Debian Med Project
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Bugs of task bio-dev
Total bugs: 78
Open bugs: 69
Fixed bugs: 9
Links to other tasks
Biology 133 (1379)
Phylogeny 3 (12)
Cloud 29 (333)
Covid-19 138 (1464)
Medical data 0 (0)
Dental 0 (0)
Epidemiology 7 (139)
Imaging 212 (1123)
Laboratory 1 (9)
Oncology 2 (39)
Pharmacology 1 (9)
Physics 26 (201)
Practice 6 (45)
Psychology 4 (42)
Research 0 (0)
Statistics 1 (3)
Tools 29 (200)
Typesetting 66 (535)
critical 0 0
grave 0 0
serious 6 3
important 10 1
normal 36 3
minor 1 1
wishlist 8 0

Summary bugs page of task Biology development

Immediately looking into bugs of the dependencies of this task is advised (702)*

Open bugs in dependent packages

6 serious, 10 important, 36 normal, 1 minor, 8 wishlist
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
749736 biococoa: GCC warnings that may lead to runtime issues with new GNUstep libraries bookworm, bullseye, buster, jessie, sid, stretch
1012919 fast5: ftbfs with GCC-12 bookworm, sid
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
1012934 gatb-core: ftbfs with GCC-12 bookworm, sid
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
1012946 htscodecs: ftbfs with GCC-12 bookworm, sid
1011977 FTBFS with OpenJDK 17: 5 failing tests bookworm, ftbfs, sid
948463 libai-fann-perl: Integer overflow leading to heap buffer overflow
599961 libbio-scf-perl: FTBFS: Neither BIG nor LITTLE endian defined
1012967 libbpp-core: ftbfs with GCC-12 bookworm, sid
1012968 libbpp-phyl: ftbfs with GCC-12 bookworm, sid
1012969 libbpp-popgen: ftbfs with GCC-12 bookworm, sid
1012970 libbpp-qt: ftbfs with GCC-12 bookworm, sid
1012971 libbpp-seq: ftbfs with GCC-12 bookworm, sid
1012972 libbpp-seq-omics: ftbfs with GCC-12 bookworm, sid
1012973 libcifpp: ftbfs with GCC-12 bookworm, sid
1012976 libfastahack: ftbfs with GCC-12 bookworm, sid
1012978 libgenome: ftbfs with GCC-12 bookworm, sid
1013664 libgoby-java: FTBFS: [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/ error: package edu.rit.pj does not exist bookworm, ftbfs, sid
1012984 libncl: ftbfs with GCC-12 bookworm, sid
1012983 libpdb-redo: ftbfs with GCC-12 bookworm, sid
1012988 librg-blast-parser-perl: ftbfs with GCC-12 bookworm, sid
1012990 librostlab-blast: ftbfs with GCC-12 bookworm, sid
1012992 libseqlib: ftbfs with GCC-12 bookworm, sid
976570 libstatgen: FTBFS on arm64: E: Build killed with signal TERM after 150 minutes of inactivity bookworm, bullseye, ftbfs, sid
225651 ncbi-tools-x11: want Cn3D++
992180 openmm FTBFS on \!amd64/arm64/ppc64el ftbfs
1013703 pyranges: FTBFS: pytest7 regression, py3.9 OK; py3.10 fails with Fatal Python error: Bus error bookworm, ftbfs, sid
1013713 python-biom-format: FTBFS: pytest7 regression, not sure what the problem is bookworm, ftbfs, sid
1009118 python3-biopython: incompatible with muscle >= 5 confirmed, fixed-upstream, upstream, wontfix
979625 autopkgtest: ModuleNotFoundError (ipytree) and AssertionError
860158 python-pbcore: prints warnings with recent h5py on ppc64el
1008452 python-streamz: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.10 3.9" returned exit code 13 bookworm, ftbfs, sid
983517 pytorch: Build documentation
997931 libtorch-dev: Caffe2Targets.cmake is broken
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
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
1013028 rdkit: ftbfs with GCC-12 bookworm, sid
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
1013275 toil: FTBFS with Python 3.10 only ftbfs

Open bugs in suggested packages

3 serious, 1 important, 3 normal, 1 minor
928076 bcbio: Workflows not ready for non-developers to depend on.
997059 intake FTBFS on IPV6-only buildds confirmed, ftbfs, ipv6
934619 libmaus2 FTBFS (mostly 32bit): error: no matching function for call fixed-upstream, ftbfs, help, upstream
947882 python3-networkx: SyntaxWarning on package upgrade fixed-upstream
1012386 python-seqcluster: FTBFS: ModuleNotFoundError: No module named 'attr' ftbfs
994459 libjs-jquery removed symlinked files moreinfo
1012141 r-bioc-dada2: FTBFS with onetbb/2021.5.0-8 in experimental ftbfs
998030 r-cran-dt: Add xdg-open app open attempts as recommended a11y

Done bugs

972537 please add --enable-ros3-vfd to the build options to allow RO access to HDF5 on S3
1011157 libsbml: FTBFS with OpenJDK 17 due to unsupported javac source/target level 6 bookworm, ftbfs, sid
997123 networkx: FTBFS: '! LaTeX Error: File `tgtermes.sty' not found.' bookworm, ftbfs, sid
1013010 openmm: ftbfs with GCC-12 bookworm, confirmed, sid, upstream
912586 python-cobra still fails it's autopkg tests bullseye, buster, help, sid
991981 python3-skbio: package installs .../dist-packages/benchmarks/..
994423 pytorch: Baseline violation on armhf bookworm, bullseye, ftbfs, sid
997488 q2cli: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.9 returned exit code 13 bookworm, confirmed, fixed-upstream, ftbfs, sid, upstream
1008352 seqan3: FTBFS: type_traits.hpp:68:37: error: no match for call to ‘(const ranges::views::zip_fn) (std::ranges::single_view<std::tuple<std::vector<seqan3::dna4, std::allocator<seqan3::dna4> >&, std::vector<seqan3::dna4, std::allocator<seqan3::dna4> >&> >, std::ranges::iota_view<int, std::unreachable_sentinel_t>)’ bookworm, ftbfs, sid
*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:
Last update: Sat, 25 Jun 2022 18:22:55 -0000