Debian Med Project
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Summary
Bugs of task bio-dev
Total bugs: 68
Open bugs: 50
Fixed bugs: 18
Links to other tasks
Tasks overview
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 0
serious 11 2
important 7 0
normal 12 1
minor 2 0
wishlist 15 0

Summary bugs page of task Biology development

Immediately looking into bugs of the dependencies of this task is advised (572)*

Open bugs in dependent packages

11 serious, 7 important, 12 normal, 2 minor, 15 wishlist
bamtools (1) Homepage: https://github.com/pezmaster31/bamtools/wiki Vcs Debian Med Packaging Team
865130 reapr FTBFS on big endian: Error sampling from files '00.Sample/fragCov.gz', '00.assembly.fa.gc.gz' upstream
biococoa (1) Homepage: http://bioinformatics.org/biococoa/ Vcs Debian Med Packaging Team
749736 biococoa: GCC warnings that may lead to runtime issues with new GNUstep libraries buster, jessie, sid, stretch
biojava4-live (1) Homepage: http://www.biojava.org Vcs Debian Med Packaging Team
843712 biojava4-live: FTBFS (failing tests)
biojava-live (2) Homepage: http://www.biojava.org Vcs Debian Med Packaging Team
659824 biojava-live: New version available
859958 biojava-live: please make the build reproducible
bioperl (1) Homepage: http://www.bioperl.org/ Vcs Debian Med Packaging Team
866073 bioperl: autopkgtest regression
fast5 (1) Homepage: https://github.com/mateidavid/fast5 Vcs Debian Med Packaging Team
876283 autopkg test command1 fails buster, sid
freecontact (1) Homepage: http://rostlab.org/ Vcs Debian Med Packaging Team
814617 freecontact: adequate reports symbol-size-mismatch /usr/bin/freecontact => _ZN11xercesc_3_16XMLUni18fgXercesLoadSchemaE
htseq (1) Homepage: http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html Vcs Debian Med Packaging Team
860674 htseq: FTBFS on i386: build-dependency not installable: python-pysam buster, sid, stretch
htslib (2) Homepage: https://github.com/samtools/htslib Vcs Debian Med Packaging Team
866137 htslib autopkgtest is broken in 1.4.1-2
871314 htslib: new version break python-pysam sid
kineticstools (1) Homepage: https://github.com/PacificBiosciences/kineticsTools Vcs Debian Med Packaging Team
860636 kineticstools: FTBFS on i386: build-dependency not installable: python-pbcore (>= 1.2.8) buster, sid, stretch
libbpp-qt (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
875009 [libbpp-qt] Future Qt4 removal from Buster upstream
libhmsbeagle (1) Homepage: https://github.com/beagle-dev/beagle-lib Vcs Debian Med Packaging Team
858524 libhmsbeagle-dev: broken symlink: /usr/include/libhmsbeagle -> libhmsbeagle-2
librostlab-blast (2) Homepage: http://rostlab.org/ Vcs Debian Med Packaging Team
832138 librostlab-blast: The package should compile without forcing the older -std=c++03
851472 librostlab-blast: autopkg test suite failure
libsbml (1) Homepage: http://www.sbml.org/ Vcs Debian Med Packaging Team
847013 src:libsbml: build python3 bindings
libvcflib (1) Homepage: https://github.com/ekg/vcflib Vcs Debian Med Packaging Team
860665 libvcflib: FTBFS on i386: build-dependency not installable: libssw-dev buster, sid, stretch
ncbi-tools6 (1) Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/ Vcs Debian Med Packaging Team
225651 ncbi-tools-x11: want Cn3D++
ngs-sdk (1) Homepage: https://github.com/ncbi/ngs Vcs Debian Med Packaging Team
813559 ngs-sdk: FTBFS: most platforms explicitly unsupported
openms (7) Homepage: http://open-ms.sourceforge.net/ Vcs The Debichem Group
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
pbbam (1) Homepage: http://pbbam.readthedocs.org/en/latest/index.html Vcs Debian Med Packaging Team
829741 pbbam: FTBFS (32-bit): pbmerge assertion failure
pbh5tools (1) Homepage: https://github.com/PacificBiosciences/pbh5tools Vcs Debian Med Packaging Team
860616 pbh5tools: FTBFS on i386: build-dependency not installable: python-pbcore buster, sid, stretch
pbseqlib (1) Homepage: https://github.com/PacificBiosciences/blasr_libcpp Vcs Debian Med Packaging Team
860671 pbseqlib: FTBFS on i386: build-dependency not installable: libpbbam-dev buster, sid, stretch
pyfai (2) Homepage: https://github.com/silx-kit/pyFAI Vcs Debian Science Maintainers
710121 pyfai: Please package the latest pyFAI
866460 pyfai: depends on obsolete python-imaging (replace with python3-pil or python-pil) buster, sid
python-biom-format (1) Homepage: http://biom-format.org/ Vcs Debian Med Packaging Team
820060 python-biom-format: broken on big-endian architectures
python-biopython (2) Homepage: http://biopython.org Vcs Debian Med Packaging Team
672407 python-biopython: duplicate mathml2.dtd
872222 python-biopython: broken symlinks: /usr/share/doc/python-biopython/{NEWS, DEPRECATED, CONTRIB} -> *.rst
python-pbcommand (1) Homepage: https://pbcommand.readthedocs.org/en/latest/ Vcs Debian Med Packaging Team
860615 python-pbcommand: FTBFS on i386: build-dependency not installable: python-pbcore buster, sid, stretch
python-pbcore (2) Homepage: https://github.com/PacificBiosciences/pbcore Vcs Debian Med Packaging Team
860158 python-pbcore: prints warnings with recent h5py on ppc64el
860644 python-pbcore: FTBFS on i386: build-dependency not installable: python-pysam (>= 0.9.0) buster, sid, stretch
python-pybedtools (1) Homepage: https://daler.github.io/pybedtools/ Vcs Debian Med Packaging Team
868927 python-pybedtools FTBFS with more than one supported Python3 version buster, patch, sid
python-pysam (2) Homepage: http://pysam.readthedocs.org/en/latest Vcs Debian Med Packaging Team
834856 python-pysam: FTBFS on 32-bit architectures: segmentation fault in testsuite help
871083 python-pysam: FTBFS: Test failures sid
python-ruffus (1) Homepage: http://www.ruffus.org.uk/ Vcs Debian Med Packaging Team
841073 python-ruffus: Needs 18 GB of RAM to build
python-skbio (1) Homepage: https://github.com/biocore/scikit-bio Vcs Debian Med Packaging Team
868962 python-skbio: FTBFS: Test failures buster, sid
rdkit (2) Homepage: http://www.rdkit.org Vcs Debichem Team
751414 rdkit: postgresql cartridge not built
872246 rdkit: FTBFS with Sphinx 1.6: Needs build-dep on latexmk buster, sid
relion (1) Homepage: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page Vcs Debian Med Packaging Team
873865 relion: Please add arm64
staden-io-lib (1) Homepage: http://staden.sourceforge.net/ Vcs Debian Med Packaging Team
710225 staden-io-lib: library name should follow ABI version (not project version)

