Summary

Bugs of task bio-dev

Total bugs: 89

Open bugs: 79

Fixed bugs: 10

Links to other tasks

Tasks overview

Biology 167 (1428)

Biology development 79 (571)

Next generation sequencing 8 (96)

Phylogeny 3 (21)

Cloud 37 (315)

Content management 0 (0)

Covid-19 134 (1151)

Medical data 1 (3)

Dental 0 (0)

Epidemiology 3 (18)

Hospital information systems 0 (0)

Imaging 231 (1075)

Imaging development 91 (602)

Laboratory 1 (9)

Oncology 3 (48)

Pharmacology 1 (9)

Physics 25 (180)

Practice 3 (27)

Psychology 7 (65)

Rehabilitation 0 (0)

Research 0 (0)

Statistics 0 (0)

Tools 33 (218)

Typesetting 67 (538)

Legend

Severity	Dependent	Suggested
critical	0	0
grave	0	0
serious	1	0
important	7	2
normal	45	3
minor	4	0
wishlist	16	1

Summary bugs page of task Biology development

Immediately looking into bugs of the dependencies of this task is advised (571)^*

Open bugs in dependent packages

1 serious, 7 important, 45 normal, 4 minor, 16 wishlist

bamtools (2) 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
983981	bamtools: ftbfs with GCC-11	bookworm, sid
biococoa (1) Homepage: http://bioinformatics.org/biococoa/ Vcs Debian Med Packaging Team
749736	biococoa: GCC warnings that may lead to runtime issues with new GNUstep libraries	bullseye, buster, jessie, sid, stretch
biojava-live (1) Homepage: http://www.biojava.org Vcs Debian Med Packaging Team
659824	biojava-live: New version available
biomaj3 (1) Homepage: https://github.com/genouest/biomaj Vcs Debian Med Packaging Team
950914	python3-biomaj3: Depends on python-influxdb wich ftbs, patch to remove dependency
cdk (1) Homepage: https://cdk.github.io/ Vcs Debian Java Maintainers
505226	Please package jchempaint
gatb-core (3) 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
984145	gatb-core: ftbfs with GCC-11	bookworm, sid
hdf5 (14) 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
972537	please add --enable-ros3-vfd to the build options to allow RO access to HDF5 on S3
973261	libhdf5-openmpi-dev: installing requires /proc being mounted
htsjdk (2) Homepage: http://samtools.github.io/htsjdk/ Vcs Debian Med Packaging Team
877590	FTBFS: error: package org.testng does not exist	bullseye, buster, sid
920588	htsjdk: Autopkgtest for htsjdk
htslib (1) Homepage: https://github.com/samtools/htslib Vcs Debian Med Packaging Team
978835	htslib: ftbfs with autoconf 2.70	bookworm, sid
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-cluster-perl (1) Homepage: https://metacpan.org/release/Bio-Cluster Vcs Debian Med Packaging Team
963866	libbio-cluster-perl: circular dependency hell
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
libbpp-core (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
984086	libbpp-core: ftbfs with GCC-11	bookworm, pending, sid
libbpp-phyl (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
984089	libbpp-phyl: ftbfs with GCC-11	bookworm, sid
libbpp-popgen (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
984091	libbpp-popgen: ftbfs with GCC-11	bookworm, sid
libbpp-qt (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
984088	libbpp-qt: ftbfs with GCC-11	bookworm, sid
libbpp-raa (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
984090	libbpp-raa: ftbfs with GCC-11	bookworm, sid
libbpp-seq (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
984094	libbpp-seq: ftbfs with GCC-11	bookworm, sid
libbpp-seq-omics (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
984092	libbpp-seq-omics: ftbfs with GCC-11	bookworm, sid
libcifpp (2) Homepage: https://github.com/PDB-REDO/libcifpp Vcs Debian Med Packaging Team
982333	libcifpp: [INTL:pt] Portuguese translation - debconf messages	l10n, patch
984093	libcifpp: ftbfs with GCC-11	bookworm, sid
libedlib (1) Homepage: https://github.com/Martinsos/edlib Vcs Debian Med Packaging Team
984103	libedlib: ftbfs with GCC-11	bookworm, sid
libfastahack (1) Homepage: https://github.com/ekg/fastahack Vcs Debian Med Packaging Team
984104	libfastahack: ftbfs with GCC-11	bookworm, sid
libgenome (1) Homepage: https://sourceforge.net/projects/libgenome/ Vcs Debian Med Packaging Team
984106	libgenome: ftbfs with GCC-11	bookworm, sid
