Debian Med Project
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Bugs of task bio
Total bugs: 147
Open bugs: 133
Fixed bugs: 14
Links to other tasks
Biology 133 (1379)
Phylogeny 3 (12)
Cloud 29 (333)
Covid-19 138 (1464)
Medical data 0 (0)
Dental 0 (0)
Epidemiology 7 (139)
Imaging 212 (1123)
Laboratory 1 (9)
Oncology 2 (39)
Pharmacology 1 (9)
Physics 26 (201)
Practice 6 (45)
Psychology 4 (42)
Research 0 (0)
Statistics 1 (3)
Tools 29 (200)
Typesetting 66 (535)
critical 0 0
grave 0 1
serious 14 5
important 27 4
normal 47 12
minor 5 0
wishlist 14 4

Summary bugs page of task Biology

Immediately looking into bugs of the dependencies of this task is advised (1379)*

Open bugs in dependent packages

14 serious, 27 important, 47 normal, 5 minor, 14 wishlist
920282 abyss fails to build on hurd - googletest EXPECT_DEATH
967243 acedb: depends on deprecated GTK 2
1012893 anfo: ftbfs with GCC-12 bookworm, sid
865130 reapr FTBFS on big endian: Error sampling from files '00.Sample/fragCov.gz', '00.assembly.fa.gc.gz' ftbfs, upstream
988848 libbamtools-doc: broken symlink: /usr/share/doc/libbamtools-dev/html/jquery.js -> ../../../javascript/jquery/jquery.js
992143 bamtools: autopkgtest failure: times out on armel
870060 bcftools FTBFS on big endian: 107 tests failed ftbfs, upstream
1010834 biosyntax-vim: Unusable with vim-addon-manager because of outdated manifest
1010836 biosyntax-gedit: No longer works with recent versions of gedit
1010653 busco: add autopkgtest to check integration with hmmer and prodigal
1012906 cif-tools: ftbfs with GCC-12 bookworm, sid
884475 clonalorigin: FTBFS on alpha: tests time out upstream, wontfix
982869 datamash FTBFS on !x86 32bit: FAIL: tests/decorate-errors ftbfs, upstream
903886 dawg: Test suite fails upstream
921566 deepnano: autopkgtest times out since 2019-01-11
1012913 dssp: ftbfs with GCC-12 bookworm, sid
846858 src:ea-utils: New version available
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
902132 falcon: FTBFS since python-networkx version 2.1-1; fails in test suite ftbfs, pending
936503 falcon: Python2 removal in sid/bullseye fixed-upstream, pending, upstream
1008220 flexbar 3.5.0-4 FTBFS against libtbb-dev 2021.5.0-7 ftbfs
1011656 flexbar ftbfs: cannot find tbb header
1012127 flexbar: FTBFS with onetbb/2021.5.0-8 in experimental ftbfs
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
1012934 gatb-core: ftbfs with GCC-12 bookworm, sid
967379 gdpc: depends on deprecated GTK 2
982103 gdpc: autopkgtest failure on s390x
732691 Pressing "alignment or Ctrl+G" only results in a dialog with a cancel button
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
1012573 harvest-tools: FTBFS with protobuf 3.20.1+ bookworm, ftbfs, patch, sid, upstream
958244 Use system libinih-dev
986193 hinge: no autopkgtest available yet newcomer
977067 igdiscover: test suite flaky, possibly on high core count machines confirmed, moreinfo, unreproducible
875328 jellyfish1: FTBFS: __sync_val_compare_and_swap_8 undefined upstream, wontfix
1008944 jellyfish1: autopkgtest failure on armhf and i386: Matrix is singular
872418 jmol: Weblinks in Help do not work
1008402 khmer: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.10 3.9" returned exit code 13 bookworm, ftbfs, sid
1009159 kmerresistance: Add autopkgtest newcomer
1012976 libfastahack: ftbfs with GCC-12 bookworm, sid
1012984 libncl: ftbfs with GCC-12 bookworm, sid
967603 ltrsift: depends on deprecated GTK 2
1013408 macsyfinder: FTBFS with Sphinx 5.0, docutils 0.18: dh_auto_test: error: pybuild --test -i python{version} -p 3.10 returned exit code 13 ftbfs
996981 multiqc: Link to jquery missing
956751 mummerplot incompatible with Debian's version of gnuplot
891197 Please switch to pcre2
956850 ncbi-blast+: Please provide /usr/bin/
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++
964082 parsinsert fails it's tests when built with -O3 bookworm, bullseye, moreinfo, sid, unreproducible
993019 perm -- Buffer overflows
1011156 picard-tools: FTBFS with OpenJDK 17 due to com.sun.javadoc removal bookworm, ftbfs, sid
1013577 picard-tools: FTBFS: error: cannot find symbol bookworm, ftbfs, sid
986194 pique: no autopkgtest available yet newcomer
1009156 pplacer: Add autopkgtest
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
1013026 quorum: ftbfs with GCC-12 bookworm, sid
642084 qutemol: Cannot start the program
939033 qutemol: Uses GifQuantizeBuffer - stops working with newer giflib
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
961234 r-cran-treescape: FTBFS on ppc64el:Segmentation fault bookworm, bullseye, ftbfs, sid
1008252 salmon: FTBFS in unstable and testing ftbfs
1008254 salmon: FTBFS with glibc 2.34 ftbfs
1011662 salmon ftbfs against onetbb/experimental: tbb api break
1011742 salmon: FTBFS with onetbb/2021.5.0-8 in experimental ftbfs
892222 seqan2: FTBFS on hppa: app_test_seqan_tcoffee fails on 2trx.mlcs.fasta upstream
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)
853113 spades: Fails to build with unhelpful error message in a "low" memory machine
976523 spades: FTBFS: jemalloc_internal.h:292:6: error: #error "No LG_QUANTUM definition for architecture; specify via CPPFLAGS" bookworm, bullseye, ftbfs, sid
1011968 spades: autopkgtest regression
956848 t-coffee: should use "example"
1013275 toil: FTBFS with Python 3.10 only 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
1002400 umap-learn: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.9 --system=custom "--test-args=PYTHONPATH={build_dir} {interpreter} -m pytest" returned exit code 13 bookworm, ftbfs, sid
1013058 uncalled: ftbfs with GCC-12 bookworm, sid
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, sid
446750 reading vmol files: coord factor ignored and misdefined
446753 pdb import is broken
716250 [Mayhem] Bug report on viewmol: readpdb crashes with exit status 139
716256 [Mayhem] Bug report on viewmol: readgamess crashes with exit status 139
875522 viewmol: Please stop installing deprecated mimelnk files
938774 viewmol: Python2 removal in sid/bullseye bookworm, bullseye, sid
967229 viewmol: Unversioned Python removal in sid/bullseye bookworm, bullseye, sid
1013064 vmatch: ftbfs with GCC-12 bookworm, sid

