Debian Med Project
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Summary
Bugs of task bio-dev
Total bugs: 177
Open bugs: 119
Fixed bugs: 58
Links to other tasks
Biology 214 (1472)
Biology development 119 (1181)
Phylogeny 9 (45)
Cloud 39 (381)
Covid-19 148 (1401)
Medical data 1 (1)
Dental 1 (3)
Epidemiology 8 (110)
Imaging 209 (1052)
Laboratory 1 (9)
Oncology 1 (3)
Pharmacology 1 (9)
Physics 25 (159)
Practice 7 (42)
Psychology 6 (46)
Research 0 (0)
Statistics 3 (7)
Tools 38 (241)
Typesetting 61 (490)
Legend
SeverityDependentSuggested
critical 0 0
grave 0 0
serious 21 2
important 16 2
normal 16 5
minor 39 5
wishlist 10 3

Summary bugs page of task Biology development

Immediately looking into bugs of the dependencies of this task is advised (1181)*

Open bugs in dependent packages

21 serious, 16 important, 16 normal, 39 minor, 10 wishlist
865130 reapr FTBFS on big endian: Error sampling from files '00.Sample/fragCov.gz', '00.assembly.fa.gc.gz' ftbfs, upstream
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
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
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
1064095 hdf5: NMU diff for 64-bit time_t transition patch, pending, sid, trixie
948463 libai-fann-perl: Integer overflow leading to heap buffer overflow
1062229 libbigwig: NMU diff for 64-bit time_t transition patch, pending, sid, trixie
1047073 libbio-asn1-entrezgene-perl: Fails to build source after successful build ftbfs, sid, trixie
599961 libbio-scf-perl: FTBFS: Neither BIG nor LITTLE endian defined
1047210 libbio-scf-perl: Fails to build source after successful build ftbfs, sid, trixie
1015473 libbpp-core: ftbfs with LTO (link time optimization) enabled sid, trixie
1062230 libbpp-core: NMU diff for 64-bit time_t transition patch, pending
1015475 libbpp-phyl: ftbfs with LTO (link time optimization) enabled sid, trixie
1062234 libbpp-phyl: NMU diff for 64-bit time_t transition patch, pending
1062232 libbpp-phyl-omics: NMU diff for 64-bit time_t transition patch, pending
1015474 libbpp-popgen: ftbfs with LTO (link time optimization) enabled sid, trixie
1062236 libbpp-popgen: NMU diff for 64-bit time_t transition patch, pending
1015476 libbpp-qt: ftbfs with LTO (link time optimization) enabled sid, trixie
1062237 libbpp-qt: NMU diff for 64-bit time_t transition patch, pending
1015477 libbpp-raa: ftbfs with LTO (link time optimization) enabled sid, trixie
1062238 libbpp-raa: NMU diff for 64-bit time_t transition patch, pending, sid, trixie
1015478 libbpp-seq: ftbfs with LTO (link time optimization) enabled sid, trixie
1062240 libbpp-seq: NMU diff for 64-bit time_t transition patch, pending
1015479 libbpp-seq-omics: ftbfs with LTO (link time optimization) enabled sid, trixie
1062239 libbpp-seq-omics: NMU diff for 64-bit time_t transition patch, pending
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
1048817 libcifpp: Fails to build source after successful build ftbfs, sid, trixie
1063191 libcifpp-data: Incorrect URL in update-libcifpp-data script patch
1015484 libedlib: ftbfs with LTO (link time optimization) enabled sid, trixie
1062316 libgkarrays: NMU diff for 64-bit time_t transition patch, pending, sid, trixie