libncl (1) Homepage: https://github.com/mtholder/ncl Vcs Debian Med Packaging Team
984188	libncl: ftbfs with GCC-11	bookworm, sid
libpdb-redo (1) Homepage: https://github.com/PDB-REDO/libpdb-redo Vcs Debian Med Packaging Team
984200	libpdb-redo: ftbfs with GCC-11	bookworm, sid
librdp-taxonomy-tree-java (1) Homepage: https://github.com/rdpstaff/TaxonomyTree Vcs Debian Med Packaging Team
982054	librdp-taxonomy-tree-java: FTBFS with OpenJDK 17 due to javadoc errors	bookworm, ftbfs, sid
librostlab-blast (2) Homepage: http://rostlab.org/ Vcs Debian Med Packaging Team
832138	librostlab-blast: The package should compile without forcing the older -std=c++03
851472	librostlab-blast: autopkg test suite failure	help
libseqlib (1) Homepage: https://github.com/walaj/SeqLib Vcs Debian Med Packaging Team
984210	libseqlib: ftbfs with GCC-11	bookworm, sid
libsmithwaterman (1) Homepage: https://github.com/ekg/smithwaterman Vcs Debian Med Packaging Team
984207	libsmithwaterman: ftbfs with GCC-11	bookworm, sid
libstatgen (1) Homepage: https://genome.sph.umich.edu/wiki/C++_Library:_libStatGen Vcs Debian Med Packaging Team
976570	libstatgen: FTBFS on arm64: E: Build killed with signal TERM after 150 minutes of inactivity	bullseye, ftbfs, sid
libtabixpp (1) Homepage: https://github.com/ekg/tabixpp Vcs Debian Med Packaging Team
986555	mark one more symbol as optional	patch
libvcflib (2) Homepage: https://github.com/vcflib/vcflib Vcs Debian Med Packaging Team
984139	freebayes: ftbfs with GCC-11	bookworm, fixed-upstream, sid, upstream
984212	libvcflib: ftbfs with GCC-11	bookworm, fixed-upstream, sid, upstream
ncbi-tools6 (1) Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/ Vcs Debian Med Packaging Team
225651	ncbi-tools-x11: want Cn3D++
nim-kexpr (1) Homepage: https://github.com/brentp/kexpr-nim Vcs Debian Med Packaging Team
985682	nim-kexpr-dev: broken long package description
pyfai (1) Homepage: https://github.com/silx-kit/pyFAI Vcs Debian Science Maintainers
966040	pyfai: Uses old name of sip module
python-biopython (1) Homepage: http://biopython.org Vcs Debian Med Packaging Team
986410	autopkg tests don't run with the same dependencies as during the build
python-cooler (2) Homepage: https://github.com/mirnylab/cooler Vcs Debian Med Packaging Team
965361	python-cooler: please make the build reproducible	patch, pending
979625	autopkgtest: ModuleNotFoundError (ipytree) and AssertionError
python-freecontact (1) Homepage: https://rostlab.org/owiki/index.php/FreeContact Vcs Debian Med Packaging Team
984302	python-freecontact: ftbfs with GCC-11	bookworm, sid
python-loompy (1) Homepage: https://github.com/linnarsson-lab/loompy Vcs Debian Med Packaging Team
970309	src:python-loompy: Please provide autopkgtest	newcomer
python-parasail (1) Homepage: https://github.com/jeffdaily/parasail-python Vcs Debian Med Packaging Team
976497	python-parasail: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.9 returned exit code 13	bullseye, ftbfs, help, sid
python-pbcore (2) Homepage: https://github.com/PacificBiosciences/pbcore Vcs Debian Med Packaging Team
860158	python-pbcore: prints warnings with recent h5py on ppc64el
919052	python-pbcore: some docs for pbcore are not found
python-ruffus (1) Homepage: http://www.ruffus.org.uk/ Vcs Debian Med Packaging Team
841073	python-ruffus: Needs 18 GB of RAM to build	help, upstream
pytorch (2) Homepage: https://pytorch.org/ Vcs Debian Deep Learning Team
983517	pytorch: Build documentation
984304	pytorch: ftbfs with GCC-11	bookworm, sid
rdkit (4) Homepage: http://www.rdkit.org Vcs Debichem Team
927955	python-rdkit: missing module pyAvalonTools
964773	rdkit: Please build rdkit with inchi support	wontfix
983040	rdkit: doesn't ship with inchi support enabled	wontfix
983077	rdkit doesn't ship with inchi support enabled	wontfix
seqan2 (2) Homepage: http://www.seqan.de/ Vcs Debian Med Packaging Team
892222	seqan2: FTBFS on hppa: app_test_seqan_tcoffee fails on 2trx.mlcs.fasta	upstream
917851	seqan2 2.4.0+dfsg-9: FTBFS, alignment problem	ftbfs
spoa (1) Homepage: https://github.com/rvaser/spoa Vcs Debian Med Packaging Team
984348	spoa: ftbfs with GCC-11	bookworm, sid

