Debian Med Project
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Summary
Bugs of task bio
Total bugs: 171
Open bugs: 135
Fixed bugs: 36
Links to other tasks
Biology 135 (1263)
Phylogeny 4 (42)
Cloud 29 (354)
Covid-19 133 (1271)
Medical data 0 (0)
Dental 0 (0)
Epidemiology 5 (74)
Imaging 211 (1007)
Laboratory 1 (9)
Oncology 0 (0)
Pharmacology 1 (9)
Physics 26 (201)
Practice 6 (45)
Psychology 2 (24)
Research 0 (0)
Statistics 0 (0)
Tools 32 (209)
Typesetting 60 (464)
Legend
SeverityDependentSuggested
critical 0 0
grave 0 1
serious 12 3
important 22 4
normal 48 14
minor 13 0
wishlist 14 4

Summary bugs page of task Biology

Immediately looking into bugs of the dependencies of this task is advised (1263)*

Open bugs in dependent packages

12 serious, 22 important, 48 normal, 13 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, ftbfs, help, 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
1018317 biomaj3-daemon: build-depends on python3-nose or uses it for autopkgtest
1010653 busco: add autopkgtest to check integration with hmmer and prodigal
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
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
1018351 fastaq: build-depends on python3-nose or uses it for autopkgtest
1008220 flexbar 3.5.0-4 FTBFS against libtbb-dev 2021.5.0-7 ftbfs, upstream
1011656 flexbar ftbfs: cannot find tbb header
1012127 flexbar: FTBFS with onetbb/2021.5.0-8 in experimental ftbfs, upstream
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
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
1020793 gmap: FTBFS on avx512 host in buster ftbfs
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
977067 igdiscover: test suite flaky, possibly on high core count machines confirmed, moreinfo, unreproducible
1018377 insilicoseq: build-depends on python3-nose or uses it for autopkgtest
1018382 iva: build-depends on python3-nose or uses it for autopkgtest
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
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
1018407 mirtop: build-depends on python3-nose or uses it for autopkgtest
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/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++
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
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
1018501 python-gffutils: build-depends on python3-nose or uses it for autopkgtest
1018560 python-pybedtools: build-depends on python3-nose or uses it for autopkgtest
1018582 python-sqt: build-depends on python3-nose or uses it for autopkgtest
642084 qutemol: Cannot start the program
939033 qutemol: Uses GifQuantizeBuffer - stops working with newer giflib
1019819 qutemol: Please transition to wxwidgets3.2
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
1018610 recan: build-depends on python3-nose or uses it for autopkgtest
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 ftbfs
1011742 salmon: FTBFS with onetbb/2021.5.0-8 in experimental ftbfs
1015654 sambamba: ftbfs with LTO (link time optimization) enabled bookworm, sid
1018636 scoary: build-depends on python3-nose or uses it for autopkgtest
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
1015668 spades: ftbfs with LTO (link time optimization) enabled bookworm, sid
1015667 spoa: ftbfs with LTO (link time optimization) enabled bookworm, sid
956848 t-coffee: should use "example" blastpgp.pl
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
1018656 umap-learn: build-depends on python3-nose or uses it for autopkgtest
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
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

Open bugs in suggested packages

1 grave, 3 serious, 4 important, 14 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.
1018312 bcbio: build-depends on python3-nose or uses it for autopkgtest
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
1018477 python-deeptools: build-depends on python3-nose or uses it for autopkgtest
1018577 python-seqcluster: build-depends on python3-nose or uses it for autopkgtest
994459 libjs-jquery removed symlinked files moreinfo
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?

Done bugs

1015861 bamtools: FTBFS with upcoming doxygen 1.9.4 ftbfs
1010834 biosyntax-vim: Unusable with vim-addon-manager because of outdated manifest
1010836 biosyntax-gedit: No longer works with recent versions of gedit
1018972 blasr autopkgtest regression with pbbam 2.1.0
1018936 busco: unsatisfiable dependency on arm64
1012906 cif-tools: ftbfs with GCC-12 bookworm, sid
1012913 dssp: ftbfs with GCC-12 bookworm, sid
1020305 src:emmax: fails to migrate to testing for too long: autopkgtest failure bookworm, sid
1014797 FTBFS: test failures with new libgd3 ftbfs, help, upstream
1019809 gentle: Please transition to wxwidgets3.2 help
972537 please add --enable-ros3-vfd to the build options to allow RO access to HDF5 on S3
1018683 igv: FTBFS (calls internet during tests) confirmed
1012953 jellyfish: ftbfs with GCC-12 bookworm, confirmed, sid, upstream
1017261 jellyfish: FTBFS: dh_missing: error: missing files, aborting bookworm, ftbfs, sid
1017989 src:jellyfish: fails to migrate to testing for too long: unresolved RC bug bookworm, sid
1020110 kaptive: FTBFS: make[1]: *** [debian/rules:12: override_dh_auto_clean] Error 25 bookworm, ftbfs, sid
1020031 khmer: FTBFS: ld: cannot find build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o: No such file or directory bookworm, ftbfs, sid
1019834 lamarc: Please transition to wxwidgets3.2
1020106 macsyfinder: FTBFS: AssertionError: "Models Parsing\nunable to parse model def[104 chars]del." != "unable to parse model definition 'foo/mod[88 chars]del." bookworm, ftbfs, sid
1016645 metaphlan2: package name and description can become confusing
1018433 paleomix: build-depends on python3-nose or uses it for autopkgtest
1016941 phyml: flaky autopkgtest on armel: test duration around autopkgtest timeout
1015136 q2cli: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.10 returned exit code 13 bookworm, ftbfs, sid
1018606 q2cli: build-depends on python3-nose or uses it for autopkgtest
1015250 q2-feature-table: Conflict with biom-format 2.1.12 upstream
1017515 q2-feature-table: needs update for python-biom-format/2.1.12-1
1018608 q2-quality-filter: build-depends on python3-nose or uses it for autopkgtest
1017514 q2-types: needs update for python-biom-format/2.1.12-1
1014100 qiime: autopkgtest needs update for new version of python-decorator bookworm, sid
1018609 qiime: build-depends on python3-nose or uses it for autopkgtest
995224 relion-cuda: FTBFS with cub 1.14 bookworm, ftbfs, sid
1020753 seqtk: reproducible-builds: Embedded build path in /usr/bin/seqtk patch
1019811 treeviewx: Please transition to wxwidgets3.2 help
1013182 twopaco FTBFS with oneTBB 2021.5.0 ftbfs
1013064 vmatch: ftbfs with GCC-12 bookworm, sid
1016743 zalign: autopkgtest failure on 32 bit architectures: Segmentation fault
*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: Sun, 02 Oct 2022 18:19:49 -0000