Python SyntaxWarning
python-pybedtools (1) Homepage: https://daler.github.io/pybedtools/ Vcs Debian Med Packaging Team
1081673	FTBFS with Python 3.13	fixed-upstream, patch, upstream
python-pysam (1) Homepage: https://pysam.readthedocs.org/en/latest Vcs Debian Med Packaging Team
1087457	python3-pysam: autopkgtest regression with htslib 1.21	upstream
python-pyspoa (1) Homepage: https://github.com/nanoporetech/pyspoa Vcs Debian Med Packaging Team
1045607	python-pyspoa: Fails to build source after successful build	ftbfs, sid, trixie
python-pyvcf (2) Homepage: https://github.com/jamescasbon/PyVCF Vcs Debian Med Packaging Team
1079359	SyntaxWarning: invalid escape sequence '\['	newcomer, upstream
1083698	python-pyvcf: (build-)depends on deprecated module python3-pkg-resources	sid, trixie
python-ruffus (2) Homepage: http://www.ruffus.org.uk/ Vcs Debian Med Packaging Team
1082265	python-ruffus FTBFS with Python 3.13
1086958	python-ruffus: Python SyntaxWarning
python-streamz (2) Homepage: https://github.com/python-streamz/streamz/ Vcs Debian Python Team
1046218	python-streamz: Fails to build source after successful build	ftbfs, sid, trixie
1083714	python-streamz: (build-)depends on deprecated module python3-pkg-resources	sid, trixie
pytorch (5) Homepage: https://pytorch.org/ Vcs Debian Deep Learning Team
983517	pytorch: Build documentation
1057644	pytorch: build for all supported Python versions	wontfix
1083727	pytorch: (build-)depends on deprecated module python3-pkg-resources	sid, trixie
1083729	pytorch: (build-)depends on deprecated module python3-pkg-resources	sid, trixie
1086773	Please drop dependency on python3-astunparse
rdkit (5) Homepage: http://www.rdkit.org Vcs Debichem Team
927955	python-rdkit: missing module pyAvalonTools
1069873	rdkit: FTBFS convert: Unable to read font (/usr/share/fonts/type1/gsfonts/n019003l.pfb).	ftbfs, sid
1077055	postgresql-16-rdkit: inchi support not included in rdkit build	moreinfo
1083076	python3-rdkit: SEGFAULT on import on armhf
1086226	rdkit: autopkgtests fail
reprof (2) Homepage: https://rostlab.org/ Vcs Debian Med Packaging Team
1045897	reprof: Fails to build source after successful build	ftbfs, sid, trixie
1049597	reprof: Fails to build binary packages again after successful build	ftbfs, sid, trixie
ruby-crb-blast (1) Homepage: https://github.com/cboursnell/crb-blast Vcs Debian Ruby Team
1045625	ruby-crb-blast: Fails to build source after successful build	ftbfs, sid, trixie
seqan2 (2) Homepage: https://www.seqan.de/ Vcs Debian Med Packaging Team
917851	seqan2 2.4.0+dfsg-9: FTBFS, alignment problem	ftbfs
1047218	seqan2: Fails to build source after successful build	ftbfs, sid, trixie
seqan3 (1) Homepage: https://www.seqan.de/ Vcs Debian Med Packaging Team
1048951	seqan3: Fails to build source after successful build	ftbfs, sid, trixie
sra-sdk (2) Homepage: https://github.com/ncbi/sra-tools/ Vcs Debian Med Packaging Team
1084404	sra-sdk: move from fuse to fuse3
1087096	sra-sdk: Python SyntaxWarning
toil (3) Homepage: https://github.com/BD2KGenomics/toil Vcs Debian Med Packaging Team
1073358	toil: FTBFS: ModuleNotFoundError: No module named 'boto'	ftbfs, sid, trixie
1084681	toil: removal of Python standard libraries in Python 3.13	fixed-upstream
1087116	toil: Python SyntaxWarning

