Debian Med Project
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Bugs of task bio
Total bugs: 138
Open bugs: 105
Fixed bugs: 33
Links to other tasks
Biology 105 (1282)
Phylogeny 8 (96)
Cloud 35 (402)
Medical data 1 (0)
Dental 1 (9)
Epidemiology 1 (30)
Imaging 200 (1074)
Laboratory 0 (0)
Oncology 0 (0)
Pharmacology 0 (0)
Physics 28 (207)
Practice 3 (9)
Psychology 10 (140)
Research 0 (0)
Statistics 2 (4)
Tools 36 (245)
Typesetting 75 (583)
critical 0 0
grave 0 2
serious 23 2
important 13 1
normal 33 5
minor 13 1
wishlist 11 1

Summary bugs page of task Biology

Immediately looking into bugs of the dependencies of this task is advised (1282)*

Open bugs in dependent packages

23 serious, 13 important, 33 normal, 13 minor, 11 wishlist
889147 abyss: PairedDBG_LoadAlgorithm test fails on sparc64 due to strict alignment violation patch, upstream
893184 artemis FTBFS with openjdk-9
890785 autodock-vina: Please provide autopkgtest newcomer
712789 Fwd: avogadro crashes patch
731226 avogadro crashes on export image upstream
874834 [avogadro] Future Qt4 removal from Buster help
852839 baitfisher: FTBFS (32-bit): mixes ::size_t and faststring::size_t fixed-upstream, help
784451 [ball] Qt4's WebKit removal buster, fixed-upstream, sid, upstream
874837 [ball] Future Qt4 removal from Buster fixed-upstream
865130 reapr FTBFS on big endian: Error sampling from files '00.Sample/fragCov.gz', '00.assembly.fa.gc.gz' upstream
819617 FTBFS: any-i386 - floating point idiosyncracies buster, sid, stretch
860682 bcftools: FTBFS on i386: Test failures buster, sid, stretch
860704 python-pysam: FTBFS on i386: build-dependency not installable: bcftools (>= 1.3.1) buster, sid, stretch
870060 bcftools FTBFS on big endian: 107 tests failed
894359 beast2-mcmc build depends on openjdk-8-jdk buster, help, sid
896483 beast-mcmc FTBFS with TeX Live 2018 patch
890116 bedtools FTBFS on 32bit: Tools failing: coverage intersect negativecontrol reldist shuffle split
890117 bedtools FTBFS on big endian: Tools failing: bamtobed bamtofastq coverage genomecov groupby intersect jaccard map merge multicov negativecontrol
894781 bedtools: autopkgtest fails while it succeeded in the past
874835 [bppphyview] Future Qt4 removal from Buster
890531 bppphyview FTBFS with libbpp-qt-dev 2.3.2-1
891730 clonalframe: Please provide autopkgtest
884475 clonalorigin: FTBFS on alpha: tests time out upstream, wontfix
896487 datamash FTBFS on !x86/ia64: FAIL: tests/datamash-output-format
846858 src:ea-utils: New version available
862118 ea-utils: New upstream version available
682042 emboss-data: ships bulky taxonomy and gene ontology data
896492 examl: autopkgtest started failing for unclear reasons, but old test logs contain error code 255 as well
890787 fastdnaml: Please provide autopkgtest
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
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
826069 ghemical: does not display color or allow building help
644397 Provide runtime detection for CPU SIMD capabilities upstream
887340 gromacs: FTBFS on x32: tests 2 and 13 time out upstream
896194 gromacs FTBFS: GpuUtilsUnitTests (Timeout)
894898 please drop the runtime dependency on python3-distutils patch
849025 jalview: FTBFS: error: cannot find symbol EnumCallback
896484 jmodeltest FTBFS with TeX Live 2018 buster, patch, sid
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
804579 logol-bin: bogus hardcoded dependency on libncursesw5 wontfix
896486 maffilter FTBFS with libbpp-phyl-omics-dev 2.4.0
890788 mipe: Please provide autopkgtest newcomer
896141 msxpertsuite: binary-all FTBFS
891197 Please switch to pcre2
225651 ncbi-tools-x11: want Cn3D++
879619 ncbi-tools6: Please provide autopkgtest
784502 [openms] Qt4's WebKit removal buster, sid
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)
853595 openms: ftbfs with GCC-7 buster, fixed-upstream, sid
865240 Please update dependencies from latex-xcolor to tl-latex-recommended buster, sid
871297 libopenms2.0: requires rebuild against GCC 7 and symbols/shlibs bump buster, sid
875073 [openms] Future Qt4 removal from Buster
881026 openms: Transition to xerces-c3.2
891732 paleomix should become binary-any
880258 picard-tools: FTBFS: error: package org.testng does not exist buster, sid
716580 [Mayhem] Bug report on populations: populations crashes with exit status 139
890993 primer3 FTBFS on big endian: test failure
895243 primer3: autopkgtest fails since 2.4.0-1 while it succeeded in the past
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
886634 pyscanfcs: Please migrate to Python 3
881555 python-csb: Please migrate away from Epydoc if possible
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
767296 rasmol: ftbfs on ppc64el -- conflict with vector keyword patch
790196 rasmol: depends on vte which is deprecated buster, help, sid
821023 rasmol: Short descriptions should begin with lowercase l10n, patch
890784 readseq: Please provide autopkgtest newcomer
847569 rsem: New version available
890782 rsem: Please add autopkgtest
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
879620 sra-sdk: Please provide autopkgtest
716373 [Mayhem] Bug report on t-coffee: t_coffee crashes with exit status 139 help
873866 tophat: Please add arm64
806214 tree-puzzle: Package fails test suite
890790 tree-puzzle: Please provide autopkgtest newcomer
846481 src:treeviewx: Please remove statically linked code copy of libncl

