Debian Med Project
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Summary
Bugs of task bio
Total bugs: 158
Open bugs: 144
Fixed bugs: 14
Links to other tasks
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 1 0
grave 0 2
serious 9 6
important 20 8
normal 45 15
minor 14 1
wishlist 18 5

Summary bugs page of task Biology

Immediately looking into bugs of the dependencies of this task is advised (1213)*

Open bugs in dependent packages

1 critical, 9 serious, 20 important, 45 normal, 14 minor, 18 wishlist
920282 abyss fails to build on hurd - googletest EXPECT_DEATH
967243 acedb: depends on deprecated GTK 2
1032625 please drop transitional package acedb-other-belvu from src:acedb
1032626 please drop transitional package acedb-other-dotter from src:acedb
1012893 anfo: ftbfs with GCC-12 bookworm, ftbfs, help, sid
1035113 arden: please add autopkgtests (to add coverage for python3-numpy)
1036488 arden: please add autopkgtests (to add coverage for python3-matplotlib)
1035116 assemblytics: please add autopkgtests (to add coverage for python3-numpy)
865130 reapr FTBFS on big endian: Error sampling from files '00.Sample/fragCov.gz', '00.assembly.fa.gc.gz' ftbfs, upstream
870060 bcftools FTBFS on big endian: 107 tests failed ftbfs, upstream
1032034 beagle: broken package on non arm64/amd64 architectures
1025424 beast-mcmc: please enable autopkgtest help
1025830 beauti2 fails to start help
1035121 bitseq: please add autopkgtests (to add coverage for python3-numpy)
1022772 btllib: fails to build on 32-bit archs
1032358 btllib: Depends on libsdsl-dev, breaking installability when not needed patch
1010653 busco: add autopkgtest to check integration with hmmer and prodigal
1032036 chromhmm: broken package on non arm64/amd64 architectures
884475 clonalorigin: FTBFS on alpha: tests time out upstream, wontfix
1035182 cutesv: please add autopkgtests (to add coverage for python3-numpy)
982869 datamash FTBFS on !x86 32bit: FAIL: tests/decorate-errors ftbfs, upstream
903886 dawg: Test suite fails upstream
862118 ea-utils: New upstream version available
682042 emboss-data: ships bulky taxonomy and gene ontology data
986043 emboss: uses media types that are not registered
750139 gamgi: Conflicting return types of function gamgi_engine_iarray_push upstream
967366 gamgi: depends on deprecated GTK 2
715937 [Mayhem] Bug report on garlic: garlic crashes with exit status 139
749656 garlic: Conflicting declarations of function BlurMainWindow_ to cause undefined behaviour
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
967379 gdpc: depends on deprecated GTK 2 wontfix
982103 gdpc: autopkgtest failure on s390x
732691 Pressing "alignment or Ctrl+G" only results in a dialog with a cancel button upstream
1033703 gffread: autopkgtest regression: test dependency not in testing bookworm-ignore
967392 ghemical: depends on deprecated GTK 2
967865 ghemical: depends on deprecated libglade2
996006 ghemical: Segmentation fault when starting
644397 Provide runtime detection for CPU SIMD capabilities upstream
983942 gromacs: ftbfs with -march=x86-64-v3
958244 Use system libinih-dev
986193 hinge: no autopkgtest available yet newcomer
1035178 hinge: please add autopkgtests (to add coverage for python3-numpy)
1036500 hinge: please add autopkgtests (to add coverage for python3-matplotlib)
1032975 igdiscover -- Broken, unusable package due to incomplete code in the binary package
1021557 jellyfish: Performance regression in 2.3.0 (orders of magnitude for some inputs) upstream
875328 jellyfish1: FTBFS: __sync_val_compare_and_swap_8 undefined upstream, wontfix
872418 jmol: Weblinks in Help do not work
1009159 kmerresistance: Add autopkgtest newcomer
1015486 libfastahack: ftbfs with LTO (link time optimization) enabled bookworm, sid
1015505 libncl: ftbfs with LTO (link time optimization) enabled bookworm, sid
1015525 libssw: ftbfs with LTO (link time optimization) enabled bookworm, sid
1032557 libvcflib breaks ABI without SONAME bump
967603 ltrsift: depends on deprecated GTK 2 upstream, wontfix
1035175 metaphlan: please add autopkgtests (to add coverage for python3-numpy)
1035188 microbegps: please add autopkgtests (to add coverage for python3-numpy)
1036480 microbegps: please add autopkgtests (to add coverage for python3-matplotlib)
996981 multiqc: Link to jquery missing
891197 Please switch to pcre2
956850 ncbi-blast+: Please provide /usr/bin/legacy_blast.pl
984871 ncbi-blast+: Missing headers for shared libraries
1010110 ncbi-blast+: terminate called after throwing an instance of 'ncbi::CIO_Exception' wontfix
225651 ncbi-tools-x11: want Cn3D++
1025370 ntcard: ftbfs with nthash 2.3.0 ftbfs, upstream
1032672 ntcard: disabling "32-bit" disabled too many archs patch
964082 parsinsert fails it's tests when built with -O3 bookworm, bullseye, moreinfo, sid, unreproducible
986194 pique: no autopkgtest available yet newcomer
1009156 pplacer: Add autopkgtest
1024889 pplacer: build-depedends on dropped package.
602610 Package freemol.mengine for full modeling capabilities
709306 pymol: Crashes when running within xrdp/vnc (no 3D support)
765794 Race condition when running scripts in "stdin" mode
783653 pymol: Segmentation fault immediately after loading pdb
1036374 [INTL:es] Spanish translation of qcumber debconf template l10n, patch
1036506 qcumber: please add autopkgtests (to add coverage for python3-matplotlib)
1030954 quorum: ftbfs with LTO (link time optimization) enabled bookworm, sid
642084 qutemol: Cannot start the program
939033 qutemol: Uses GifQuantizeBuffer - stops working with newer giflib
1024661 r-bioc-bitseq: orphaned upstream and blocking BioC 3.16 transition ftbfs
1033853 r-bioc-megadepth: autopkgtest regression: different output bookworm-ignore
961234 r-cran-treescape: FTBFS on ppc64el:Segmentation fault bookworm, bullseye, ftbfs, sid
909766 Use Debian packaged spdlog instead of code copy of old version help, upstream
976588 rapmap: FTBFS on arm64 (when trying to build arch:all) bookworm, bullseye, ftbfs, sid
1027384 rnahybrid: please enable riscv64 build ftbfs, pending
1015654 sambamba: ftbfs with LTO (link time optimization) enabled bookworm, sid
917851 seqan2 2.4.0+dfsg-9: FTBFS, alignment problem ftbfs
967743 seqtools: depends on deprecated GTK 2
848589 snap-aligner: Build requires 188 GB of memory (fortunately not used, just allocated)
1031465 snippy: FTBFS: make[2]: *** [Makefile:32: S1/snps.tab] Error 2 bookworm, ftbfs, sid
1029202 snippy: Error when using snpeff 5.1 upstream
976523 spades: FTBFS: jemalloc_internal.h:292:6: error: #error "No LG_QUANTUM definition for architecture; specify via CPPFLAGS" bookworm, bullseye, ftbfs, sid
1015668 spades: ftbfs with LTO (link time optimization) enabled bookworm, sid
1015667 spoa: ftbfs with LTO (link time optimization) enabled bookworm, sid
1033089 subread: reproducible-builds: Embedded build path in various binaries patch
956848 t-coffee: should use "example" blastpgp.pl
1031192 toil: FTBFS (The job JobClass is requesting 2.0 cores) ftbfs
846481 src:treeviewx: Please remove statically linked code copy of libncl
981874 trinityrnaseq: flaky autopkgtest bookworm, bullseye, sid
1004773 trinityrnaseq: test loops until disk full (with r-cran-readr from unstable on arm64)
1006336 trinityrnaseq: autopkgtest regression in testing: segmentation fault
980509 umap-learn: Binary package name should be python3-umap-learn pending
976511 vg: FTBFS on arm64: configure: error: Could not find a version of the library! bookworm, bullseye, ftbfs, sid
987184 vg -- excessive variants built, and not tested
1013061 vg: ftbfs with GCC-12 bookworm, ftbfs, sid
1015699 vg: ftbfs with LTO (link time optimization) enabled bookworm, sid
1035276 xpore: please add autopkgtests (to add coverage for python3-numpy)

