Debian Med Project
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Summary
Bugs of task bio-dev
Total bugs: 163
Open bugs: 135
Fixed bugs: 28
Links to other tasks
Biology 314 (1752)
Phylogeny 13 (57)
Cloud 54 (309)
Covid-19 163 (1387)
Medical data 1 (1)
Dental 1 (3)
Epidemiology 4 (75)
Imaging 227 (1030)
Laboratory 1 (9)
Oncology 1 (3)
Pharmacology 1 (9)
Physics 27 (176)
Practice 7 (42)
Psychology 8 (42)
Research 0 (0)
Statistics 3 (7)
Tools 38 (241)
Typesetting 63 (508)
Legend
SeverityDependentSuggested
critical 0 0
grave 0 0
serious 0 2
important 18 2
normal 23 11
minor 60 9
wishlist 9 1

Summary bugs page of task Biology development

Immediately looking into bugs of the dependencies of this task is advised (729)*

Open bugs in dependent packages

18 important, 23 normal, 60 minor, 9 wishlist
865130 reapr FTBFS on big endian: Error sampling from files '00.Sample/fragCov.gz', '00.assembly.fa.gc.gz' ftbfs, upstream
1043881 bamtools: Fails to build source after successful build ftbfs, sid, trixie
1043774 bio-tradis: Fails to build source after successful build ftbfs, sid, trixie
749736 biococoa: GCC warnings that may lead to runtime issues with new GNUstep libraries bookworm, bullseye, buster, jessie, sid, stretch, trixie
1043996 biosquid: Fails to build source after successful build ftbfs, sid, trixie
1049808 biosquid: Fails to build binary packages again after successful build ftbfs, sid, trixie
1056799 cyvcf2: ftbfs with cython 3.0.x sid, trixie
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
1046620 htseq: Fails to build source after successful build ftbfs, sid, trixie
948463 libai-fann-perl: Integer overflow leading to heap buffer overflow
1047073 libbio-asn1-entrezgene-perl: Fails to build source after successful build ftbfs, sid, trixie
1046631 libbio-samtools-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
1015475 libbpp-phyl: ftbfs with LTO (link time optimization) enabled sid, trixie
1015474 libbpp-popgen: ftbfs with LTO (link time optimization) enabled sid, trixie
1015476 libbpp-qt: ftbfs with LTO (link time optimization) enabled sid, trixie
1015477 libbpp-raa: ftbfs with LTO (link time optimization) enabled sid, trixie
1015478 libbpp-seq: ftbfs with LTO (link time optimization) enabled sid, trixie
1015479 libbpp-seq-omics: ftbfs with LTO (link time optimization) enabled sid, trixie
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
1015484 libedlib: ftbfs with LTO (link time optimization) enabled sid, trixie
1048671 libedlib: Fails to build source after successful build ftbfs, sid, trixie
1015486 libfastahack: ftbfs with LTO (link time optimization) enabled sid, trixie
1046227 libgo-perl: Fails to build source after successful build ftbfs, sid, trixie
1047938 libjloda-java: Fails to build source after successful build ftbfs, sid, trixie
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
1046603 libpll: Fails to build source after successful build ftbfs, sid, trixie
1049759 libpll: Fails to build binary packages again 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
1047821 libseqlib: 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
1015525 libssw: ftbfs with LTO (link time optimization) enabled experimental, sid, trixie
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
1057440 libvcflib: 1
1045603 libwfa2: Fails to build source after successful build ftbfs, 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
1044055 mirtop: test failure with pandas 2.0
225651 ncbi-tools-x11: want Cn3D++
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
1056438 pyfai's autopkg tests fail with Python 3.12 sid, trixie
1044064 pyranges: FTBFS with pandas 2.0
1044072 python-anndata: FTBFS with pandas 2.0
1056455 python-anndata's autopkg tests fail with Python 3.12 sid, trixie
1044074 python-biom-format: FTBFS with pandas 2.0
1055709 python-bx ftbfs with Python 3.12 sid, trixie
1053940 python-cooler: test failure with pandas 2.1
1056464 python-csb's autopkg tests fail with Python 3.12 sid, trixie
1044056 python-nanoget: test failure with pandas 2.0
1046425 python-pairix: Fails to build source after successful build ftbfs, sid, trixie
1046452 python-pymummer: Fails to build source after successful build ftbfs, pending, sid, trixie
1045607 python-pyspoa: Fails to build source after successful build ftbfs, sid, trixie
1046140 python-pyvcf: Fails to build source after successful build ftbfs, pending, sid, trixie
1044065 python-skbio: FTBFS with pandas 2.0
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 (and cython 3.0.5) sid, trixie
1056873 python-skbio: ftbfs with cython 3.0.x sid, trixie
1049145 python-sqt: 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
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
1055696 python3-rdkit: unusable with Python 3.12 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

