Debian Med Project
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Summary
Bugs of task bio
Total bugs: 184
Open bugs: 116
Fixed bugs: 68
Links to other tasks
Biology 116 (1040)
Phylogeny 5 (30)
Cloud 34 (372)
Medical data 1 (0)
Dental 0 (0)
Epidemiology 1 (9)
Imaging 208 (1113)
Laboratory 0 (0)
Oncology 0 (0)
Pharmacology 3 (27)
Physics 27 (213)
Practice 2 (0)
Psychology 8 (93)
Research 0 (0)
Statistics 2 (6)
Tools 36 (219)
Typesetting 88 (602)
Legend
SeverityDependentSuggested
critical 0 0
grave 0 2
serious 13 1
important 15 1
normal 40 6
minor 3 3
wishlist 28 4

Summary bugs page of task Biology

Immediately looking into bugs of the dependencies of this task is advised (1040)*

Open bugs in dependent packages

13 serious, 15 important, 40 normal, 3 minor, 28 wishlist
852839 baitfisher: FTBFS (32-bit): mixes ::size_t and faststring::size_t
784451 [ball] Qt4's WebKit removal buster, fixed-upstream, sid, upstream
867660 ball: FTBFS with sip 4.19.x: sip: File::CannotWrite has not been defined fixed-upstream, patch
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
747337 broken autopkgtest: missing dependency, not testing installed package, test failures upstream
860655 blasr: FTBFS on i386: unsatisfiable build-dependencies: libpbseq-dev (>= 0~20160912), libpbbam-dev buster, sid, stretch
864439 bowtie: FTBFS on mips64el - /usr/bin/ld: .gnu.hash is incompatible with the MIPS ABI
864448 bowtie FTBFS on mips64el: /usr/bin/ld: .gnu.hash is incompatible with the MIPS ABI
874835 [bppphyview] Future Qt4 removal from Buster
715691 [Mayhem] Bug report on bppsuite: bppalnscore crashes with exit status 139
715692 [Mayhem] Bug report on bppsuite: bppancestor crashes with exit status 139
715693 [Mayhem] Bug report on bppsuite: bppconsense crashes with exit status 139
715694 [Mayhem] Bug report on bppsuite: bppdist crashes with exit status 139
715695 [Mayhem] Bug report on bppsuite: bppml crashes with exit status 139
860639 circlator: FTBFS on i386: unsatisfiable build-dependencies: python3-pysam (>= 0.8.1), spades, bwa (>= 0.7.12) buster, sid, stretch
874845 [clonalframe] Future Qt4 removal from Buster upstream
860690 crac: FTBFS on i386: build-dependency not installable: libjellyfish-2.0-dev buster, sid, stretch
846858 src:ea-utils: New version available
862118 ea-utils: New upstream version available
682042 emboss-data: ships bulky taxonomy and gene ontology data
864376 falcon: properly fix test failure: Task Node(1-preads_ovl/m_00001) failed with exit-code=256
864378 falcon accidentally still built on x32
860653 fitgcp: FTBFS on i386: build-dependency not installable: python-pysam buster, sid, stretch
759006 flexbar: FTBFS on hppa: Flexbar.h:258: undefined reference to `tbb::pipeline::run(unsigned int)'
814617 freecontact: adequate reports symbol-size-mismatch /usr/bin/freecontact => _ZN11xercesc_3_16XMLUni18fgXercesLoadSchemaE
860661 fsm-lite: FTBFS on i386: build-dependency not installable: libsdsl-dev buster, sid, stretch
750139 gamgi: Conflicting return types of function gamgi_engine_iarray_push
669296 garlic: debcheckout fails pending
715937 [Mayhem] Bug report on garlic: garlic crashes with exit status 139
749656 garlic: Conflicting declarations of function BlurMainWindow_ to cause undefined behaviour
872431 garlic FTCBFS: uses the build architecture compiler patch
873859 gasic: Please add arm64
732691 Pressing "alignment or Ctrl+G" only results in a dialog with a cancel button
826069 ghemical: does not display color or allow building help
