Debian Med Project
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Summary
Bugs of task bio-dev
Total bugs: 202
Open bugs: 141
Fixed bugs: 61
Links to other tasks
Biology 325 (1747)
Phylogeny 15 (90)
Cloud 52 (288)
Covid-19 173 (1328)
Medical data 1 (1)
Dental 1 (3)
Epidemiology 3 (60)
Imaging 229 (1000)
Laboratory 1 (9)
Oncology 1 (3)
Pharmacology 1 (9)
Physics 29 (204)
Practice 7 (42)
Psychology 7 (39)
Research 0 (0)
Statistics 2 (4)
Tools 38 (241)
Typesetting 69 (559)
Legend
SeverityDependentSuggested
critical 0 0
grave 0 0
serious 1 2
important 10 2
normal 22 8
minor 72 14
wishlist 9 1

Summary bugs page of task Biology development

Immediately looking into bugs of the dependencies of this task is advised (662)*

Open bugs in dependent packages

1 serious, 10 important, 22 normal, 72 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
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
1043774 bio-tradis: Fails to build source after successful build ftbfs, 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
1044467 genometools: Fails to build source after successful build ftbfs, sid, trixie
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
1048106 htscodecs: Fails to build source after successful build ftbfs, sid, trixie
1049483 htscodecs: Fails to build binary packages again after successful build ftbfs, sid, trixie
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 bookworm, sid, trixie
1015475 libbpp-phyl: ftbfs with LTO (link time optimization) enabled bookworm, sid, trixie
1015474 libbpp-popgen: ftbfs with LTO (link time optimization) enabled bookworm, sid, trixie
1015476 libbpp-qt: ftbfs with LTO (link time optimization) enabled bookworm, sid, trixie
1015477 libbpp-raa: ftbfs with LTO (link time optimization) enabled bookworm, sid, trixie
1015478 libbpp-seq: ftbfs with LTO (link time optimization) enabled bookworm, sid, trixie
1015479 libbpp-seq-omics: ftbfs with LTO (link time optimization) enabled bookworm, 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 bookworm, sid, trixie
1048671 libedlib: Fails to build source after successful build ftbfs, sid, trixie
1015486 libfastahack: ftbfs with LTO (link time optimization) enabled bookworm, sid, trixie
1045612 libgoby-java: Fails to build source after successful build ftbfs, pending, 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 bookworm, sid, trixie
1015505 libncl: ftbfs with LTO (link time optimization) enabled bookworm, 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 bookworm, sid, trixie
1015526 libtabixpp: ftbfs with LTO (link time optimization) enabled bookworm, sid, trixie
1049726 libtabixpp: Fails to build binary packages again after successful build ftbfs, sid, trixie
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
992180 openmm FTBFS on \!amd64/arm64/hurd-i386/i386/ppc64el ftbfs
1044064 pyranges: FTBFS with pandas 2.0
1044072 python-anndata: FTBFS with pandas 2.0
1044074 python-biom-format: FTBFS with pandas 2.0
1045930 python-cutadapt: Fails to build source after successful build ftbfs, pending, sid, trixie
1049497 python-dendropy: Fails to build binary packages again after successful build ftbfs, sid, trixie
1044056 python-nanoget: test failure with pandas 2.0
1046425 python-pairix: Fails to build source after successful build ftbfs, sid, trixie
1044066 python-pyani: FTBFS with pandas 2.0
1042651 python-pybedtools: FTBFS with Sphinx 7.1, docutils 0.20: error: invalid command 'build_sphinx' ftbfs
1048006 python-pybedtools: Fails to build source after successful build ftbfs, sid, trixie
1046452 python-pymummer: Fails to build source after successful build ftbfs, sid, trixie
1047165 python-pysam: Fails to build source after successful build ftbfs, 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, 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
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
1045932 python-tinyalign: Fails to build source after successful build ftbfs, pending, sid, trixie
983517 pytorch: Build documentation
1045833 r-cran-gprofiler2: Fails to build source after successful build ftbfs, sid, trixie
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
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
1045316 snakemake: Fails to build source after successful build ftbfs, pending, sid, trixie
1015667 spoa: ftbfs with LTO (link time optimization) enabled bookworm, sid, trixie
1040391 sra-toolkit: broken symlink: /usr/lib/debian-med/bin/kget -> ../../../bin/vdb-get
1042198 unifrac: FTBFS: AssertionError: 0.9999999403953552 != 1.0 ftbfs, sid, trixie
1048281 unifrac-tools: Fails to build source after successful build ftbfs, sid, trixie

Open bugs in suggested packages

2 serious, 2 important, 8 normal, 14 minor, 1 wishlist
1043819 bbhash: Fails to build source after successful build ftbfs, sid, trixie
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, 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
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
1044060 q2-quality-control: test failure with pandas 2.0
1048362 q2-taxa: Fails to build source after successful build ftbfs, sid, trixie
1044068 q2templates: FTBFS with pandas 2.0
1024580 r-bioc-affxparser: FTBFS on hppa - cannot handle R_PARISC_PCREL17F ftbfs, patch
1049205 r-bioc-affyio: Fails to build source after successful build ftbfs, sid, trixie
1049248 r-bioc-makecdfenv: Fails to build source after successful build ftbfs, sid, trixie
998030 r-cran-dt: Add xdg-open app open attempts as recommended a11y
1045485 r-cran-fastcluster: Fails to build source after successful build ftbfs, sid, trixie
1049523 r-cran-fastcluster: Fails to build binary packages again after successful build ftbfs, sid, trixie
1049550 terraphast: Fails to build binary packages again after successful build ftbfs, sid, trixie