Open bugs in suggested packages

2 serious, 2 important, 11 normal, 9 minor, 1 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
1032358 btllib: Depends on libsdsl-dev, breaking installability when not needed patch
1043870 concurrentqueue: Fails to build source after successful build ftbfs, sid, trixie
976506 conda-package-handling: FTBFS in bullseye (failing tests) bullseye, ftbfs, patch, pending, sid, trixie
1052523 conda-package-handling: please remove extraneous dependency on python3-six
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
1044050 intake: FTBFS with pandas 2.0
1050623 intake: autopkgtest needs update for dask 2023.8.0 ftbfs, sid, trixie
934619 libmaus2 FTBFS (mostly 32bit): error: no matching function for call fixed-upstream, ftbfs, help, upstream
1049859 minimap: Fails to build binary packages again after successful build ftbfs, sid, trixie
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)
1045829 q2-demux: Fails to build source after successful build ftbfs, sid, trixie
1053942 q2-demux: test failure with pandas 2.1
1044060 q2-quality-control: test failure with pandas 2.0
1048362 q2-taxa: Fails to build source after successful build ftbfs, sid, trixie
1053943 q2-taxa: test failure with pandas 2.1
1053944 q2-types: test failure with pandas 2.1
1044068 q2templates: FTBFS with pandas 2.0
1024580 r-bioc-affxparser: FTBFS on hppa - cannot handle R_PARISC_PCREL17F ftbfs, patch
1049550 terraphast: Fails to build binary packages again after successful build ftbfs, sid, trixie

Done bugs

1043819 bbhash: Fails to build source after successful build ftbfs, sid, trixie
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
1055447 htsjdk: FTBFS: 35741 tests completed, 9 failed, 10 skipped ftbfs, sid
1045612 libgoby-java: Fails to build source after successful build ftbfs, sid, trixie
1032532 libthread-pool: fails to compile on 32bit platforms patch
1057253 libvcflib: add support for loongarch64 patch
992180 openmm FTBFS on \!amd64/arm64/hurd-i386/i386/ppc64el ftbfs
1054763 openmm: FTBFS: make[1]: *** [debian/rules:38: override_dh_auto_test] Error 2 ftbfs, sid, trixie
1056323 python-biom-format: FTBFS with Python 3.12 (test failures) ftbfs, patch, sid, trixie
1055708 python-biopython's autopkg tests fail with Python 3.12 sid, trixie
1030885 python-cogent: FTBFS (some tests require more than one CPU) ftbfs, patch
1044066 python-pyani: FTBFS with pandas 2.0
1054591 python3-pyflow: ${VERSION} not expanded in package metadata, causing PEP-440 validation failures
1047165 python-pysam: Fails to build source after successful build ftbfs, sid, trixie
1055505 python-pysam new upstream needed to build with Python 3.12 sid, trixie, upstream
1056037 python-sqt ftbfs with Python 3.12 sid, trixie
994423 pytorch: Baseline violation on armhf bookworm, bullseye, ftbfs, sid
1050175 Missing symbol when importing torch
1029700 q2-quality-control: tests fail with scipy 1.10
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
1054790 rdkit: FTBFS: make[1]: *** [debian/rules:88: override_dh_auto_configure] Error 2 ftbfs, sid, trixie
1053509 shasta: autopkgtest regression on arm64: is memory suddenly not enough?
1045316 snakemake: Fails to build source after successful build ftbfs, sid, trixie
1031192 toil: FTBFS (The job JobClass is requesting 2.0 cores) ftbfs
1048281 unifrac-tools: Fails to build source after successful build ftbfs, sid, trixie
*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: Tue, 05 Dec 2023 16:26:56 -0000