871727 grinder: FTBFS when debhelper does not export PERL_USE_UNSAFE_INC
644397 Provide runtime detection for CPU SIMD capabilities upstream
866137 htslib autopkgtest is broken in 1.4.1-2
871314 htslib: new version break python-pysam sid
860640 iva: FTBFS on i386: build-dependency not installable: python3-pysam buster, sid, stretch
849025 jalview: FTBFS: error: cannot find symbol EnumCallback
712791 jmol - exporting the image as PDF saves only partial image patch
872418 jmol: Weblinks in Help do not work
875585 FTBFS with Java 9: AWT api changes
851830 arm64 has flaky tests
860636 kineticstools: FTBFS on i386: build-dependency not installable: python-pbcore (>= 1.2.8) buster, sid, stretch
860665 libvcflib: FTBFS on i386: build-dependency not installable: libssw-dev buster, sid, stretch
804579 logol-bin: bogus hardcoded dependency on libncursesw5
765285 mapsembler2: FTBFS on mips mipsel ppc sparc when 8 byte __sync* builtins are used
860672 mhap: FTBFS on i386: build-dependency not installable: libssw-java buster, sid, stretch
225651 ncbi-tools-x11: want Cn3D++
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, 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
860676 pbalign: FTBFS on i386: build-dependency not installable: python-pbcore (>= 0.8.5) buster, sid, stretch
860631 pbbarcode: FTBFS on i386: unsatisfiable build-dependencies: python-pbcore, pbh5tools buster, sid, stretch
860711 pbdagcon: FTBFS on i386: unsatisfiable build-dependencies: libpbseq-dev, libpbbam-dev buster, sid, stretch
860669 pbgenomicconsensus: FTBFS on i386: build-dependency not installable: python-pbcore (>= 1.2.9) buster, sid, stretch
860616 pbh5tools: FTBFS on i386: build-dependency not installable: python-pbcore buster, sid, stretch
874155 FTBFS with Java 9: overrides core packages help, upstream
716580 [Mayhem] Bug report on populations: populations crashes with exit status 139
875097 [populations] Future Qt4 removal from Buster
813250 prime-phylo: FTBFS on hppa: undefined boost references
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
820308 qiime: many unsatisfiable dependencies
860688 rapmap: FTBFS on i386: build-dependency not installable: libjellyfish-2.0-dev buster, sid, stretch
767296 rasmol: ftbfs on ppc64el -- conflict with vector keyword patch
790196 rasmol: depends on vte which is deprecated buster, sid, stretch
821023 rasmol: Short descriptions should begin with lowercase l10n, patch
873865 relion: Please add arm64
861281 rnahybrid: FTBFS on armel help
847569 rsem: New version available
860681 salmon: FTBFS on i386: unsatisfiable build-dependencies: libjellyfish-2.0-dev (> 2.2.3-2), libbwa-dev buster, sid, stretch
871315 samtools: new version breaks python-pysam sid
860643 sga: FTBFS on i386: build-dependency not installable: python-pysam buster, sid, stretch
848589 snap-aligner: Build requires 188 GB of memory (fortunately not used, just allocated)
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
818505 sortmerna FTBFS on !x86 buster, sid
853113 spades: Fails to build with unhelpful error message in a "low" memory machine
860677 spades: FTBFS on i386: unsatisfiable build-dependencies: libssw-dev, bwa buster, sid, stretch
710225 staden-io-lib: library name should follow ABI version (not project version)
716373 [Mayhem] Bug report on t-coffee: t_coffee crashes with exit status 139 help
780816 tophat: contains and uses convience copy of samtools 0.1.18
873866 tophat: Please add arm64
806214 tree-puzzle: Package fails test suite
846481 src:treeviewx: Please remove statically linked code copy of libncl

