Debian Med Project
Help us to see Debian used by medical practitioners and biomedical researchers! Join us on the Salsa page.
Bugs of task bio
Total bugs: 151
Open bugs: 114
Fixed bugs: 37
Links to other tasks
Biology 114 (1337)
Phylogeny 9 (93)
Cloud 43 (411)
Medical data 1 (0)
Dental 1 (30)
Epidemiology 3 (69)
Imaging 227 (1359)
Imaging development 101 (1082)
Laboratory 0 (0)
Oncology 0 (0)
Pharmacology 0 (0)
Physics 26 (219)
Practice 3 (30)
Psychology 11 (122)
Research 0 (0)
Statistics 3 (7)
Tools 37 (246)
Typesetting 81 (601)
critical 0 0
grave 0 2
serious 23 2
important 12 0
normal 39 7
minor 18 1
wishlist 9 1

Summary bugs page of task Biology

Immediately looking into bugs of the dependencies of this task is advised (1337)*

Open bugs in dependent packages

23 serious, 12 important, 39 normal, 18 minor, 9 wishlist
889147 abyss: PairedDBG_LoadAlgorithm test fails on sparc64 due to strict alignment violation patch, upstream
909710 altree: Please provide autopkgtest newcomer
712789 Fwd: avogadro crashes patch
731226 avogadro crashes on export image upstream
874834 [avogadro] Future Qt4 removal from Buster help
784451 [ball] Qt4's WebKit removal buster, fixed-upstream, sid, upstream
874837 [ball] Future Qt4 removal from Buster fixed-upstream
905443 ball: FTBFS - test failures ftbfs
865130 reapr FTBFS on big endian: Error sampling from files '00.Sample/fragCov.gz', '00.assembly.fa.gc.gz' ftbfs, upstream
819617 FTBFS: any-i386 - floating point idiosyncracies buster, ftbfs, sid, stretch
860682 bcftools: FTBFS on i386: Test failures buster, ftbfs, sid, stretch
860704 python-pysam: FTBFS on i386: build-dependency not installable: bcftools (>= 1.3.1) buster, ftbfs, sid, stretch
870060 bcftools FTBFS on big endian: 107 tests failed ftbfs
894359 beast2-mcmc build depends on openjdk-8-jdk buster, help, sid
890116 bedtools FTBFS on 32bit: Tools failing: coverage intersect negativecontrol reldist shuffle split ftbfs
890117 bedtools FTBFS on big endian: Tools failing: bamtobed bamtofastq coverage genomecov groupby intersect jaccard map merge multicov negativecontrol ftbfs
906811 FTBFS: libconfig.h: No such file or directory ftbfs, pending
909711 clearcut: Please provide autopkgtest newcomer
891730 clonalframe: Please provide autopkgtest
884475 clonalorigin: FTBFS on alpha: tests time out upstream, wontfix
904145 concavity FTCBFS: uses a C compiler for C++ sources patch, upstream
896487 datamash FTBFS on !x86/ia64: FAIL: tests/datamash-output-format fixed-upstream, ftbfs, patch
903886 dawg: Test suite fails upstream
846858 src:ea-utils: New version available
862118 ea-utils: New upstream version available
682042 emboss-data: ships bulky taxonomy and gene ontology data
909706 epcr: Please provide autopkgtest newcomer
896492 examl: autopkgtest started failing for unclear reasons, but old test logs contain error code 255 as well
902132 falcon: FTBFS since python-networkx version 2.1-1; fails in test suite ftbfs
909713 fastlink: Please provide autopkgtest newcomer
897109 fastqc: autopkgtest fails with new version while succeeded in the past; htsjdk.samtools.util.RuntimeIOException: Stream closed
907624 ffindex: ffindex_modify segfaults during autopkgtest ftbfs
814617 freecontact: adequate reports symbol-size-mismatch /usr/bin/freecontact => _ZN11xercesc_3_16XMLUni18fgXercesLoadSchemaE
750139 gamgi: Conflicting return types of function gamgi_engine_iarray_push upstream
903048 gamgi: Please do not depend on transitional dummy pkg ttf-dejavu
907905 garli: FTBFS randomly (failing tests) 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
