Debian Med Project
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Summary
Bugs of task bio
Total bugs: 211
Open bugs: 155
Fixed bugs: 56
Links to other tasks
Biology 155 (1342)
Phylogeny 3 (21)
Cloud 33 (291)
Covid-19 131 (1115)
Medical data 1 (3)
Dental 0 (0)
Epidemiology 3 (18)
Imaging 227 (1053)
Laboratory 1 (9)
Oncology 1 (9)
Pharmacology 1 (9)
Physics 25 (180)
Practice 3 (27)
Psychology 5 (47)
Research 0 (0)
Statistics 0 (0)
Tools 33 (218)
Typesetting 68 (547)
Legend
SeverityDependentSuggested
critical 0 0
grave 1 0
serious 4 1
important 25 4
normal 81 9
minor 10 1
wishlist 12 7

Summary bugs page of task Biology

Immediately looking into bugs of the dependencies of this task is advised (1342)*

Open bugs in dependent packages

1 grave, 4 serious, 25 important, 81 normal, 10 minor, 12 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
962675 can cdbfasta be marked Multi-Arch: foreign?
970597 src:changeo: no autopkgtest available yet newcomer
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
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
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
984139 freebayes: ftbfs with GCC-11 bookworm, sid
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
982692 gemma: FTBFS: dh_auto_test: error: make -j1 check returned exit code 2 bullseye, ftbfs, moreinfo, sid, unreproducible
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
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
983579 jalview: [INTL:de] initial German debconf translation l10n, patch
983580 jalview: Questions/Corrections for Debconf template
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
984073 kallisto: ftbfs with GCC-11 bookworm, sid
851830 arm64 has flaky tests
984079 khmer: ftbfs with GCC-11 bookworm, 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
984212 libvcflib: ftbfs with GCC-11 bookworm, sid
967603 ltrsift: depends on deprecated GTK 2
984226 mapsembler2: ftbfs with GCC-11 bookworm, sid
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, sid
891197 Please switch to pcre2
956850 ncbi-blast+: Please provide /usr/bin/legacy_blast.pl
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
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
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
970598 src:seqsero: no autopkgtest available yet newcomer
967743 seqtools: depends on deprecated GTK 2
983700 sga: reduce Build-Depends patch
970404 shovill: Please provide autopkgtest
984334 skewer: ftbfs with GCC-11 bookworm, sid
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
956848 t-coffee: should use "example" blastpgp.pl
984367 tigr-glimmer: ftbfs with GCC-11 bookworm, sid
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

1 serious, 4 important, 9 normal, 1 minor, 7 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.
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
982699 intake: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.9 returned exit code 13 bullseye, ftbfs, sid
970309 src:python-loompy: Please provide autopkgtest newcomer
982139 q2-quality-control: test skipped on ppc64el

Done bugs

982608 axe-demultiplexer: FTCBFS: unsatisfiable python3-sphinx dependency patch
982965 bedops: reduce Build-Depends patch
982168 biomaj3-daemon: autopkgtest failure: No module named 'biomaj3_daemon'
983142 circlator: reproducible builds: Generated tarball includes file mode patch
982989 codonw FTCBFS: Multiple reasons patch
956675 cyvcf2: test failures on ppc64el and s390x bullseye, ftbfs, sid
982290 disulfinder FTCBFS: hard codes the build architecture compiler g++ patch, upstream
982352 drop-seq-tools: Excessive dependendies
982617 drop-seq: autopkgtest regression confirmed
980765 eigensoft: absolute path to fixgreen in /usr/bin/ploteig
981684 src:estscan: fails to migrate to testing for too long: FTBFS on mipsel bullseye, ftbfs, sid
909713 fastlink: Please provide autopkgtest newcomer
980484 gmap FTCBFS: AC_RUN_IFELSE patch, upstream
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
849025 jalview: FTBFS: error: cannot find symbol EnumCallback ftbfs
973431 jellyfish ftbfs when built with -O3 bullseye, ftbfs, sid
976340 jellyfish FTBFS with -I in builddir ftbfs
958471 src:kineticstools: Non-free data included in source
954270 kmc: autopgktest times out on multimulticore hosts confirmed
982045 libssw: FTBFS with OpenJDK 17 due to unsupported javac source/target level 6 bookworm, ftbfs, sid
933928 macsyfinder: Port to Python3 needed fixed-upstream
936977 macsyfinder: Python2 removal in sid/bullseye bullseye, fixed-upstream, sid
970875 mash: inconsistent results on 32 vs 64 bits architectures
981293 metastudent-data breaks metastudent autopkgtest: 255 bullseye, help, sid, upstream
981294 src:metastudent-data: fails to migrate to testing for too long: autopkgtest regression bullseye, sid
890788 mipe: Please provide autopkgtest newcomer
982718 msxpertsuite: FTBFS: [ERROR] LazyFont - Failed to read font file /usr/share/texlive/texmf-dist/fonts/opentype/public/stix2-otf/STIX2Math.otf <java.io.FileNotFoundException: /usr/share/texlive/texmf-dist/fonts/opentype/public/stix2-otf/STIX2Math.otf (No such file or directory)>java.io.FileNotFoundException: /usr/share/texlive/texmf-dist/fonts/opentype/public/stix2-otf/STIX2Math.otf (No such file or directory) bullseye, ftbfs, patch, sid
960634 nanopolish: FTBFS on ppc64el (as well as ppc64 and powerpc), enumerator conflict ftbfs
983767 nanopolish ftbfs with the nocheck profile
981926 neobio: FTBFS with OpenJDK 17 due to unsupported javac source/target level 6 bookworm, ftbfs, sid
975588 openms: FTBFS against boost_1.74 ftbfs
982567 openms build-depends on removed package. upstream
982181 pbsuite: autopkgtest regression
974003 src:plink2: fails to migrate to testing for too long: FTBFS on ppc64el bullseye, sid
962190 primer3: please disable Big Endian tests on autopkgtests too patch
905206 profnet: autopkgtest regression upstream
982098 python-anndata: autopkgtest failure on 32bit
974839 q2-feature-classifier: unsatisfiable build-dependency
983027 r-bioc-mutationalpatterns: autopkgtest regression in testing: no package called ‘BSgenome.Hsapiens.UCSC.hg19’
982115 r-bioc-scater: autopkgtest failure on i386
982421 r-cran-seurat: autopkgtest failure on i386/armhf patch
982912 repeatmasker-recon FTCBFS: hardcodes "make" in d/rules patch
983723 rna-star FTBFS on ppc64el due to -march=native ftbfs
984328 seer: ftbfs with GCC-11 bookworm, sid
972603 seqan: Needs update for new googletest
980685 seqan: FTBFS: dh_auto_test: error: cd obj-x86_64-linux-gnu && make -j4 test ARGS\+=-j4 returned exit code 2 bullseye, ftbfs, sid
972752 seqan2: FTBFS with DEB_BUILD_OPTIONS=reproducible=+fixfilepath patch
982212 simka: autopkgtest needs same architecture list as simka
890790 tree-puzzle: Please provide autopkgtest newcomer
979760 vdjtools: autopkgtest failure: "java: not found"
982116 vdjtools: autopkgtest fails due to slightly differing result on !x86
982930 wham-align: FTCBFS: multiple reasons 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:
critical10
grave10
serious10
important5
normal3
minor1
wishlist0
Last update: Thu, 04 Mar 2021 15:51:12 -0000