Debian Med Project
Help us to see Debian used by medical practitioners and biomedical researchers! Join us on the Salsa page.
Summary
Bugs of task bio
Total bugs: 193
Open bugs: 167
Fixed bugs: 26
Links to other tasks
Biology 167 (1428)
Phylogeny 3 (21)
Cloud 37 (315)
Covid-19 134 (1151)
Medical data 1 (3)
Dental 0 (0)
Epidemiology 3 (18)
Imaging 231 (1075)
Laboratory 1 (9)
Oncology 3 (48)
Pharmacology 1 (9)
Physics 25 (180)
Practice 3 (27)
Psychology 7 (65)
Research 0 (0)
Statistics 0 (0)
Tools 33 (218)
Typesetting 67 (538)
Legend
SeverityDependentSuggested
critical 0 0
grave 1 0
serious 5 0
important 27 4
normal 85 10
minor 9 1
wishlist 17 8

Summary bugs page of task Biology

Immediately looking into bugs of the dependencies of this task is advised (1428)*

Open bugs in dependent packages

1 grave, 5 serious, 27 important, 85 normal, 9 minor, 17 wishlist
920282 abyss fails to build on hurd - googletest EXPECT_DEATH
967243 acedb: depends on deprecated GTK 2
982365 ball: reduce Build-Depends
865130 reapr FTBFS on big endian: Error sampling from files '00.Sample/fragCov.gz', '00.assembly.fa.gc.gz' ftbfs, upstream
983981 bamtools: ftbfs with GCC-11 bookworm, sid
819617 FTBFS: any-i386 - floating point idiosyncracies bullseye, buster, ftbfs, sid, stretch
860682 bcftools: FTBFS on i386: Test failures bullseye, buster, ftbfs, sid, stretch
860704 python-pysam: FTBFS on i386: build-dependency not installable: bcftools (>= 1.3.1) bullseye, buster, ftbfs, sid, stretch
870060 bcftools FTBFS on big endian: 107 tests failed ftbfs, upstream
983631 blasr FTCBFS: multiple reasons patch
986203 bustools: Please provide autopkgtest newcomer
962675 can cdbfasta be marked Multi-Arch: foreign?
984015 cif-tools: ftbfs with GCC-11 bookworm, sid
884475 clonalorigin: FTBFS on alpha: tests time out upstream, wontfix
984018 clonalorigin: ftbfs with GCC-11 bookworm, sid
978784 clustalw: ftbfs with autoconf 2.70 bookworm, sid
978794 crac: ftbfs with autoconf 2.70 bookworm, sid
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
984034 density-fitness: ftbfs with GCC-11 bookworm, sid
984036 disulfinder: ftbfs with GCC-11 bookworm, sid
984042 dssp: ftbfs with GCC-11 bookworm, sid
846858 src:ea-utils: New version available
862118 ea-utils: New upstream version available
984043 ea-utils: ftbfs with GCC-11 bookworm, sid
986197 ecopcr: Please provide autopkgtest newcomer
682042 emboss-data: ships bulky taxonomy and gene ontology data
982036 emboss: FTBFS with OpenJDK 17 due to com.sun.net.ssl removal bookworm, ftbfs, help, sid
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 bullseye, fixed-upstream, pending, sid, upstream
984055 fastqtl: ftbfs with GCC-11 bookworm, sid
986201 fsm-lite: Please provide autopkgtest newcomer
750139 gamgi: Conflicting return types of function gamgi_engine_iarray_push upstream
967366 gamgi: depends on deprecated GTK 2
907905 garli: FTBFS randomly (failing tests) fixed-upstream, ftbfs, upstream
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
984145 gatb-core: ftbfs with GCC-11 bookworm, sid
967379 gdpc: depends on deprecated GTK 2
981876 gdpc: flaky autopkgtest on i386 bullseye, sid
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
981688 graphlan: Wrong homepage
644397 Provide runtime detection for CPU SIMD capabilities upstream
921784 gromacs: unhelpful error message from mpicxx.openmpi unreproducible
983942 gromacs: ftbfs with -march=x86-64-v3
984161 gromacs: ftbfs with GCC-11 bookworm, sid
958244 Use system libinih-dev
986193 hinge: no autopkgtest available yet newcomer
978835 htslib: ftbfs with autoconf 2.70 bookworm, sid
977067 igdiscover: test suite flaky, possibly on high core count machines confirmed, moreinfo, unreproducible
978837 indelible: ftbfs with autoconf 2.70 bookworm, sid
978841 infernal: ftbfs with autoconf 2.70 bookworm, sid
985567 jalview: [INTL:fr] French templates translation l10n, patch, pending
978843 jellyfish: ftbfs with autoconf 2.70 bookworm, sid