732691 Pressing "alignment or Ctrl+G" only results in a dialog with a cancel button
890789 gff2aplot: Please provide autopkgtest newcomer
909714 gff2aplot: Please provide autopkgtest newcomer
826069 ghemical: does not display color or allow building help
909715 glam2: Please provide autopkgtest newcomer
644397 Provide runtime detection for CPU SIMD capabilities upstream
909763 hinge FTBFS with spdlog 1:1.1.0-1 ftbfs, help
909707 hyphy: Please provide autopkgtest newcomer
909716 idba: Please provide autopkgtest newcomer
849025 jalview: FTBFS: error: cannot find symbol EnumCallback ftbfs
906371 jmodeltest: FTBFS in buster/sid ftbfs, help
712791 jmol - exporting the image as PDF saves only partial image patch
872418 jmol: Weblinks in Help do not work
851830 arm64 has flaky tests
902591 kineticstools: autopkgtest failure with NumPy 1.14
909708 loki: Please provide autopkgtest newcomer
890788 mipe: Please provide autopkgtest newcomer
891197 Please switch to pcre2
901028 ncbi-entrez-direct: New upstream version available
225651 ncbi-tools-x11: want Cn3D++
908353 ncbi-tools6 FTCBFS: uses the build architecture compiler patch, pending
816562 libopenms2.0: fails to upgrade from 'jessie' - trying to overwrite /usr/share/man/man3/libopenms.3.gz
822412 openms: non-free WSDL-Schema (ND); incomplete copyright (missing DSL, BSL-1.0 licenses)
906561 openms: Homepage: field needs updating
906666 openms FTBFS on armel/armhf: error: expected class-name before '{' token ftbfs
903759 pdb2pqr: autopkgtest regression
880258 picard-tools: FTBFS: error: package org.testng does not exist buster, sid
905645 picard-tools: autopkgtest regression: Option 'ALIGNMENT_STATUS' is required.
895243 primer3: autopkgtest fails since 2.4.0-1 while it succeeded in the past
905206 profnet: autopkgtest regression
897605 profphd failure in stretch
602610 Package freemol.mengine for full modeling capabilities
651609 pymol: Setting-Error: type read mismatch (int) 667
703782 pymol: Unable to launch the Menu
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
897431 pymol: Public modules must be in the python-pymol package
910686 Pymol 2.2.0 sources available from github
881555 python-csb: Please migrate away from Epydoc if possible
905055 python-treetime: broken symlinks: /usr/bin/* -> ../share/treetime/*.py
909784 python-treetime: Incomplete debian/copyright?
883260 qcumber: [INLT:ru] Russian translation of debconf template l10n, patch
820308 qiime: many unsatisfiable dependencies
887943 rapmap: FTBFS on mips64el: both tests fail help, upstream
909766 rapmap FTBFS with spdlog 1:1.1.0-1 ftbfs, help
790196 rasmol: depends on vte which is deprecated buster, help, patch, sid
909709 raster3d: Please provide autopkgtest newcomer
909767 salmon FTBFS with spdlog 1:1.1.0-1 ftbfs
907489 sambamba FTBFS fixed-upstream, ftbfs, help, upstream
890185 seqan2: FTBFS on ia64
892222 seqan2: FTBFS on hppa: app_test_seqan_tcoffee fails on 2trx.mlcs.fasta upstream
892223 seqan2: FTBFS on sparc64: 39 tests failed out of 403 upstream
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
716373 [Mayhem] Bug report on t-coffee: t_coffee crashes with exit status 139 help
909530 t-coffee: autopkgtest regression help, unreproducible
873866 tophat: Please add arm64
806214 tree-puzzle: Package fails test suite
890790 tree-puzzle: Please provide autopkgtest newcomer
909717 tree-puzzle: Please provide autopkgtest newcomer
846481 src:treeviewx: Please remove statically linked code copy of libncl
897877 trinityrnaseq: ftbfs with GCC-8 buster, fixed-upstream, ftbfs, sid

