Debian Med Project
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Summary
Bugs of task bio-dev
Total bugs: 101
Open bugs: 82
Fixed bugs: 19
Links to other tasks
Tasks overview
Biology 141 (1417)
Phylogeny 3 (12)
Cloud 29 (354)
Covid-19 135 (1331)
Medical data 0 (0)
Dental 0 (0)
Epidemiology 5 (74)
Imaging 212 (1057)
Laboratory 1 (9)
Oncology 0 (0)
Pharmacology 1 (9)
Physics 26 (201)
Practice 6 (45)
Psychology 2 (24)
Research 0 (0)
Statistics 0 (0)
Tools 32 (209)
Typesetting 60 (464)
Legend
SeverityDependentSuggested
critical 0 0
grave 0 0
serious 5 1
important 11 1
normal 28 6
minor 19 2
wishlist 9 0

Summary bugs page of task Biology development

Immediately looking into bugs of the dependencies of this task is advised (659)*

Open bugs in dependent packages

5 serious, 11 important, 28 normal, 19 minor, 9 wishlist
bamtools (3) 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
988848 libbamtools-doc: broken symlink: /usr/share/doc/libbamtools-dev/html/jquery.js -> ../../../javascript/jquery/jquery.js
992143 bamtools: autopkgtest failure: times out on armel
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 bookworm, bullseye, buster, jessie, sid, stretch
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
1015412 gatb-core: ftbfs with LTO (link time optimization) enabled bookworm, sid
gfapy (1) Homepage: https://github.com/ggonnella/gfapy Vcs Debian Med Packaging Team
1018365 gfapy: build-depends on python3-nose or uses it for autopkgtest
hdf5 (12) 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
htsjdk (1) Homepage: https://samtools.github.io/htsjdk/ Vcs Debian Med Packaging Team
1011977 FTBFS with OpenJDK 17: 5 failing tests bookworm, ftbfs, 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-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
1015473 libbpp-core: ftbfs with LTO (link time optimization) enabled bookworm, sid
libbpp-phyl (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
1015475 libbpp-phyl: ftbfs with LTO (link time optimization) enabled bookworm, sid
libbpp-popgen (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
1015474 libbpp-popgen: ftbfs with LTO (link time optimization) enabled bookworm, sid
libbpp-qt (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
1015476 libbpp-qt: ftbfs with LTO (link time optimization) enabled bookworm, sid
libbpp-raa (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
1015477 libbpp-raa: ftbfs with LTO (link time optimization) enabled bookworm, sid
libbpp-seq (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
1015478 libbpp-seq: ftbfs with LTO (link time optimization) enabled bookworm, sid
libbpp-seq-omics (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
1015479 libbpp-seq-omics: ftbfs with LTO (link time optimization) enabled bookworm, sid
libedlib (1) Homepage: https://github.com/Martinsos/edlib Vcs Debian Med Packaging Team
1015484 libedlib: ftbfs with LTO (link time optimization) enabled bookworm, sid
libfastahack (1) Homepage: https://github.com/ekg/fastahack Vcs Debian Med Packaging Team
1015486 libfastahack: ftbfs with LTO (link time optimization) enabled bookworm, sid
libgenome (1) Homepage: https://sourceforge.net/projects/libgenome/ Vcs Debian Med Packaging Team
1015488 libgenome: ftbfs with LTO (link time optimization) enabled bookworm, sid
libmuscle (1) Homepage: http://sourceforge.net/p/mauve/code/HEAD/tree/muscle/trunk/ Vcs Debian Med Packaging Team
1015504 libmuscle: ftbfs with LTO (link time optimization) enabled bookworm, sid
libncl (1) Homepage: https://github.com/mtholder/ncl Vcs Debian Med Packaging Team
1015505 libncl: ftbfs with LTO (link time optimization) enabled bookworm, sid
librg-blast-parser-perl (1) Homepage: https://rostlab.org/ Vcs Debian Med Packaging Team
1012988 librg-blast-parser-perl: ftbfs with GCC-12 bookworm, ftbfs, sid
librostlab-blast (1) Homepage: https://rostlab.org/ Vcs Debian Med Packaging Team
1012990 librostlab-blast: ftbfs with GCC-12 bookworm, sid
libseqlib (1) Homepage: https://github.com/walaj/SeqLib Vcs Debian Med Packaging Team
1015520 libseqlib: ftbfs with LTO (link time optimization) enabled bookworm, sid
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 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 bookworm, bullseye, ftbfs, sid