983273 jellyfish: Homepage: needs updating
875328 jellyfish1: FTBFS: __sync_val_compare_and_swap_8 undefined upstream, wontfix
978842 jellyfish1: ftbfs with autoconf 2.70 bookworm, sid
712791 jmol - exporting the image as PDF saves only partial image patch
872418 jmol: Weblinks in Help do not work
981989 jmol: FTBFS with OpenJDK 17 due to JSObject.getWindow() removal bookworm, ftbfs, sid
986592 kleborate: flaky arm64 autopkgtest: Mutex is not owned by current thread bullseye, help, sid
851830 arm64 has flaky tests
984079 khmer: ftbfs with GCC-11 bookworm, pending, sid
983930 kmc: ftbfs with -march=x86-64-v2
984080 lamarc: ftbfs with GCC-11 bookworm, sid
984081 lastz: ftbfs with GCC-11 bookworm, sid
984104 libfastahack: ftbfs with GCC-11 bookworm, sid
984188 libncl: ftbfs with GCC-11 bookworm, sid
984207 libsmithwaterman: ftbfs with GCC-11 bookworm, sid
984139 freebayes: ftbfs with GCC-11 bookworm, fixed-upstream, sid, upstream
984212 libvcflib: ftbfs with GCC-11 bookworm, fixed-upstream, sid, upstream
967603 ltrsift: depends on deprecated GTK 2
984226 mapsembler2: ftbfs with GCC-11 bookworm, sid
984973 mash FTCBFS -- multiple reasons patch
982005 mauve-aligner: FTBFS with OpenJDK 17 due to rmic removal bookworm, ftbfs, sid
984243 mothur: ftbfs with GCC-11 bookworm, sid
956751 mummerplot incompatible with Debian's version of gnuplot
984250 murasaki: ftbfs with GCC-11 bookworm, patch, sid
983767 nanopolish ftbfs with the nocheck profile
891197 Please switch to pcre2
956850 ncbi-blast+: Please provide /usr/bin/legacy_blast.pl
984871 ncbi-blast+: Missing headers for shared libraries
225651 ncbi-tools-x11: want Cn3D++
935340 obitools: Port to Python3 needed upstream
964082 parsinsert fails it's tests when built with -O3 bullseye, moreinfo, sid, unreproducible
983630 pbdagcon FTCBFS: python3 dependency not installable patch
978880 phyx: ftbfs with autoconf 2.70 bookworm, sid
985144 pigx-rnaseq -- Fails to build reproducibly: different binaries on usrmerge system patch
986194 pique: no autopkgtest available yet newcomer
984293 plink: ftbfs with GCC-11 bookworm, sid
970599 src:prime-phylo: no autopkgtest available yet newcomer
897605 profphd failure in stretch
942064 profphd: autopkgtest failure bullseye, help, sid
984301 proftmb: ftbfs with GCC-11 bookworm, sid
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
929700 pymol: Deprecation warning during startup
986253 build with pie again patch
642084 qutemol: Cannot start the program
939033 qutemol: Uses GifQuantizeBuffer - stops working with newer giflib
984316 qutemol: ftbfs with GCC-11 bookworm, sid
961234 r-cran-treescape: FTBFS on ppc64el:Segmentation fault 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) bullseye, ftbfs, sid
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
985069 seqprep FTCBFS -- multiple reasons patch
967743 seqtools: depends on deprecated GTK 2
983700 sga: reduce Build-Depends patch, pending
970404 shovill: Please provide autopkgtest
984334 skewer: ftbfs with GCC-11 bookworm, sid
985071 smalt: native FTBFS with DEB_BUILD_OPTIONS=nocheck
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" bullseye, ftbfs, sid
984348 spoa: ftbfs with GCC-11 bookworm, sid
984978 subread FTCBFS -- multiple reasons patch
956848 t-coffee: should use "example" blastpgp.pl
984367 tigr-glimmer: ftbfs with GCC-11 bookworm, sid
984958 tnseq-transit: spews SyntaxWarning during installation
984369 tortoize: ftbfs with GCC-11 bookworm, sid
846481 src:treeviewx: Please remove statically linked code copy of libncl
981874 trinityrnaseq: flaky autopkgtest bullseye, sid
984370 tvc: ftbfs with GCC-11 bookworm, sid
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! bullseye, ftbfs, 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 bullseye, sid
967229 viewmol: Unversioned Python removal in sid/bullseye bullseye, sid
978918 vsearch: ftbfs with autoconf 2.70 bookworm, sid
978928 zalign: ftbfs with autoconf 2.70 bookworm, sid