Open bugs in suggested packages

1 grave, 14 serious, 3 important, 6 normal, 5 minor, 2 wishlist

bbhash (1) Homepage: https://github.com/rizkg/BBHash Vcs Debian Med Packaging Team
1049876	bbhash: FTBFS on 32 bit architectures	ftbfs, sid, trixie
bcbio (2) Homepage: https://github.com/bcbio/bcbio-nextgen Vcs Debian Med Packaging Team
928076	bcbio: Workflows not ready for non-developers to depend on.
1018312	bcbio: build-depends on python3-nose or uses it for autopkgtest	sid, trixie
btllib (3) Homepage: https://github.com/bcgsc/btllib Vcs Debian Med Packaging Team
1022772	btllib: fails to build on 32-bit archs	wontfix
1032358	btllib: Depends on libsdsl-dev, breaking installability when not needed	patch, pending
1058455	btllib: add build support for loongarch64	patch
concurrentqueue (1) Homepage: https://github.com/cameron314/concurrentqueue Vcs Debian Med Packaging Team
1043870	concurrentqueue: Fails to build source after successful build	ftbfs, sid, trixie
genomicsdb (1) Homepage: https://www.genomicsdb.org/ Vcs Debian Med Packaging Team
1086565	genomicsdb: FTBFS with fmtlib 10	ftbfs
intake (3) Homepage: https://github.com/intake/intake Vcs Debian Med Packaging Team
1063953	intake: autopkgtest regression with pytest 8
1064752	intake: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12 3.11" returned exit code 13	ftbfs, sid, trixie
1067969	python3-intake: Please replace python3-appdirs dependency with platformdirs	sid, trixie
libmaus2 (2) Homepage: https://gitlab.com/german.tischler/libmaus2 Vcs Debian Med Packaging Team
934619	libmaus2 FTBFS (mostly 32bit): error: no matching function for call	fixed-upstream, ftbfs, help, upstream
1069691	libmaus2: FTBFS on arm64: what(): AutoArray<unsigned long,alloc_type_memalign_cacheline> failed to allocate 1398102 elements (11184816 bytes)	confirmed, ftbfs, upstream
networkx (1) Homepage: https://networkx.github.io/ Vcs Debian OpenStack
1083502	networkx: (build-)depends on deprecated module python3-pkg-resources	sid, trixie
python-ncls (1) Homepage: https://github.com/biocore-ntnu/ncls Vcs Debian Python Team
1046648	python-ncls: Fails to build source after successful build	ftbfs, sid, trixie
python-pyflow (2) Homepage: https://illumina.github.io/pyflow/ Vcs Debian Med Packaging Team
1080766	Missing Build-Depends on python3-setuptools	sid, trixie, wontfix
1081243	python3-pyflow: helloWorld and other examples not runnable, possibly since python2 dropped	upstream, wontfix
python-seqcluster (1) Homepage: https://github.com/lpantano/seqcluster Vcs Debian Med Packaging Team
1035277	python-seqcluster: please add autopkgtests (to add coverage for python3-numpy)
q2-alignment (1) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1076318	q2-alignment hard-codes python 3.11 without depending on it	sid, trixie
q2cli (1) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1076080	q2cli: FTBFS in sid (python3.12)	ftbfs
q2-demux (1) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1076315	q2-demux hard-codes python 3.11 without depending on it	sid, trixie
q2-feature-classifier (1) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1071882	q2-feature-classifier: FTBFS: unsatisfiable build-dependencies	ftbfs
q2-phylogeny (1) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1076317	q2-phylogeny hard-codes python 3.11 without depending on it
q2-quality-control (1) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1076914	q2-quality-control: FTBFS: rm: cannot remove '/<<PKGBUILDDIR>>/debian//usr/lib/python3/dist-packages/run_decontam.R': No such file or directory	ftbfs
q2-types (2) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1065333	q2-types: test data heavily outweighs actual code
1076316	q2-types hard-codes python 3.11 without depending on it	sid, trixie
qiime (2) Homepage: https://qiime2.org Vcs Debian Med Packaging Team
1076314	qiime hard-codes python 3.11 without depending on it	sid, trixie
1084668	qiime: removal of Python standard libraries in Python 3.13
r-bioc-mofa (1) Homepage: https://bioconductor.org/packages/MOFA/ Vcs Debian R Packages Maintainers
1085689	r-bioc-mofa: Python SyntaxWarning
r-bioc-org.hs.eg.db (1) Homepage: https://bioconductor.org/packages/data/experiment/org.Hs.eg.db/ Vcs Debian R Packages Maintainers
1083247	r-bioc-org.hs.eg.db: homepage defunct, standardize
sumalibs (1) Homepage: https://git.metabarcoding.org/obitools/sumalibs Vcs Debian Med Packaging Team
1075544	sumalibs: ftbfs with GCC-14	ftbfs, sid, trixie