Open bugs in suggested packages

2 important, 3 normal, 1 wishlist

bcbio (1) Homepage: https://github.com/bcbio/bcbio-nextgen Vcs Debian Med Packaging Team
928076	bcbio: Workflows not ready for non-developers to depend on.
intake (1) Homepage: https://github.com/intake/intake Vcs Debian Med Packaging Team
970312	src:intake: Please provide autopkgtest	newcomer
libfreecontact-perl (1) Homepage: https://rostlab.org/owiki/index.php/FreeContact Vcs Debian Med Packaging Team
984107	libfreecontact-perl: ftbfs with GCC-11	bookworm, sid
libmaus2 (1) Homepage: https://gitlab.com/german.tischler/libmaus2 Vcs Debian Med Packaging Team
934619	libmaus2 FTBFS (mostly 32bit): error: no matching function for call	ftbfs, help, upstream
networkx (1) Homepage: https://networkx.github.io/ Vcs Sandro Tosi
947882	python3-networkx: SyntaxWarning on package upgrade	fixed-upstream
q2-quality-control (1) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
982139	q2-quality-control: test skipped on ppc64el

Done bugs

bamtools (1) Homepage: https://github.com/pezmaster31/bamtools/wiki Vcs Debian Med Packaging Team
987023	bamtools: autopkgtest failure: times out on armhf and s390x
freecontact (1) Homepage: http://rostlab.org/ Vcs Debian Med Packaging Team
986524	freecontact: FTBFS: devlibs error: There is no package matching [libgfortran-8-dev] and noone provides it, please report bug to d-shlibs maintainer	bullseye, ftbfs, sid
htslib (3) Homepage: https://github.com/samtools/htslib Vcs Debian Med Packaging Team
749367	htslib FTBFS on testing for mips/mipsel	bullseye, buster, moreinfo, patch, sid, stretch
800469	htslib FTBFS on armhf, bus error.	bullseye, buster, ftbfs, patch, sid, stretch
849667	htslib: FTBFS on armhf: [test] Bus error	bullseye, buster, ftbfs, patch, sid, stretch
kineticstools (1) Homepage: https://github.com/PacificBiosciences/kineticsTools Vcs Debian Med Packaging Team
958471	src:kineticstools: Non-free data included in source
python-cobra (1) Homepage: https://opencobra.github.io/cobrapy/ Vcs Debian Med Packaging Team
912586	python-cobra still fails it's autopkg tests	bullseye, buster, help, sid
python-intervaltree-bio (1) Homepage: https://github.com/konstantint/intervaltree-bio Vcs Debian Med Packaging Team
920545	python-intervaltree breaks python-intervaltree-bio autopkgtest	help, patch, upstream
r-cran-dt (1) Homepage: https://cran.r-project.org/package=DT Vcs Debian R Packages Maintainers
985281	r-cran-dt: unhandled symlink to directory conversion: /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables-extensions -> ../../../../../../share/javascript/jquery-datatables-extensions
snakemake (1) Homepage: https://snakemake.readthedocs.io/ Vcs Debian Med Packaging Team
986768	snakemake: autopkgtest regression: Missing input files for rule remote_ancient

^*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