Open bugs in suggested packages

2 serious, 1 normal
pbcopper (1) Homepage: https://github.com/PacificBiosciences/pbcopper Vcs Debian Med Packaging Team
852654 src:pbcopper: no point to releasing it without `unanimity`
r-bioc-iranges (1) Homepage: https://bioconductor.org/packages/IRanges/ Vcs Debian Med Packaging Team
855625 r-bioc-iranges: ships dangling symlink /usr/share/doc/r-bioc-iranges/RleTricks.pdf
samtools (1) Homepage: http://www.htslib.org/ Vcs Debian Med Packaging Team
871315 samtools: new version breaks python-pysam sid

Done bugs

biojava4-live (1) Homepage: http://www.biojava.org Vcs Debian Med Packaging Team
875334 FTBFS with Java 9: javax.xml.bind
bioperl (1) Homepage: http://www.bioperl.org/ Vcs Debian Med Packaging Team
873745 bioperl: please Build-Depend on rename buster, sid
bioperl-run (1) Homepage: http://search.cpan.org/dist/BioPerl-Run/ Vcs Debian Med Packaging Team
868073 bioperl-run: FTBFS: t/Bowtie.t failure buster, sid, upstream
bio-tradis (1) Homepage: https://github.com/sanger-pathogens/Bio-Tradis Vcs Debian Med Packaging Team
866074 bio-tradis: autopkgtest regression
fast5 (1) Homepage: https://github.com/mateidavid/fast5 Vcs Debian Med Packaging Team
875991 fast5: FTBFS: debian/python-fast5-bin/usr/bin/ is not a directory
htseq (1) Homepage: http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html Vcs Debian Med Packaging Team
742921 python-htseq: python.numpy dtype size error
htslib (3) Homepage: https://github.com/samtools/htslib Vcs Debian Med Packaging Team
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
libbpp-phyl (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
871085 libbpp-phyl: FTBFS: collect2: error: ld returned 1 exit status buster, sid
libchado-perl (1) Homepage: http://gmod.org/wiki/Chado Vcs Debian Med Packaging Team
854341 libchado-perl: FTBFS: The following enviroment variables not detected: CHADO_DB_USERNAME help, moreinfo, unreproducible
ngs-sdk (1) Homepage: https://github.com/ncbi/ngs Vcs Debian Med Packaging Team
866514 src:ngs.sdk: Excessive build-depends complicate python3 transition patch
python-biomaj3 (3) Homepage: https://github.com/genouest/biomaj Vcs Debian Med Packaging Team
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
python-biotools (1) Homepage: https://github.com/sonwell/biotools Vcs Debian Med Packaging Team
866528 src:python-biotools: Inappropriate use of arch:any vice arch:all patch
python-cogent (1) Homepage: http://pycogent.org/ Vcs Debian Med Packaging Team
730515 cd-hit-est is cdhit-est in Debian [Why?]
r-bioc-shortread (1) Homepage: https://bioconductor.org/packages/ShortRead/ Vcs Debian Med Packaging Team
845752 r-bioc-shortread FTBFS on armel: Error: segfault from C stack overflow
*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