Done bugs

biojava6-live (1) Homepage: https://www.biojava.org Vcs Debian Med Packaging Team
1078612	biojava6-live: will FTBFS during trixie support period	ftbfs
consensuscore (1) Homepage: https://github.com/PacificBiosciences/ConsensusCore Vcs Debian Med Packaging Team
1067499	libconsensuscore-dev: ships /usr/include/meson.build
ffindex (2) Homepage: https://github.com/ahcm/ffindex Vcs Debian Med Packaging Team
1084923	ffindex: Drop openmpi for 32-bit systems
1086910	ffindex: depends on openmpi on 32-bit architectures
genomicsdb (1) Homepage: https://www.genomicsdb.org/ Vcs Debian Med Packaging Team
1079485	libgenomicsdb1: Built with default MPI, but depends on openmpi-bin
gfapy (1) Homepage: https://github.com/ggonnella/gfapy Vcs Debian Med Packaging Team
1085607	gfapy: Python SyntaxWarning
gffread (1) Homepage: https://ccb.jhu.edu/software/stringtie/gff.shtml Vcs Debian Med Packaging Team
1033703	gffread: autopkgtest regression: test dependency not in testing	bookworm-ignore
htsjdk (1) Homepage: https://samtools.github.io/htsjdk/ Vcs Debian Med Packaging Team
1055447	htsjdk: FTBFS: 35741 tests completed, 9 failed, 10 skipped	bookworm, ftbfs, sid, trixie
htslib (3) Homepage: https://github.com/samtools/htslib Vcs Debian Med Packaging Team
1086364	metabat: FTBFS: Package 'bzip2', required by 'htslib', not found	ftbfs, sid, trixie
1086367	libhts-dev: Missing dependency on libbz2-dev	ftbfs
1086368	libhts-dev: Missing dependency on libbz2-dev	ftbfs
libbio-db-hts-perl (1) Homepage: https://metacpan.org/release/Bio-DB-HTS Vcs Debian Med Packaging Team
1086359	libbio-db-hts-perl: FTBFS: This module requires HTSlib (http://htslib.org/)	ftbfs, sid, trixie
libpdb-redo (3) Homepage: https://github.com/PDB-REDO/libpdb-redo Vcs Debian Med Packaging Team
1046388	libpdb-redo: Fails to build source after successful build	ftbfs, sid, trixie
1085426	libpdb-redo: FTBFS: error: âProgressâ is not a member of âcifâ; did you mean âprogress_barâ	ftbfs, sid, trixie
1086519	libpdb-redo3 - hardcoded dependency on libcifpp5
libssw (1) Homepage: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library Vcs Debian Med Packaging Team
1015525	libssw: ftbfs with LTO (link time optimization) enabled	experimental, sid, trixie
mirtop (1) Homepage: https://github.com/miRTop/mirtop Vcs Debian Med Packaging Team
1084347	python-seqcluster: FTBFS: ModuleNotFoundError: No module named 'six'	ftbfs, sid, trixie
ncbi-vdb (1) Homepage: https://github.com/ncbi/ncbi-vdb Vcs Debian Med Packaging Team
1075868	ncbi-vdb: FTBFS with MbedTLS 3.6	ftbfs
pbseqlib (1) Homepage: https://github.com/PacificBiosciences/blasr_libcpp Vcs Debian Med Packaging Team
1086515	pbseqlib: Please drop BD on libbz2-dev
propka (1) Homepage: http://propka.org Vcs Debian Med Packaging Team
1083559	propka: (build-)depends on deprecated module python3-pkg-resources	sid, trixie
python-bcbio-gff (1) Homepage: https://github.com/chapmanb/bcbb/tree/master/gff Vcs Debian Med Packaging Team