libtabixpp (1) Homepage: https://github.com/ekg/tabixpp Vcs Debian Med Packaging Team
1015526 libtabixpp: ftbfs with LTO (link time optimization) enabled bookworm, sid
mirtop (1) Homepage: https://github.com/miRTop/mirtop Vcs Debian Med Packaging Team
1018407 mirtop: build-depends on python3-nose or uses it for autopkgtest
ncbi-tools6 (1) Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/ Vcs Debian Med Packaging Team
225651 ncbi-tools-x11: want Cn3D++
openmm (1) Homepage: https://simtk.org/home/openmm Vcs Debichem Team
992180 openmm FTBFS on \!amd64/arm64/ppc64el ftbfs
pbbam (1) Homepage: https://pbbam.readthedocs.org/en/latest/index.html Vcs Debian Med Packaging Team
1018972 blasr autopkgtest regression with pbbam 2.1.0
pyfai (2) Homepage: https://github.com/silx-kit/pyFAI Vcs Debian PaN Maintainers
1018811 pyfai: autopkgtest regression on armel and i386 patch
1020073 pyfai: FTBFS: distutils.errors.DistutilsError: Command '['/usr/bin/python3.10', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/tmp/tmpymrbi1ta', '--quiet', 'setuptools<60.0.0']' returned non-zero exit status 1. bookworm, ftbfs, sid
python-biom-format (1) Homepage: https://biom-format.org/ Vcs Debian Med Packaging Team
1018464 python-biom-format: build-depends on python3-nose or uses it for autopkgtest
python-biopython (1) Homepage: https://biopython.org Vcs Debian Med Packaging Team
1009118 python3-biopython: incompatible with muscle >= 5 confirmed, fixed-upstream, upstream, wontfix
python-cooler (1) Homepage: https://github.com/mirnylab/cooler Vcs Debian Med Packaging Team
979625 autopkgtest: ModuleNotFoundError (ipytree) and AssertionError
python-deeptools (1) Homepage: https://github.com/deeptools/deepTools Vcs Debian Med Packaging Team
1018477 python-deeptools: build-depends on python3-nose or uses it for autopkgtest
python-gffutils (1) Homepage: https://daler.github.io/gffutils Vcs Debian Med Packaging Team
1018501 python-gffutils: build-depends on python3-nose or uses it for autopkgtest
python-pbcore (2) Homepage: https://github.com/PacificBiosciences/pbcore Vcs Debian Med Packaging Team
860158 python-pbcore: prints warnings with recent h5py on ppc64el
1018551 python-pbcore: build-depends on python3-nose or uses it for autopkgtest
python-pyani (1) Homepage: https://github.com/widdowquinn/pyani Vcs Debian Med Packaging Team
1018559 python-pyani: build-depends on python3-nose or uses it for autopkgtest
python-pybedtools (1) Homepage: https://daler.github.io/pybedtools/ Vcs Debian Med Packaging Team
1018560 python-pybedtools: build-depends on python3-nose or uses it for autopkgtest
python-pymummer (1) Homepage: https://github.com/sanger-pathogens/pymummer Vcs Debian Med Packaging Team
1018565 python-pymummer: build-depends on python3-nose or uses it for autopkgtest
python-skbio (1) Homepage: https://github.com/biocore/scikit-bio Vcs Debian Med Packaging Team
1017574 python3-skbio: autopkgtest fail with pandas 1.4
python-sqt (1) Homepage: https://bitbucket.org/marcelm/sqt Vcs Debian Med Packaging Team
1018582 python-sqt: build-depends on python3-nose or uses it for autopkgtest
pytorch (2) Homepage: https://pytorch.org/ Vcs Debian Deep Learning Team
983517 pytorch: Build documentation
997931 libtorch-dev: Caffe2Targets.cmake is broken
rdkit (6) 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
990653 rdkit-doc: broken symlinks: /usr/share/doc/rdkit/html/_static/{jquery,underscore}.js
1015650 rdkit: ftbfs with LTO (link time optimization) enabled bookworm, sid
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
seqan3 (1) Homepage: https://www.seqan.de/ Vcs Debian Med Packaging Team
1020035 seqan3: FTBFS: char_traits.h:431:56: error: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets 4 and 3 may overlap up to 9223372036854775813 bytes at offset -3 [-Werror=restrict] bookworm, ftbfs, sid
snakemake (1) Homepage: https://snakemake.readthedocs.io/ Vcs Debian Med Packaging Team
1019317 snakemake: HTML dashboard (--gui) is broken due to use of local jquery/bootstrap patch
spoa (1) Homepage: https://github.com/rvaser/spoa Vcs Debian Med Packaging Team
1015667 spoa: ftbfs with LTO (link time optimization) enabled bookworm, sid

