Debian Med Project
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Summary
Bugs of task bio-dev
Total bugs: 56
Open bugs: 34
Fixed bugs: 22
Links to other tasks
Tasks overview
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)
Legend
SeverityDependentSuggested
critical 0 0
grave 0 0
serious 11 1
important 4 0
normal 8 0
minor 2 0
wishlist 8 0

Summary bugs page of task Biology development

Immediately looking into bugs of the dependencies of this task is advised (478)*

Open bugs in dependent packages

11 serious, 4 important, 8 normal, 2 minor, 8 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 (1) Homepage: http://www.biojava.org Vcs Debian Med Packaging Team
659824 biojava-live: New version available
freecontact (1) Homepage: http://rostlab.org/ Vcs Debian Med Packaging Team
814617 freecontact: adequate reports symbol-size-mismatch /usr/bin/freecontact => _ZN11xercesc_3_16XMLUni18fgXercesLoadSchemaE
htsjdk (1) Homepage: http://samtools.github.io/htsjdk/ Vcs Debian Med Packaging Team
877590 FTBFS: error: package org.testng does not exist buster, sid
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 help
ncbi-tools6 (2) Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/ Vcs Debian Med Packaging Team
225651 ncbi-tools-x11: want Cn3D++
879619 ncbi-tools6: Please provide autopkgtest
ngs-sdk (1) Homepage: https://github.com/ncbi/ngs Vcs Debian Med Packaging Team
813559 ngs-sdk: FTBFS: most platforms explicitly unsupported
openms (8) 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, 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
pbbam (1) Homepage: http://pbbam.readthedocs.org/en/latest/index.html Vcs Debian Med Packaging Team
829741 pbbam: FTBFS (32-bit): pbmerge assertion failure fixed-upstream
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 (1) Homepage: http://biopython.org Vcs Debian Med Packaging Team
883860 python-biopython: SeqRecord broken on Debian packages when python-biopython-sql package is not installed upstream
python-csb (1) Homepage: https://github.com/csb-toolbox/CSB Vcs Debian Med Packaging Team
881555 python-csb: Please migrate away from Epydoc if possible
python-pbcore (1) Homepage: https://github.com/PacificBiosciences/pbcore Vcs Debian Med Packaging Team
860158 python-pbcore: prints warnings with recent h5py on ppc64el
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
894326 python-skbio FTBFS with dh-python >= 3.20180313
rdkit (3) Homepage: http://www.rdkit.org Vcs Debichem Team
751414 rdkit: postgresql cartridge not built
881562 rdkit: Please migrate away from Epydoc if possible
894202 rdkit FTBFS on 32bit: test hang
ruby-bio (1) Homepage: http://bioruby.org/ Vcs Debian Ruby Extras Maintainers
890691 ruby-bio FTBFS with ruby 2.5 buster, sid
ruby-crb-blast (1) Homepage: https://github.com/cboursnell/crb-blast Vcs Debian Ruby Extras Maintainers
892066 ruby-crb-blast FTBFS: test failures

Open bugs in suggested packages

1 serious
pbcopper (1) Homepage: https://github.com/PacificBiosciences/pbcopper Vcs Debian Med Packaging Team
852654 src:pbcopper: no point to releasing it without `unanimity`

Done bugs

bamtools (1) Homepage: https://github.com/pezmaster31/bamtools/wiki Vcs Debian Med Packaging Team
894886 libbamtools-dev needs Breaks+Replaces: libbamtools2.4.0 (<< 2.5.1+dfsg-2~)
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
htsjdk (1) Homepage: http://samtools.github.io/htsjdk/ Vcs Debian Med Packaging Team
894289 htsjdk FTBFS with openjdk-9
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-core (3) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
890400 libbpp-core3: ABI change without soname chenge
890405 libbpp-core3: ABI change without soname chenge
894751 license missing
libbpp-phyl (2) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
890136 libbpp-phyl: FTBFS on mipsel: Test took too much time
895339 libbpp-phyl: FTBFS: Could not find compatible version of bpp-seq
libbpp-popgen (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
895213 libbpp-popgen ftbfs on all architectures except on amd64 buster, sid
libbpp-seq-omics (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
895212 libbpp-seq-omics ftbfs on all archs except amd64 buster, sid
libseqlib (1) Homepage: https://github.com/walaj/SeqLib Vcs Debian Med Packaging Team
891745 libseqlib-dev: /usr/include/SeqLib/BamWalker.h includes file locations no longer provided by libhts-dev
libsmithwaterman (2) Homepage: https://github.com/ekg/smithwaterman Vcs Debian Med Packaging Team
895502 libsmithwaterman FTBFS on 32bit: missing symbol
895527 libsmithwaterman FTBFS on mips/mipsel: symbol differences
mgltools-vision (1) Homepage: http://mgltools.scripps.edu/ Vcs Debian Med Packaging Team
883845 mgltools-vision: Source includes "Vision/doc/Examples/lena.jpg" listed in Files-Excluded header
python-biopython (1) Homepage: http://biopython.org Vcs Debian Med Packaging Team
672407 python-biopython: duplicate mathml2.dtd
python-cogent (1) Homepage: http://pycogent.org/ Vcs Debian Med Packaging Team
730515 cd-hit-est is cdhit-est in Debian [Why?]
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
rdkit (1) Homepage: http://www.rdkit.org Vcs Debichem Team
893177 rdkit ftbfs with new glibc/2.27
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
*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: Sat, 21 Apr 2018 18:31:21 -0000