1085892	python-bcbio-gff: Python SyntaxWarning
python-biopython (1) Homepage: https://biopython.org Vcs Debian Med Packaging Team
1086156	ftbfs: test failure: DSSP failed to produce an output	ftbfs
python-pbcore (1) Homepage: https://github.com/PacificBiosciences/pbcore Vcs Debian Med Packaging Team
1083675	python-pbcore: (build-)depends on deprecated module python3-pkg-resources	sid, trixie
python-pyfaidx (1) Homepage: https://github.com/mdshw5/pyfaidx Vcs Debian Med Packaging Team
1083691	python-pyfaidx: (build-)depends on deprecated module python3-pkg-resources	sid, trixie
python-pyflow (1) Homepage: https://illumina.github.io/pyflow/ Vcs Debian Med Packaging Team
1054591	python3-pyflow: ${VERSION} not expanded in package metadata, causing PEP-440 validation failures
python-treetime (1) Homepage: https://github.com/neherlab/treetime Vcs Debian Med Packaging Team
1086965	python-treetime: Python SyntaxWarning
pytorch (5) Homepage: https://pytorch.org/ Vcs Debian Deep Learning Team
994423	pytorch: Baseline violation on armhf	bookworm, bullseye, experimental, ftbfs, sid, trixie
1056388	FTBFS with fmtlib 10	fixed-upstream, ftbfs
1060097	pytorch: FBFS: /<<PKGBUILDDIR>>/aten/src/ATen/native/quantized/cpu/qlinear_prepack.cpp:249:103: error: cannot convert âdnnl::memory::data_typeâ to âconst ideep::dims&â {aka âconst std::vector<long int>&â}	ftbfs
1070379	pytorch: CVE-2024-31580 CVE-2024-31583 CVE-2024-31584	security, upstream
1085004	pytorch: FTBFS: error: no matching function for call to âllvm::TargetMachine::registerPassBuilderCallbacks(llvm::PassBuilder&, bool)â	ftbfs
r-bioc-annotationhub (1) Homepage: https://bioconductor.org/packages/AnnotationHub/ Vcs Debian R Packages Maintainers
1034852	r-bioc-annotationhub: autopkgtest regression: download failed	bookworm-ignore
r-bioc-biomart (1) Homepage: https://bioconductor.org/packages/biomaRt/ Vcs Debian R Packages Maintainers
1039501	r-bioc-biomart: autopkgtest regression: Failure ('test_ensembl_ssl_settings.R:71')
r-bioc-structuralvariantannotation (1) Homepage: https://bioconductor.org/packages/StructuralVariantAnnotation/ Vcs Debian R Packages Maintainers
1025045	r-bioc-structuralvariantannotation: Test failures in autopkgtest	bookworm-ignore, upstream
rdkit (1) Homepage: http://www.rdkit.org Vcs Debichem Team
1085248	src:rdkit: fails to migrate to testing for too long	sid, trixie
relion (1) Homepage: https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page Vcs Debian Med Packaging Team
1086914	relion: depends on openmpi on 32-bit architectures	sid, trixie
seqan3 (1) Homepage: https://www.seqan.de/ Vcs Debian Med Packaging Team
1087373	seqan3: FTBFS: Some parallel tests fail on single-cpu systems	ftbfs
sra-sdk (1) Homepage: https://github.com/ncbi/sra-tools/ Vcs Debian Med Packaging Team
1040391	sra-toolkit: broken symlink: /usr/lib/debian-med/bin/kget -> ../../../bin/vdb-get

^*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:

critical	10
grave	10
serious	10
important	5
normal	3
minor	1
wishlist	0