Debian Med Project
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Summary
Bugs of task bio-dev
Total bugs: 78
Open bugs: 70
Fixed bugs: 8
Links to other tasks
Tasks overview
Biology 144 (1213)
Phylogeny 5 (33)
Cloud 24 (210)
Covid-19 125 (1193)
Medical data 0 (0)
Dental 0 (0)
Epidemiology 6 (99)
Imaging 219 (1019)
Laboratory 1 (9)
Oncology 1 (5)
Pharmacology 1 (9)
Physics 26 (210)
Practice 4 (27)
Psychology 4 (28)
Research 0 (0)
Statistics 2 (4)
Tools 36 (236)
Typesetting 66 (536)
Legend
SeverityDependentSuggested
critical 0 1
grave 1 0
serious 2 3
important 12 2
normal 16 5
minor 19 1
wishlist 8 0

Summary bugs page of task Biology development

Immediately looking into bugs of the dependencies of this task is advised (537)*

Open bugs in dependent packages

1 grave, 2 serious, 12 important, 16 normal, 19 minor, 8 wishlist
bamtools (1) Homepage: https://github.com/pezmaster31/bamtools/wiki Vcs Debian Med Packaging Team
865130 reapr FTBFS on big endian: Error sampling from files '00.Sample/fragCov.gz', '00.assembly.fa.gc.gz' ftbfs, upstream
biococoa (1) Homepage: https://bioinformatics.org/biococoa/ Vcs Debian Med Packaging Team
749736 biococoa: GCC warnings that may lead to runtime issues with new GNUstep libraries bookworm, bullseye, buster, jessie, sid, stretch
gatb-core (3) Homepage: https://github.com/GATB/gatb-core Vcs Debian Med Packaging Team
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
gffread (1) Homepage: https://ccb.jhu.edu/software/stringtie/gff.shtml Vcs Debian Med Packaging Team
1033703 gffread: autopkgtest regression: test dependency not in testing bookworm-ignore
hdf5 (17) Homepage: http://hdfgroup.org/HDF5/ Vcs Gilles Filippini
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
libai-fann-perl (1) Homepage: https://metacpan.org/release/AI-FANN Vcs Debian Perl Group
948463 libai-fann-perl: Integer overflow leading to heap buffer overflow
libbio-scf-perl (1) Homepage: https://metacpan.org/release/Bio-SCF Vcs Debian Perl Group
599961 libbio-scf-perl: FTBFS: Neither BIG nor LITTLE endian defined
libbpp-core (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
1015473 libbpp-core: ftbfs with LTO (link time optimization) enabled bookworm, sid
libbpp-phyl (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
1015475 libbpp-phyl: ftbfs with LTO (link time optimization) enabled bookworm, sid
libbpp-popgen (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
1015474 libbpp-popgen: ftbfs with LTO (link time optimization) enabled bookworm, sid
libbpp-qt (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
1015476 libbpp-qt: ftbfs with LTO (link time optimization) enabled bookworm, sid
libbpp-raa (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
1015477 libbpp-raa: ftbfs with LTO (link time optimization) enabled bookworm, sid
libbpp-seq (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
1015478 libbpp-seq: ftbfs with LTO (link time optimization) enabled bookworm, sid
libbpp-seq-omics (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
1015479 libbpp-seq-omics: ftbfs with LTO (link time optimization) enabled bookworm, sid
libedlib (1) Homepage: https://github.com/Martinsos/edlib Vcs Debian Med Packaging Team
1015484 libedlib: ftbfs with LTO (link time optimization) enabled bookworm, sid
libfastahack (1) Homepage: https://github.com/ekg/fastahack Vcs Debian Med Packaging Team
1015486 libfastahack: ftbfs with LTO (link time optimization) enabled bookworm, sid
libgenome (1) Homepage: https://sourceforge.net/projects/libgenome/ Vcs Debian Med Packaging Team
1015488 libgenome: ftbfs with LTO (link time optimization) enabled bookworm, sid
libmuscle (1) Homepage: http://sourceforge.net/p/mauve/code/HEAD/tree/muscle/trunk/ Vcs Debian Med Packaging Team
1015504 libmuscle: ftbfs with LTO (link time optimization) enabled bookworm, sid
libncl (1) Homepage: https://github.com/mtholder/ncl Vcs Debian Med Packaging Team
1015505 libncl: ftbfs with LTO (link time optimization) enabled bookworm, sid
libseqlib (1) Homepage: https://github.com/walaj/SeqLib Vcs Debian Med Packaging Team
1015520 libseqlib: ftbfs with LTO (link time optimization) enabled bookworm, sid
libssw (1) Homepage: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library Vcs Debian Med Packaging Team
1015525 libssw: ftbfs with LTO (link time optimization) enabled bookworm, sid
libtabixpp (1) Homepage: https://github.com/ekg/tabixpp Vcs Debian Med Packaging Team
1015526 libtabixpp: ftbfs with LTO (link time optimization) enabled bookworm, sid
libvcflib (1) Homepage: https://github.com/vcflib/vcflib Vcs Debian Med Packaging Team
1032557 libvcflib breaks ABI without SONAME bump
ncbi-tools6 (1) Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/ Vcs Debian Med Packaging Team
225651 ncbi-tools-x11: want Cn3D++
openmm (1) Homepage: https://simtk.org/home/openmm Vcs Debichem Team
992180 openmm FTBFS on \!amd64/arm64/hurd-i386/i386/ppc64el ftbfs
python-biopython (1) Homepage: https://biopython.org Vcs Debian Med Packaging Team
1036174 FTBFS with nocheck option confirmed, ftbfs
python-pysam (1) Homepage: https://pysam.readthedocs.org/en/latest Vcs Debian Med Packaging Team
1027386 pysam -- no definition for bam_dup1 confirmed
pytorch (4) Homepage: https://pytorch.org/ Vcs Debian Deep Learning Team
983517 pytorch: Build documentation
1024903 pytorch: CVE-2022-45907: torch.jit.annotations.parse_type_line prone to command injection 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
rdkit (6) Homepage: http://www.rdkit.org Vcs Debichem Team
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
seqan2 (1) Homepage: https://www.seqan.de/ Vcs Debian Med Packaging Team
917851 seqan2 2.4.0+dfsg-9: FTBFS, alignment problem ftbfs
spoa (1) Homepage: https://github.com/rvaser/spoa Vcs Debian Med Packaging Team
1015667 spoa: ftbfs with LTO (link time optimization) enabled bookworm, sid
toil (1) Homepage: https://github.com/BD2KGenomics/toil Vcs Debian Med Packaging Team
1031192 toil: FTBFS (The job JobClass is requesting 2.0 cores) ftbfs