Open bugs in suggested packages

4 important, 10 normal, 1 minor, 8 wishlist
916406 libarb-dev: Missing symbols in static libraries
918015 [INTL:sv] Swedish strings for arb debconf l10n, patch
926017 arb: Typo in package description: "website links unreachable, description outdated"
928076 bcbio: Workflows not ready for non-developers to depend on.
986487 caftools: FTBFS with glibc >= 2.32 patch
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
972537 please add --enable-ros3-vfd to the build options to allow RO access to HDF5 on S3
973261 libhdf5-openmpi-dev: installing requires /proc being mounted
970312 src:intake: Please provide autopkgtest newcomer
970309 src:python-loompy: Please provide autopkgtest newcomer
982139 q2-quality-control: test skipped on ppc64el
986200 sift: Please provide autopkgtest newcomer

Done bugs

984889 assembly-stats natively FTBFS: error: gtest/gtest.h: No such file or directory patch
984890 assembly-stats FTCBFS: uses DEB_BUILD_GNU_TYPE patch
987023 bamtools: autopkgtest failure: times out on armhf and s390x
970597 src:changeo: no autopkgtest available yet newcomer
985596 emboss has mailcap entries with quoted %-escapes patch, security
986524 freecontact: FTBFS: devlibs error: There is no package matching [libgfortran-8-dev] and noone provides it, please report bug to d-shlibs maintainer bullseye, ftbfs, sid
982692 gemma: FTBFS: dh_auto_test: error: make -j1 check returned exit code 2 bullseye, ftbfs, sid
985004 gemma: flaky armhf autopkgtest: regularly times out after 2:47 h bullseye, sid
985157 gromacs-data: broken bash-completion scripts for gmx
986238 gubbins: broken symlink: /usr/bin/gubbins_drawer -> ../share/gubbins/gubbins_drawer.py
749367 htslib FTBFS on testing for mips/mipsel bullseye, buster, moreinfo, patch, sid, stretch
800469 htslib FTBFS on armhf, bus error. bullseye, buster, ftbfs, patch, sid, stretch
849667 htslib: FTBFS on armhf: [test] Bus error bullseye, buster, ftbfs, patch, sid, stretch
961382 hyphy: baseline violation on amd64/i386
977992 hyphy: FTBFS on hurd-i386: wrong reference to the build directory patch
985284 hyphy-common: unhandled symlink to directory conversion: /usr/lib/hyphy -> ../share/hyphy
985448 jalview: please make the build reproducible patch
958471 src:kineticstools: Non-free data included in source
954270 kmc: autopgktest times out on multimulticore hosts confirmed
962190 primer3: please disable Big Endian tests on autopkgtests too patch
905206 profnet: autopkgtest regression upstream
985523 radiant: broken symlink: /usr/bin/ktImportMETAREP-blast -> ../share/perl5/KronaTools/scripts/ImportMETAREP-blast.pl
986307 scrappie: flaky armhf autopkgtest: Invalid control character at: line 1 column 91 (char 90) bullseye, sid
970598 src:seqsero: no autopkgtest available yet newcomer
984854 seqsero: Seqsero invokes python2.7 during execution
986256 simka: flaky amd64 autopkgtest: regularly times out after 2:47 h bullseye, sid
*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: Fri, 16 Apr 2021 16:07:23 -0000