Done bugs

1043827 biomaj3: Fails to build source after successful build ftbfs, sid, trixie
1049886 btllib: FTBFS on armhf due to tests timing out ftbfs, sid, trixie
1045100 conda-package-handling: Fails to build source after successful build ftbfs, sid, trixie
1045084 ctdopts: Fails to build source after successful build ftbfs, sid, trixie
1044618 cwlformat: Fails to build source after successful build ftbfs, sid, trixie
1044843 fast5: Fails to build source after successful build ftbfs, sid, trixie
1015412 gatb-core: ftbfs with LTO (link time optimization) enabled bookworm, sid, trixie
1044916 gfapy: 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
1015488 libgenome: ftbfs with LTO (link time optimization) enabled bookworm, sid, trixie
1042662 librostlab: FTBFS with Sphinx 7.1, docutils 0.20: make: *** [debian/rules:8: binary] Error 25 ftbfs
1015520 libseqlib: ftbfs with LTO (link time optimization) enabled bookworm, sid, trixie
1042116 libstatgen: FTBFS: dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols file: see diff output below ftbfs, sid, trixie
1032532 libthread-pool: fails to compile on 32bit platforms patch
1043584 pbbam FTBFS with pbcopper 2.2.0 ftbfs, sid, trixie
1045826 pyfastx: Fails to build source after successful build ftbfs, sid, trixie
1042046 pyranges: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.11 returned exit code 13 ftbfs, sid, trixie
1046655 python-bcbio-gff: Fails to build source after successful build ftbfs, sid, trixie
1047173 python-bel-resources: Fails to build source after successful build ftbfs, sid, trixie
1045752 python-bioframe: Fails to build source after successful build ftbfs, sid, trixie
1048964 python-cgelib: Fails to build source after successful build ftbfs, sid, trixie
1047698 python-cigar: Fails to build source after successful build ftbfs, sid, trixie
1042310 python-cobra: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.11 returned exit code 13 ftbfs, sid, trixie
1045711 python-cooler: Fails to build source after successful build ftbfs, sid, trixie
1049301 python-csb: Fails to build source after successful build ftbfs, sid, trixie
1045708 python-dendropy: Fails to build source after successful build ftbfs, sid, trixie
1049164 python-gffutils: Fails to build source after successful build ftbfs, sid, trixie
1048197 python-intervaltree-bio: Fails to build source after successful build ftbfs, sid, trixie
1048906 python-nanoget: Fails to build source after successful build ftbfs, sid, trixie
1045604 python-pangolearn: Fails to build source after successful build ftbfs, sid, trixie
1047143 python-parasail: Fails to build source after successful build ftbfs, sid, trixie
1048696 python-wdlparse: Fails to build source after successful build ftbfs, sid, trixie
994423 pytorch: Baseline violation on armhf bookworm, bullseye, ftbfs, sid
1024903 pytorch: CVE-2022-45907: torch.jit.annotations.parse_type_line prone to command injection fixed-upstream, security, upstream
1031687 libtorch-dev: ATEN_INCLUDE_DIR in ATenConfig.cmake uses build path
1035458 libtorch-dev: broken symlinks: /usr/lib/x86_64-linux-gnu/libcaffe2_*.so -> libcaffe2_*.so.1.13
1037824 pytorch: ftbfs with GCC-13 experimental, ftbfs, sid, trixie
1050175 Missing symbol when importing torch
1051258 pytorch2 ftbfs on ppc64el fixed-upstream, patch, sid, trixie
1051828 pytorch: needs-root for autopkgtests?
1048491 q2-alignment: Fails to build source after successful build ftbfs, sid, trixie
1045721 q2cli: Fails to build source after successful build ftbfs, sid, trixie
1047153 q2-metadata: Fails to build source after successful build ftbfs, sid, trixie
1029700 q2-quality-control: tests fail with scipy 1.10
1045458 q2-quality-filter: Fails to build source after successful build 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')
1024661 r-bioc-bitseq: orphaned upstream and blocking BioC 3.16 transition ftbfs
1050026 r-bioc-metagenomeseq: autopkgtest regression upstream
1025045 r-bioc-structuralvariantannotation: Test failures in autopkgtest bookworm-ignore, upstream
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, trixie
1037837 rdkit: ftbfs with GCC-13 ftbfs, sid, trixie
1039561 seqan3's autopkg tests fail to build sid, trixie
1041371 seqan3 autopkg test fails sid, trixie
1042196 shasta: FTBFS: Base.hpp:35:18: error: ‘uint8_t’ was not declared in this scope ftbfs, sid, trixie
1031192 toil: FTBFS (The job JobClass is requesting 2.0 cores) ftbfs
1047298 toil: Fails to build source after successful build ftbfs, sid, trixie
1037879 unifrac-tools: ftbfs with GCC-13 ftbfs, sid, trixie
1042340 xxsds-dynamic: FTBFS: make: *** [debian/rules:9: binary] Error 2 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: Thu, 21 Sep 2023 18:19:08 -0000