Open bugs in suggested packages

1 critical, 3 serious, 2 important, 5 normal, 1 minor
bcbio (2) Homepage: https://github.com/bcbio/bcbio-nextgen Vcs Debian Med Packaging Team
928076 bcbio: Workflows not ready for non-developers to depend on.
1018312 bcbio: build-depends on python3-nose or uses it for autopkgtest
btllib (2) Homepage: https://github.com/bcgsc/btllib Vcs Debian Med Packaging Team
1022772 btllib: fails to build on 32-bit archs
1032358 btllib: Depends on libsdsl-dev, breaking installability when not needed patch
conda-package-handling (1) Homepage: https://github.com/conda/conda-package-handling Vcs Debian Med Packaging Team
976506 conda-package-handling: FTBFS in bullseye (failing tests) bullseye, ftbfs, patch, sid
libmaus2 (1) Homepage: https://gitlab.com/german.tischler/libmaus2 Vcs Debian Med Packaging Team
934619 libmaus2 FTBFS (mostly 32bit): error: no matching function for call fixed-upstream, ftbfs, help, upstream
python-seqcluster (1) Homepage: https://github.com/lpantano/seqcluster Vcs Debian Med Packaging Team
1035277 python-seqcluster: please add autopkgtests (to add coverage for python3-numpy)
r-bioc-affxparser (1) Homepage: https://bioconductor.org/packages/affxparser/ Vcs Debian R Packages Maintainers
1024580 r-bioc-affxparser: FTBFS on hppa - cannot handle R_PARISC_PCREL17F ftbfs, patch
r-bioc-annotationhub (1) Homepage: https://bioconductor.org/packages/AnnotationHub/ Vcs Debian R Packages Maintainers
1034852 r-bioc-annotationhub: autopkgtest regression: download failed bookworm-ignore
r-bioc-bitseq (1) Homepage: https://bioconductor.org/packages/BitSeq/ Vcs Debian R Packages Maintainers
1024661 r-bioc-bitseq: orphaned upstream and blocking BioC 3.16 transition ftbfs
r-bioc-structuralvariantannotation (1) Homepage: https://bioconductor.org/packages/StructuralVariantAnnotation/ Vcs Debian R Packages Maintainers
1025045 r-bioc-structuralvariantannotation: Test failures in autopkgtest bookworm-ignore, upstream
r-cran-dt (1) Homepage: https://cran.r-project.org/package=DT Vcs Debian R Packages Maintainers
998030 r-cran-dt: Add xdg-open app open attempts as recommended a11y

Done bugs

freecontact (1) Homepage: https://rostlab.org/ Vcs Debian Med Packaging Team
1036260 freecontact: FTBFS in testing: make[1]: *** [debian/rules:29: override_dh_install] Error 1 bookworm, confirmed, ftbfs, patch, sid
hdf5 (1) Homepage: http://hdfgroup.org/HDF5/ Vcs Gilles Filippini
972537 please add --enable-ros3-vfd to the build options to allow RO access to HDF5 on S3
libthread-pool (1) Homepage: https://github.com/rvaser/thread_pool Vcs Debian Med Packaging Team
1032532 libthread-pool: fails to compile on 32bit platforms patch
python-cobra (1) Homepage: https://opencobra.github.io/cobrapy/ Vcs Debian Med Packaging Team
912586 python-cobra still fails it's autopkg tests bullseye, buster, help, sid
python-skbio (1) Homepage: https://github.com/biocore/scikit-bio Vcs Debian Med Packaging Team
991981 python3-skbio: package installs .../dist-packages/benchmarks/..
pytorch (1) Homepage: https://pytorch.org/ Vcs Debian Deep Learning Team
994423 pytorch: Baseline violation on armhf bookworm, bullseye, ftbfs, sid
q2-metadata (1) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1029699 q2-metadata: tests fail with scipy 1.10
q2-quality-control (1) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1029700 q2-quality-control: tests fail with scipy 1.10
*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, 01 Jun 2023 04:55:13 -0000