1057518 libgoby-java: FTBFS with default Java 21 ftbfs
1015504 libmuscle: ftbfs with LTO (link time optimization) enabled sid, trixie
1015505 libncl: ftbfs with LTO (link time optimization) enabled sid, trixie
1046388 libpdb-redo: Fails to build source after successful build ftbfs, sid, trixie
1046372 librcsb-core-wrapper: Fails to build source after successful build ftbfs, sid, trixie
1047025 librostlab: Fails to build source after successful build ftbfs, sid, trixie
1048643 librostlab-blast: Fails to build source after successful build ftbfs, sid, trixie
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
1063136 libslow5lib: NMU diff for 64-bit time_t transition patch, pending, sid, trixie
1015525 libssw: ftbfs with LTO (link time optimization) enabled experimental, sid, trixie
1063137 libtabixpp: NMU diff for 64-bit time_t transition patch, pending, sid, trixie
1045603 libwfa2: Fails to build source after successful build ftbfs, sid, trixie
1062731 libwfa2: NMU diff for 64-bit time_t transition patch, pending, sid, trixie
1062681 macromoleculebuilder: NMU diff for 64-bit time_t transition patch, pending, sid, trixie
1046152 mcl: Fails to build source after successful build ftbfs, sid, trixie
1046060 minimap2: Fails to build source after successful build ftbfs, sid, trixie
225651 ncbi-tools-x11: want Cn3D++
1064245 ncbi-tools6: NMU diff for 64-bit time_t transition patch, pending, sid, trixie
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
1061814 openmm fails its autopkg tests with Python 3.12 ftbfs, patch, sid, trixie
1063095 openmm: NMU diff for 64-bit time_t transition patch, pending, sid, trixie
1061938 pyfai: Segfault when closing a dialg
1044072 python-anndata: FTBFS with pandas 2.0 sid, trixie
1064147 ftbfs: test failures affecting Bio.SeqIO.SeqXmIIO ftbfs, sid
1058479 python-cogent: please (temporarily) drop python3-numba dependencies wontfix
1063974 python-gffutils: autopkgtest regression with pytest 8
1058482 python-loompy: please (temporarily) drop python3-numba dependencies
1045607 python-pyspoa: Fails to build source after successful build ftbfs, sid, trixie
1046218 python-streamz: Fails to build source after successful build ftbfs, sid, trixie
983517 pytorch: Build documentation
1056388 FTBFS with fmtlib 10 fixed-upstream, ftbfs
1057644 pytorch: build for all supported Python versions wontfix
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
1064311 rdkit: NMU diff for 64-bit time_t transition patch, sid, trixie
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
1045625 ruby-crb-blast: Fails to build source after successful build ftbfs, sid, trixie
917851 seqan2 2.4.0+dfsg-9: FTBFS, alignment problem ftbfs
1047218 seqan2: Fails to build source after successful build ftbfs, sid, trixie
1048951 seqan3: Fails to build source after successful build ftbfs, sid, trixie
1015667 spoa: ftbfs with LTO (link time optimization) enabled experimental, sid, trixie
1040391 sra-toolkit: broken symlink: /usr/lib/debian-med/bin/kget -> ../../../bin/vdb-get
1053411 sra-sdk: FTBFS with re2 >= 20230601 (which requires abseil) upstream
1063189 staden-io-lib: NMU diff for 64-bit time_t transition patch, pending, sid, trixie

