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
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
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
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
1018365 gfapy: build-depends on python3-nose or uses it for autopkgtest
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
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
1015473 libbpp-core: ftbfs with LTO (link time optimization) enabled bookworm, sid
1015475 libbpp-phyl: ftbfs with LTO (link time optimization) enabled bookworm, sid
1015474 libbpp-popgen: ftbfs with LTO (link time optimization) enabled bookworm, sid
1015476 libbpp-qt: ftbfs with LTO (link time optimization) enabled bookworm, sid
1015477 libbpp-raa: ftbfs with LTO (link time optimization) enabled bookworm, sid
1015478 libbpp-seq: ftbfs with LTO (link time optimization) enabled bookworm, sid
1015479 libbpp-seq-omics: ftbfs with LTO (link time optimization) enabled bookworm, sid
1015484 libedlib: ftbfs with LTO (link time optimization) enabled bookworm, sid
1015486 libfastahack: ftbfs with LTO (link time optimization) enabled bookworm, sid
1015488 libgenome: ftbfs with LTO (link time optimization) enabled bookworm, sid
1015504 libmuscle: ftbfs with LTO (link time optimization) enabled bookworm, sid
1015505 libncl: ftbfs with LTO (link time optimization) enabled bookworm, sid
1012988 librg-blast-parser-perl: ftbfs with GCC-12 bookworm, ftbfs, sid
1012990 librostlab-blast: ftbfs with GCC-12 bookworm, sid
1015520 libseqlib: ftbfs with LTO (link time optimization) enabled bookworm, sid
1015525 libssw: ftbfs with LTO (link time optimization) enabled bookworm, sid
976570 libstatgen: FTBFS on arm64: E: Build killed with signal TERM after 150 minutes of inactivity bookworm, bullseye, ftbfs, sid
1015526 libtabixpp: ftbfs with LTO (link time optimization) enabled bookworm, sid
1018407 mirtop: build-depends on python3-nose or uses it for autopkgtest
225651 ncbi-tools-x11: want Cn3D++
992180 openmm FTBFS on \!amd64/arm64/ppc64el ftbfs
1018972 blasr autopkgtest regression with pbbam 2.1.0
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
1018464 python-biom-format: build-depends on python3-nose or uses it for autopkgtest
1009118 python3-biopython: incompatible with muscle >= 5 confirmed, fixed-upstream, upstream, wontfix
979625 autopkgtest: ModuleNotFoundError (ipytree) and AssertionError
1018477 python-deeptools: build-depends on python3-nose or uses it for autopkgtest
1018501 python-gffutils: build-depends on python3-nose or uses it for autopkgtest
860158 python-pbcore: prints warnings with recent h5py on ppc64el
1018551 python-pbcore: build-depends on python3-nose or uses it for autopkgtest
1018559 python-pyani: build-depends on python3-nose or uses it for autopkgtest
1018560 python-pybedtools: build-depends on python3-nose or uses it for autopkgtest
1018565 python-pymummer: build-depends on python3-nose or uses it for autopkgtest
1017574 python3-skbio: autopkgtest fail with pandas 1.4
1018582 python-sqt: build-depends on python3-nose or uses it for autopkgtest
983517 pytorch: Build documentation
997931 libtorch-dev: Caffe2Targets.cmake is broken
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
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
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
1019317 snakemake: HTML dashboard (--gui) is broken due to use of local jquery/bootstrap patch
1015667 spoa: ftbfs with LTO (link time optimization) enabled bookworm, sid

Open bugs in suggested packages

1 serious, 1 important, 6 normal, 2 minor
928076 bcbio: Workflows not ready for non-developers to depend on.
1018312 bcbio: build-depends on python3-nose or uses it for autopkgtest
1018334 cwlformat: build-depends on python3-nose or uses it for autopkgtest
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
1018577 python-seqcluster: build-depends on python3-nose or uses it for autopkgtest
994459 libjs-jquery removed symlinked files moreinfo
998030 r-cran-dt: Add xdg-open app open attempts as recommended a11y
1015655 samtools-legacy: ftbfs with LTO (link time optimization) enabled bookworm, sid

Done bugs

1015861 bamtools: FTBFS with upcoming doxygen 1.9.4 ftbfs
1018320 biomaj3: build-depends on python3-nose or uses it for autopkgtest
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
972537 please add --enable-ros3-vfd to the build options to allow RO access to HDF5 on S3
1012983 libpdb-redo: ftbfs with GCC-12 bookworm, sid
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
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
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
1018608 q2-quality-filter: build-depends on python3-nose or uses it for autopkgtest
1017514 q2-types: needs update for python-biom-format/2.1.12-1
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
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
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