Open bugs in suggested packages

2 grave, 1 serious, 1 important, 6 normal, 3 minor, 4 wishlist
862913 [INTL:id] initial Indonesian debconf translation l10n, patch
580670 autodocktools: Please split out non-gui/biochemistry-oriented python bits
585244 autodocktools: Python string exceptions no more allowed in Python 2.6 upstream
732858 Add MariaDB as alternative dependency
803116 biomaj: references to non-existent license "CeCILL-A"
848497 src:biomaj: New upstream version available
732862 Add MariaDB as an alternative dependency
866980 biomaj-watcher: fails to upgrade from 'jessie': Exception in thread "main" java.lang.UnsupportedClassVersionError: WatcherConfigurator : Unsupported major.minor version 52.0
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
796771 science-geography: Depends on no longer built qgis-plugin-grass
861038 emboss-explorer: broken symlink: /usr/share/doc/emboss-explorer/html -> ../../EMBOSS/doc/html/emboss/apps
855485 runPmv script does not work
855494 mgltools-pmv: runPmv does not start
855701 runPmv script does not work
868885 ugene wont find translate

Done bugs

749733 adun.app: GCC warnings that may lead to runtime issues with new GNUstep libraries buster, jessie, sid, stretch
857283 arb-common: broken symlinks: /usr/lib/arb/bin/mafft-*, /etc/arb/inputMasks/format.readme
866151 arb: transfig package renamed to fig2dev patch
874352 baitfisher: homepage URL incorrect
868958 bcftools FTBFS on 32bit: test failures
780428 beast-mcmc: restrict arch from all to amd64
866074 bio-tradis: autopkgtest regression
868794 libbpp-qt-dev: postinst removal makes bppphyview FTBFS buster, sid
868924 bppphyview: FTBFS: TreeDocument.h:47:27: fatal error: Bpp/Phyl/Io.all: No such file or directory buster, sid
871164 bppphyview: FTBFS: TreeDocument.h:47:10: fatal error: Bpp/Phyl/Io.all: No such file or directory buster, sid
871098 bppsuite: FTBFS: CMakeFiles/bppmixedlikelihoods.dir/bppMixedLikelihoods.cpp.o:(.data.rel.ro._ZTVN3bpp24ConstantRateDistributionE[_ZTVN3bpp24ConstantRateDistributionE]+0x278): undefined reference to `virtual thunk to bpp::AbstractParameterAliasable::getAliases[abi:cxx11]() const' buster, sid
871390 canu: FTBFS: merTrim/merTrim.C:1785:26: error: format not a string literal and no format arguments [-Werror=format-security] buster, sid
874851 [clustalx] Future Qt4 removal from Buster upstream
871234 cufflinks: FTBFS with GCC-7: error: type/value mismatch at argument 1 in template parameter list for 'template<class _Tp> struct std::hash' buster, help, sid
865132 diamond-aligner FTBFS on ppc64el: undefined reference to Fixed_score_buffer
853375 disulfinder: ftbfs with GCC-7 buster, sid
853396 fastx-toolkit: ftbfs with GCC-7 buster, sid
873429 flexbar builds with -march=native
866646 freebayes FTBFS with libhts-dev 1.4.1-2
826458 gbrowse: Unescaped left brace in regex is deprecated
833885 gbrowse: ships a deterministic/predictable OpenID consumer secret security
857213 gbrowse: broken symlink: /usr/share/gbrowse/htdocs/i -> debian/gbrowse/var/cache/gbrowse/images
874042 hmmer2: please Build-Depend on rename
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
863015 jellyfish: please make the output reproducible patch
865608 jellyfish shouldn't disable PIE patch
871697 jellyfish: Please add arm64
872262 jellyfish FTBFS with gcc 7 buster, patch, sid
873318 jellyfish does not actually disable parallel building
862380 khmer: FTBFS with Python 3.6 buster, patch, sid
872180 kraken builds for all archs, but depends on amd64-only package
872232 macsyfinder: FTBFS with Sphinx 1.6: Needs build-dep on latexmk
866442 mobyle: depends on obsolete python-imaging (replace with python3-pil or python-pil) buster, sid
873864 mrs: Please add arm64
873892 msxpertsuite: FTBFS: latex interference under make install
874530 msxpertsuite: FTBFS: cannot find .../massxpert-doc.pdf
853568 nanopolish: ftbfs with GCC-7 buster, help, sid
873994 FTBFS with Java 9 due to -source/-target only
853609 perm: ftbfs with GCC-7 buster, sid
870228 physamp: fails to upgrade from 'stretch' - trying to overwrite /usr/bin/bppphysamp
861367 pirs: Please do not depend on transitional dummy pkg ttf-liberation
865655 pirs shouldn't disable PIE patch
848332 src:poa: Please add autopkgtest newcomer
864558 poa FTCBFS: uses the build architecture compiler, runs tests despite DEB_BUILD_OPTIONS=nocheck patch
853621 primer3: ftbfs with GCC-7 buster, sid
865191 probabel FTBFS on big endian: FAIL: 5 upstream
848333 src:proda: Please add autopkgtest newcomer
866547 python-biomaj3 encoding issue during build fixed-upstream, patch
866548 src:python-biomaj3: Excessive build-depends complicate python3 transition patch
871160 python-biomaj3: FTBFS: UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 1781: ordinal not in range(128) buster, sid
730515 cd-hit-est is cdhit-est in Debian [Why?]
862039 r-bioc-gviz: accesses the internet during build
871333 r-bioc-rtracklayer: FTBFS: Error: package or namespace load failed for 'rtracklayer' in dyn.load(file, DLLpath = DLLpath, ...): sid
845753 r-cran-treescape FTBFS on armhf, i386: Error: segfault from C stack overflow
875789 FTBFS with Java 9: tests error out help
853656 sga: ftbfs with GCC-7 buster, sid
874424 soapdenovo: please Build-Depend on rename buster, sid
874425 soapdenovo2: please Build-Depend on rename buster, sid
848464 stacks-web: Should Depends/Recommends the metapackage default-mysql-*
868864 stacks doesn't migrate to testing, dependency doesn't exist on some architectures buster, sid
853677 t-coffee: ftbfs with GCC-7 buster, sid
853681 theseus: ftbfs with GCC-7 buster, sid
853687 trinityrnaseq: ftbfs with GCC-7 buster, sid
860645 trinityrnaseq: FTBFS on i386: unsatisfiable build-dependencies: jellyfish (>= 2.1.4), parafly buster, sid, stretch
865262 trinityrnaseq: please build-depend on automake, not obsolete automake1.11
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:
critical10
grave10
serious10
important5
normal3
minor1
wishlist0
Last update: Wed, 20 Sep 2017 19:25:48 -0000