Open bugs in suggested packages

2 grave, 6 serious, 8 important, 15 normal, 1 minor, 5 wishlist
916406 libarb-dev: Missing symbols in static libraries
918015 [INTL:sv] Swedish strings for arb debconf l10n, patch
1026401 arb: [INTL:pt_BR] Brazilian Portuguese debconf templates translation l10n, patch
928076 bcbio: Workflows not ready for non-developers to depend on.
1018312 bcbio: build-depends on python3-nose or uses it for autopkgtest
976506 conda-package-handling: FTBFS in bullseye (failing tests) bullseye, ftbfs, patch, sid
1030327 science-numericalcomputation: please stop recommending python3-theano as it is being removed
1032638 please drop transitional package science-electronics from src:debian-science
995966 epigrass: epirunner and epidash fail to run due to missing dash modules pending
998265 epigrass: autopkgtest regression: The 'panel' distribution was not found
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
1027386 pysam -- no definition for bam_dup1 confirmed
1035277 python-seqcluster: please add autopkgtests (to add coverage for python3-numpy)
1034852 r-bioc-annotationhub: autopkgtest regression: download failed bookworm-ignore
1025045 r-bioc-structuralvariantannotation: Test failures in autopkgtest bookworm-ignore, upstream
1036681 relion-cuda: FTBFS with CUDA 12: nvcc fatal : Value 'sm_35' is not defined for option 'gpu-architecture' ftbfs, sid
986200 sift: Please provide autopkgtest newcomer
987606 sift: does not autobuild on buildds
1010358 ugene: Fix for non-constant SIGSTKSZ ftbfs, patch, pending
1018252 Is ugene still non-free?
1032688 ugene: unused build-dependency on removed libprocps-dev patch

Done bugs

1010834 biosyntax-vim: Unusable with vim-addon-manager because of outdated manifest
1010836 biosyntax-gedit: No longer works with recent versions of gedit
1029689 emperor: tests fail with scipy 1.10
1032566 fastqc: new upstream version 0.12.1
1036260 freecontact: FTBFS in testing: make[1]: *** [debian/rules:29: override_dh_install] Error 1 bookworm, confirmed, ftbfs, patch, sid
972537 please add --enable-ros3-vfd to the build options to allow RO access to HDF5 on S3
1025739 hmmer2: missing source for configure
1035484 jmol: broken symlink: /usr/share/jmol/JSpecView.jar -> ../java/JSpecView.jar
1004053 kallisto: reproducible-builds: timestamps and build path embedded in test suite metadata patch
1036743 kleborate: debsums reports modified files after apt-get upgrade && apt-get dist-upgrade
1016941 phyml: flaky autopkgtest on armel: test duration around autopkgtest timeout
1034552 pullseq hangs on arm64
1029699 q2-metadata: tests fail with scipy 1.10
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