Open bugs in suggested packages

1 grave, 5 serious, 4 important, 12 normal, 4 wishlist
916406 libarb-dev: Missing symbols in static libraries
918015 [INTL:sv] Swedish strings for arb debconf l10n, patch
928076 bcbio: Workflows not ready for non-developers to depend on.
1011982 science-config: configuration file "90science-config" is missing semi-colon. Causes "unable to parse the config file" errors
995966 epigrass: epirunner and epidash fail to run due to missing dash modules
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
997059 intake FTBFS on IPV6-only buildds confirmed, ftbfs, ipv6
1013703 pyranges: FTBFS: pytest7 regression, py3.9 OK; py3.10 fails with Fatal Python error: Bus error bookworm, ftbfs, sid
1012386 python-seqcluster: FTBFS: ModuleNotFoundError: No module named 'attr' ftbfs
994459 libjs-jquery removed symlinked files moreinfo
995224 relion-cuda: FTBFS with cub 1.14 bookworm, ftbfs, sid
986200 sift: Please provide autopkgtest newcomer
987606 sift: does not autobuild on buildds
1010358 ugene: Fix for non-constant SIGSTKSZ patch

Done bugs

1008719 /usr/bin/avogadro2: molecules are loaded but nothing is displayed
1009383 gromacs: FTBFS: AttributeError: module 'collections' has no attribute 'Iterable' bookworm, experimental, ftbfs, sid
972537 please add --enable-ros3-vfd to the build options to allow RO access to HDF5 on S3
1012071 igv: FTBFS with OpenJDK 17 due to removed public constructor bookworm, ftbfs, sid
1011184 jalview: FTBFS with OpenJDK 17 due to JSObject.getWindow() removal bookworm, ftbfs, sid
1012953 jellyfish: ftbfs with GCC-12 bookworm, confirmed, sid, upstream
1011541 src:jellyfish1: fails to migrate to testing for too long: autopkgtest regression bookworm, sid
1013000 mira: ftbfs with GCC-12 bookworm, sid
1013608 ncbi-entrez-direct: FTBFS: cannot find package "" bookworm, ftbfs, sid
997488 q2cli: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.9 returned exit code 13 bookworm, confirmed, fixed-upstream, ftbfs, sid, upstream
1011412 r-bioc-scater: autopkgtest regression in testing bookworm, sid
1013030 rna-star: ftbfs with GCC-12 bookworm, sid
1012257 libsnpeff-java-doc: Unnecessary dependency on libfreemarker-java-doc
1010788 spades: Mismatch correction / --careful mode broken by Debian patch
*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:
Last update: Sat, 25 Jun 2022 18:22:55 -0000