Open bugs in suggested packages

1 serious, 1 important, 6 normal, 2 minor
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
cwlformat (1) Homepage: https://github.com/rabix/cwl-format Vcs Debian Med Packaging Team
1018334 cwlformat: build-depends on python3-nose or uses it for autopkgtest
intake (1) Homepage: https://github.com/intake/intake Vcs Debian Med Packaging Team
997059 intake FTBFS on IPV6-only buildds confirmed, ftbfs, ipv6
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 fixed-upstream, ftbfs, help, upstream
networkx (1) Homepage: https://networkx.github.io/ Vcs Sandro Tosi
947882 python3-networkx: SyntaxWarning on package upgrade fixed-upstream
python-seqcluster (1) Homepage: https://github.com/lpantano/seqcluster Vcs Debian Med Packaging Team
1018577 python-seqcluster: build-depends on python3-nose or uses it for autopkgtest
q2templates (1) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
994459 libjs-jquery removed symlinked files moreinfo
r-cran-dt (1) Homepage: https://cran.r-project.org/package=DT Vcs Debian R Packages Maintainers
998030 r-cran-dt: Add xdg-open app open attempts as recommended a11y
samtools-legacy (1) Homepage: https://www.htslib.org/ Vcs Debian Med Packaging Team
1015655 samtools-legacy: ftbfs with LTO (link time optimization) enabled bookworm, sid

Done bugs

bamtools (1) Homepage: https://github.com/pezmaster31/bamtools/wiki Vcs Debian Med Packaging Team
1015861 bamtools: FTBFS with upcoming doxygen 1.9.4 ftbfs
biomaj3 (1) Homepage: https://github.com/genouest/biomaj Vcs Debian Med Packaging Team
1018320 biomaj3: build-depends on python3-nose or uses it for autopkgtest
golang-github-biogo-hts (1) Homepage: https://github.com/biogo/hts Vcs Debian Go Packaging Team
1017270 golang-github-biogo-hts: FTBFS: dh_auto_test: error: cd obj-x86_64-linux-gnu && go test -vet=off -v -p 8 github.com/biogo/hts/bam github.com/biogo/hts/bgzf github.com/biogo/hts/bgzf/cache github.com/biogo/hts/bgzf/index github.com/biogo/hts/cram github.com/biogo/hts/cram/encoding/itf8 github.com/biogo/hts/cram/encoding/ltf8 github.com/biogo/hts/csi github.com/biogo/hts/fai github.com/biogo/hts/internal github.com/biogo/hts/sam github.com/biogo/hts/tabix returned exit code 1 bookworm, ftbfs, sid
hdf5 (1) Homepage: http://hdfgroup.org/HDF5/ Vcs Gilles Filippini
972537 please add --enable-ros3-vfd to the build options to allow RO access to HDF5 on S3
libpdb-redo (1) Homepage: https://github.com/PDB-REDO/libpdb-redo Vcs Debian Med Packaging Team
1012983 libpdb-redo: ftbfs with GCC-12 bookworm, sid
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-skbio (1) Homepage: https://github.com/biocore/scikit-bio Vcs Debian Med Packaging Team
991981 python3-skbio: package installs .../dist-packages/benchmarks/..
pytorch (3) Homepage: https://pytorch.org/ Vcs Debian Deep Learning Team
994423 pytorch: Baseline violation on armhf bookworm, bullseye, ftbfs, sid
1004782 pytorch: FTBFS with ffmpeg 5.0 bookworm, ftbfs, sid
1009200 pytorch: (autopkgtest) needs update for python3.10: 'float' object cannot be interpreted as an integer bookworm, sid
q2-feature-table (2) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1015250 q2-feature-table: Conflict with biom-format 2.1.12 upstream
1017515 q2-feature-table: needs update for python-biom-format/2.1.12-1
q2-quality-filter (1) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1018608 q2-quality-filter: build-depends on python3-nose or uses it for autopkgtest
q2-types (1) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1017514 q2-types: needs update for python-biom-format/2.1.12-1
q2cli (2) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1015136 q2cli: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.10 returned exit code 13 bookworm, ftbfs, sid
1018606 q2cli: build-depends on python3-nose or uses it for autopkgtest
qiime (2) Homepage: https://qiime2.org Vcs Debian Med Packaging Team
1014100 qiime: autopkgtest needs update for new version of python-decorator bookworm, sid
1018609 qiime: build-depends on python3-nose or uses it for autopkgtest
r-bioc-dada2 (1) Homepage: https://bioconductor.org/packages/dada2/ Vcs Debian R Packages Maintainers
1019131 r-bioc-dada2: autopkgtest regression in testing
*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: Sat, 24 Sep 2022 04:19:27 -0000