Open bugs in suggested packages

2 grave, 2 serious, 7 normal, 1 minor, 1 wishlist
580670 autodocktools: Please split out non-gui/biochemistry-oriented python bits
715587 [Mayhem] Bug report on cain-solvers: HomogeneousHistogramsAverage crashes with exit status 139 help
715588 [Mayhem] Bug report on cain-solvers: HomogeneousHistogramsAverageAps crashes with exit status 139 help
772407 science-config: bashism in /bin/sh script
881612 debian-science: s/libalberta2-dev/libalberta-dev/
901047 debian-science: s/spglib/libsymspg-dev/
907898 gmap: autopkgtest regression
895765 igv: FTBFS with java 9 ftbfs
855485 runPmv script does not work
855494 mgltools-pmv: runPmv does not start
855701 runPmv script does not work
868885 ugene wont find translate
887305 ugene: FTBFS error: invalid use of incomplete type 'const struct google_breakpad::ucontext' buster, ftbfs, sid

Done bugs

749733 GCC warnings that may lead to runtime issues with new GNUstep libraries buster, jessie, sid, stretch
909103 consider switching alter-sequence-alignment to Architecture: all
852839 baitfisher: FTBFS (32-bit): mixes ::size_t and faststring::size_t fixed-upstream, ftbfs, help
907559 cgview: Does not start
896931 fastqc: If the package libfindbin-libs-perl is not installed, fastqc exits with an error immediately.
910324 freebayes parallel FTBFS ftbfs
873859 gasic: Please add arm64
826458 gbrowse: Unescaped left brace in regex is deprecated
833885 gbrowse: ships a deterministic/predictable OpenID consumer secret security
902820 gmap: FTBFS on stretch/amd64 if CPU has SSE2 and nothing more ftbfs
908386 gmap: please limit to Architecture: amd64 ftbfs
749367 htslib FTBFS on testing for mips/mipsel buster, moreinfo, patch, sid, stretch
800469 htslib FTBFS on armhf, bus error. buster, ftbfs, patch, sid, stretch
849667 htslib: FTBFS on armhf: [test] Bus error buster, ftbfs, patch, sid, stretch
905438 htslib: FTBFS on i386: 2 tests fail ftbfs
908501 Does not depend on zlib1g-dev
907819 jellyfish: Does not build on paths containing "-L" resulting in random FTBFS when built by sbuild ftbfs
906481 libfastahack: FTBFS in buster/sid (ld: cannot find -lfastahack) buster, ftbfs, patch, sid
908426 metaphlan2 depends on libjs-twitter-bootstrap that will not be in buster
883845 mgltools-vision: Source includes "Vision/doc/Examples/lena.jpg" listed in Files-Excluded header
884525 mobyle: Mobyle javascript includes Google analytics beacon security, upstream
908786 mothur-mpi contains the same binary as mothur
910421 murasaki-mpi: broken symlinks: /usr/share/man/man1/*-mpi.1.gz -> *.1.gz
871297 libopenms2.0: requires rebuild against GCC 7 and symbols/shlibs bump buster, sid
905706 libpicard-java-doc: ships /usr/share/javascript/jquery/jquery.min.js
910750 pycorrfit: build-deps on libpython3-all-dev but only builds for one python3 version
879617 pyscanfcs: Please provide autopkgtest
886634 pyscanfcs: Please migrate to Python 3 fixed-upstream
730515 cd-hit-est is cdhit-est in Debian [Why?]
860652 snap-aligner: FTBFS on i386: SNAPLib/SortedDataWriter.cpp:338:70: error: no matching function for call to 'max(long unsigned int, _int64)' buster, ftbfs, sid, stretch
906509 sra-sdk: FTBFS in buster (unknown type name 'HttpProxy') ftbfs
910414 ssake-examples: broken symlink: /usr/share/doc/ssake/examples/ -> ../tools/
848464 stacks-web: Should Depends/Recommends the metapackage default-mysql-*
908459 theseus FTBFS with gcc 8 ftbfs
909759 tnseq-transit is not installable
860645 trinityrnaseq: FTBFS on i386: unsatisfiable build-dependencies: jellyfish (>= 2.1.4), parafly buster, sid, stretch
902190 vcftools: CVE-2018-11099 CVE-2018-11129 CVE-2018-11130 fixed-upstream, security
*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: Tue, 16 Oct 2018 06:52:44 -0000