Debian Med Project
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Summary
Bugs of task bio-dev
Total bugs: 68
Open bugs: 39
Fixed bugs: 29
Links to other tasks
Tasks overview
Biology 102 (1265)
Phylogeny 6 (57)
Cloud 35 (441)
Medical data 1 (0)
Dental 2 (39)
Epidemiology 3 (48)
Imaging 219 (1259)
Laboratory 0 (0)
Oncology 0 (0)
Pharmacology 0 (0)
Physics 26 (219)
Practice 4 (39)
Psychology 12 (152)
Research 0 (0)
Statistics 3 (7)
Tools 38 (249)
Typesetting 81 (601)
Legend
SeverityDependentSuggested
critical 0 0
grave 1 0
serious 12 1
important 4 0
normal 12 0
minor 2 0
wishlist 7 0

Summary bugs page of task Biology development

Immediately looking into bugs of the dependencies of this task is advised (574)*

Open bugs in dependent packages

1 grave, 12 serious, 4 important, 12 normal, 2 minor, 7 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' ftbfs, 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
ffindex (1) Homepage: http://www.splashground.de/~andy/programs/FFindex/ Vcs Debian Med Packaging Team
907624 ffindex: ffindex_modify segfaults during autopkgtest ftbfs
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
htslib (1) Homepage: https://github.com/samtools/htslib Vcs Debian Med Packaging Team
905438 htslib: FTBFS on i386: 2 tests fail ftbfs
kineticstools (1) Homepage: https://github.com/PacificBiosciences/kineticsTools Vcs Debian Med Packaging Team
902591 kineticstools: autopkgtest failure with NumPy 1.14
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
librcsb-core-wrapper (1) Homepage: http://sw-tools.rcsb.org/apps/CORE-WRAPPER/index.html Vcs Debian Med Packaging Team
897795 librcsb-core-wrapper: ftbfs with GCC-8 buster, ftbfs, patch, sid
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 (3) Homepage: http://www.sbml.org/ Vcs Debian Med Packaging Team
847013 src:libsbml: build python3 bindings help
896531 libsbml5-perl: Can't locate loadable object for module LibSBML patch
901455 FTBFS in sid: package com.sun.tools.doclets.standard is not visible ftbfs
ncbi-tools6 (2) Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/ Vcs Debian Med Packaging Team
225651 ncbi-tools-x11: want Cn3D++
908353 ncbi-tools6 FTCBFS: uses the build architecture compiler patch, pending
ngs-sdk (1) Homepage: https://github.com/ncbi/ngs Vcs Debian Med Packaging Team
813559 ngs-sdk: FTBFS: most platforms explicitly unsupported ftbfs
openms (4) Homepage: http://open-ms.sourceforge.net/ Vcs The Debichem Group
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
pbbam (3) Homepage: http://pbbam.readthedocs.org/en/latest/index.html Vcs Debian Med Packaging Team
829741 pbbam: FTBFS (32-bit): pbmerge assertion failure fixed-upstream, ftbfs
908269 pbbam: autopkgtest regression
909071 pbbam: FTBFS on every release architecture where it previously built
pyfai (1) Homepage: https://github.com/silx-kit/pyFAI Vcs Debian Science Maintainers
908615 pyfai: FTBFS and autopkgtest fails with python3.7 in supported versions ftbfs
python-biom-format (2) Homepage: http://biom-format.org/ Vcs Debian Med Packaging Team
820060 python-biom-format: broken on big-endian architectures
896953 python-biom-format: autopkgtest fails with new version while succeeded in the past; autodep8 not ready yet
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-cobra (1) Homepage: http://opencobra.github.io/cobrapy/ Vcs Debian Med Packaging Team
904709 python-cobra ftbfs (test failures) buster, ftbfs, sid
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
906156 python-skbio ftbfs in unstable, and autopkg tests fail (Python 3.7 tests) buster, ftbfs, sid, upstream
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 ftbfs

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

bioperl-run (1) Homepage: https://metacpan.org/release/BioPerl-Run Vcs Debian Med Packaging Team
906337 bioperl-run: FTBFS in buster/sid (autobuilder hangs) ftbfs, help
ffindex (1) Homepage: http://www.splashground.de/~andy/programs/FFindex/ Vcs Debian Med Packaging Team
905334 ffindex: missing build dependency on cmake ftbfs
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 (4) 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, ftbfs, patch, sid, stretch
849667 htslib: FTBFS on armhf: [test] Bus error buster, ftbfs, patch, sid, stretch
908501 Does not depend on zlib1g-dev
kmer (3) Homepage: http://kmer.sourceforge.net Vcs Debian Med Packaging Team
906932 kmer FTBFS in clean unstable chroot
906980 kmer: autopkgtest fails with segfault in testing/unstable while it passes in stable
907007 kmer FTBFS on arm64: recompile with -fPIC buster, ftbfs, patch, sid
libbiod (1) Homepage: https://github.com/biod/BioD Vcs Debian Med Packaging Team
907451 libbiod FTBFS: Error: cannot implicitly convert expression ftbfs, help
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
897780 libbpp-core: ftbfs with GCC-8 buster, ftbfs, sid
libbpp-phyl (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
906478 libbpp-phyl: FTBFS in buster/sid (dh_makeshlibs fails) ftbfs
libbpp-phyl-omics (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
897781 libbpp-phyl-omics: ftbfs with GCC-8 buster, ftbfs, sid
libbpp-popgen (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
897782 libbpp-popgen: ftbfs with GCC-8 buster, ftbfs, sid
libbpp-qt (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
897783 libbpp-qt: ftbfs with GCC-8 buster, ftbfs, sid
libbpp-seq (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
897784 libbpp-seq: ftbfs with GCC-8 buster, ftbfs, sid
libbpp-seq-omics (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
897785 libbpp-seq-omics: ftbfs with GCC-8 buster, ftbfs, sid
libfastahack (2) Homepage: https://github.com/ekg/fastahack Vcs Debian Med Packaging Team
906481 libfastahack: FTBFS in buster/sid (ld: cannot find -lfastahack) buster, ftbfs, patch, sid
907210 libfastahack: ftbfs on some architectures (symbols)
libmems (1) Homepage: http://sourceforge.net/p/mauve/code/HEAD/tree/libMems/trunk/ Vcs Debian Med Packaging Team
907417 libmems: Wrong library Provides for libraries with different ABI patch
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
ncbi-vdb (1) Homepage: https://github.com/ncbi/ncbi-vdb Vcs Debian Med Packaging Team
907358 ncbi-vdb: fix broken library on i386 help, patch
openms (1) Homepage: http://open-ms.sourceforge.net/ Vcs The Debichem Group
871297 libopenms2.0: requires rebuild against GCC 7 and symbols/shlibs bump buster, sid
python-cogent (1) Homepage: http://pycogent.org/ Vcs Debian Med Packaging Team
730515 cd-hit-est is cdhit-est in Debian [Why?]
python-pysam (1) Homepage: http://pysam.readthedocs.org/en/latest Vcs Debian Med Packaging Team
905548 python-pysam: FTBFS - tests fail: AttributeError: 'module' object has no attribute 'HAVE_LIBCURL' ftbfs
r-cran-rnexml (1) Homepage: https://cran.r-project.org/package=RNeXML Vcs Debian R Packages Maintainers
898207 r-cran-rnexml: autopkgtest regression
*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, 19 Sep 2018 18:29:03 -0000