Open bugs in suggested packages

2 serious, 2 important, 5 normal, 5 minor, 3 wishlist
1049876 bbhash: FTBFS on 32 bit architectures ftbfs, sid, trixie
928076 bcbio: Workflows not ready for non-developers to depend on.
1018312 bcbio: build-depends on python3-nose or uses it for autopkgtest
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
1043870 concurrentqueue: Fails to build source after successful build ftbfs, sid, trixie
1045042 ctdconverter: Fails to build source after successful build ftbfs, sid, trixie
1049797 freecontact: Fails to build binary packages again after successful build ftbfs, sid, trixie
1062403 freecontact: NMU diff for 64-bit time_t transition patch, pending, sid, trixie
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
934619 libmaus2 FTBFS (mostly 32bit): error: no matching function for call fixed-upstream, ftbfs, help, upstream
1060444 python3-networkx: postinst warning
1064503 Please pacakge new upstream release 3.2.1
1046648 python-ncls: Fails to build source after successful build ftbfs, sid, trixie
1035277 python-seqcluster: please add autopkgtests (to add coverage for python3-numpy)

Done bugs

1043996 biosquid: Fails to build source after successful build experimental, ftbfs, sid, trixie
1049808 biosquid: Fails to build binary packages again after successful build experimental, ftbfs, sid, trixie
1061931 biosquid: NMU diff for 64-bit time_t transition patch
1058768 cyvcf2: ftbfs and autopkgtest regression with htslib 1.19 fixed-upstream, ftbfs, upstream
1062588 ffindex: NMU diff for 64-bit time_t transition patch, sid, trixie
1062071 genometools: NMU diff for 64-bit time_t transition patch
1033703 gffread: autopkgtest regression: test dependency not in testing bookworm-ignore
972537 please add --enable-ros3-vfd to the build options to allow RO access to HDF5 on S3
1062344 htslib: NMU diff for 64-bit time_t transition patch
1059716 libdivsufsort: packaging help likely needed
1048671 libedlib: Fails to build source after successful build ftbfs, sid, trixie
1047938 libjloda-java: Fails to build source after successful build ftbfs, sid, trixie
1062416 libmems: NMU diff for 64-bit time_t transition patch, sid, trixie
1062580 libpwiz: NMU diff for 64-bit time_t transition patch, sid, trixie
1062602 librcsb-core-wrapper: NMU diff for 64-bit time_t transition patch, sid, trixie
1062612 librostlab: NMU diff for 64-bit time_t transition patch
1062619 libsbml: NMU diff for 64-bit time_t transition patch
1015526 libtabixpp: ftbfs with LTO (link time optimization) enabled sid, trixie
1049726 libtabixpp: Fails to build binary packages again after successful build ftbfs, sid, trixie
1062695 libvbz-hdf-plugin: NMU diff for 64-bit time_t transition patch, sid, trixie
1044055 mirtop: test failure with pandas 2.0
1064195 ncbi-tools6: NMU diff for 64-bit time_t transition patch, pending, sid, trixie
1056438 pyfai's autopkg tests fail with Python 3.12 sid, trixie
1044064 pyranges: FTBFS with pandas 2.0 help, sid, trixie
1044074 python-biom-format: FTBFS with pandas 2.0 sid, trixie
1059948 python-biom-format: please remove stale extraneous build-dep on python3-future
1053940 python-cooler: test failure with pandas 2.1 sid, trixie
1059845 Add support for loong64
1044056 python-nanoget: test failure with pandas 2.0 sid, trixie
1060973 python-pbcore: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12 3.11" returned exit code 13 ftbfs, moreinfo, sid, trixie, unreproducible
1054591 python3-pyflow: ${VERSION} not expanded in package metadata, causing PEP-440 validation failures
1048510 python-skbio: Fails to build source after successful build ftbfs, sid, trixie
1049511 python-skbio: Fails to build binary packages again after successful build ftbfs, sid, trixie
1056047 python-skbio: FTBFS with Python 3.12 (test failures) sid, trixie
1063584 python-skbio: tests fail with scipy 1.11
994423 pytorch: Baseline violation on armhf bookworm, bullseye, experimental, ftbfs, sid, trixie
1050175 Missing symbol when importing torch
1060097 pytorch: FBFS: /<<PKGBUILDDIR>>/aten/src/ATen/native/quantized/cpu/qlinear_prepack.cpp:249:103: error: cannot convert ‘dnnl::memory::data_type’ to ‘const ideep::dims&’ {aka ‘const std::vector<long int>&’} ftbfs
1045829 q2-demux: Fails to build source after successful build ftbfs, sid, trixie
1053942 q2-demux: test failure with pandas 2.1
1029700 q2-quality-control: tests fail with scipy 1.10
1044060 q2-quality-control: test failure with pandas 2.0 experimental, help, sid, trixie
1048362 q2-taxa: Fails to build source after successful build ftbfs, sid, trixie
1053943 q2-taxa: test failure with pandas 2.1 help
1044068 q2templates: FTBFS with pandas 2.0 sid, trixie
1053944 q2-types: test failure with pandas 2.1 help
1060965 q2cli: AttributeError: module 'bibtexparser' has no attribute 'bparser' ftbfs, sid, trixie
1060987 q2cli: AttributeError: module 'bibtexparser' has no attribute 'bparser' ftbfs, sid, trixie
1034852 r-bioc-annotationhub: autopkgtest regression: download failed bookworm-ignore
1039501 r-bioc-biomart: autopkgtest regression: Failure ('test_ensembl_ssl_settings.R:71')
1025045 r-bioc-structuralvariantannotation: Test failures in autopkgtest bookworm-ignore, upstream
1063431 src:r-cran-future.apply: fails to migrate to testing for too long: autopkgtest failure sid, trixie, upstream
1064953 rdkit: Please provide cmake files
1061761 snakemake ftbfs with Python 3.12 as default ftbfs, sid, trixie
1049550 terraphast: Fails to build binary packages again after successful build ftbfs, sid, trixie
1058654 toil: python3-boto is being removed from the archive upstream
1061852 toil fails its autopkg tests with Python 3.12 ftbfs, sid, trixie
1057537 vdjtools: FTBFS with default Java 21 ftbfs
*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: Thu, 29 Feb 2024 18:19:22 -0000