Open bugs in suggested packages

2 grave, 2 serious, 1 important, 5 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/
895765 igv: FTBFS with java 9
855485 runPmv script does not work
855494 mgltools-pmv: runPmv does not start
855701 runPmv script does not work
893526 mrs: FTBFS on 32-bit arches - error: format not a string literal and no format arguments buster, sid
868885 ugene wont find translate
887305 ugene: FTBFS error: invalid use of incomplete type 'const struct google_breakpad::ucontext' buster, sid

Done bugs

749733 GCC warnings that may lead to runtime issues with new GNUstep libraries buster, jessie, sid, stretch
894903 please drop the runtime dependency on python3-distutils patch
717209 avogadro: Visualizing orbitals generated with MOLCAS
894886 libbamtools-dev needs Breaks+Replaces: libbamtools2.4.0 (<< 2.5.1+dfsg-2~)
894143 bedops-doc: fails to upgrade from 'testing' - trying to overwrite /usr/share/doc/bedops/html/_downloads/Frequencies-DHSs.bed.starch.gz
894156 bedops FTBFS on mips/mipsel: Memory exhausted patch
891335 clonalframe: FTBFS with glibc 2.27: error: 'UNDERFLOW' was not declared in this scope help, patch, upstream
873859 gasic: Please add arm64
826458 gbrowse: Unescaped left brace in regex is deprecated
833885 gbrowse: ships a deterministic/predictable OpenID consumer secret security
749367 htslib FTBFS on testing for mips/mipsel buster, moreinfo, patch, sid, stretch
800469 htslib FTBFS on armhf, bus error. buster, patch, sid, stretch
849667 htslib: FTBFS on armhf: [test] Bus error buster, patch, sid, stretch
875585 FTBFS with Java 9: AWT api changes buster, patch, sid
889506 last-align: Please make build compatible with -Wl,--as-needed patch
895502 libsmithwaterman FTBFS on 32bit: missing symbol
895527 libsmithwaterman FTBFS on mips/mipsel: symbol differences
879622 macs: Please provide autopkgtest
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
893354 mrs: please update for g++7 + boost 1.65 compatibility patch
895299 mustang FTCBFS: uses a non-standard variable for the c++ compiler patch, upstream
894329 picard-tools FTBFS with openjdk-9
894473 prodigal FTBFS on armel/armhf: Build killed with signal TERM after 150 minutes of inactivity buster, patch, sid
895344 psortb: build compatibility with -Wl,--as-needed patch
879617 pyscanfcs: Please provide autopkgtest
730515 cd-hit-est is cdhit-est in Debian [Why?]
873865 relion: Please add arm64
893664 sambamba: Fails to build on i386 upstream
860652 snap-aligner: FTBFS on i386: SNAPLib/SortedDataWriter.cpp:338:70: error: no matching function for call to 'max(long unsigned int, _int64)' buster, sid, stretch
848464 stacks-web: Should Depends/Recommends the metapackage default-mysql-*
860645 trinityrnaseq: FTBFS on i386: unsatisfiable build-dependencies: jellyfish (>= 2.1.4), parafly buster, sid, stretch
855340 Spurious build dep on libssl-dev
*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, 21 Apr 2018 18:31:21 -0000