Summary

Bugs of task bio-dev

Total bugs: 48

Open bugs: 44

Fixed bugs: 4

Links to other tasks

Tasks overview

Biology 119 (849)

Biology development 44 (324)

Next generation sequencing 14 (120)

Phylogeny 8 (66)

Cloud 40 (324)

Content management 0 (0)

Medical data 1 (9)

Dental 0 (0)

Epidemiology 0 (0)

Hospital information systems 1 (9)

Imaging 178 (940)

Imaging development 93 (815)

Laboratory 0 (0)

Oncology 1 (15)

Pharmacology 1 (9)

Physics 31 (273)

Practice 2 (9)

Psychology 6 (63)

Rehabilitation 1 (9)

Research 0 (0)

Statistics 2 (6)

Tools 34 (204)

Typesetting 95 (523)

Legend

Severity	Dependent	Suggested
critical	0	0
grave	0	0
serious	2	1
important	7	1
normal	15	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 (324)^*

Open bugs in dependent packages

2 serious, 7 important, 15 normal, 2 minor, 15 wishlist

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	jessie, sid, stretch
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
biojava4-live (1) Homepage: http://www.biojava.org Vcs Debian Med Packaging Team
843712	biojava4-live: FTBFS (failing tests)
ffindex (1) Homepage: http://www.splashground.de/~andy/programs/FFindex/ Vcs Debian Med Packaging Team
851658	ffindex: autopkgtests need 6GB of memory to run
freecontact (2) Homepage: http://rostlab.org/ Vcs Debian Med Packaging Team
814617	freecontact: adequate reports symbol-size-mismatch /usr/bin/freecontact => _ZN11xercesc_3_16XMLUni18fgXercesLoadSchemaE
853405	freecontact: ftbfs with GCC-7	buster, sid
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	sid, stretch
htslib (4) Homepage: https://github.com/samtools/htslib Vcs Debian Med Packaging Team
749367	htslib FTBFS on testing for mips/mipsel	moreinfo, patch, sid, stretch
774109	htslib: FTBFS on hppa
800469	htslib FTBFS on armhf, bus error.	patch, sid, stretch
849667	htslib: FTBFS on armhf: [test] Bus error	patch, sid, stretch
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)	sid, stretch
libbpp-seq-omics (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
853482	libbpp-seq-omics: ftbfs with GCC-7	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
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	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 (4) Homepage: http://open-ms.sourceforge.net/ Vcs The Debichem Group
784502	[openms] Qt4's WebKit removal
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
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	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	sid, stretch
pyfai (1) Homepage: https://github.com/silx-kit/pyFAI Vcs Debian Science Maintainers
710121	pyfai: Please package the latest pyFAI
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
672407	python-biopython: duplicate mathml2.dtd
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	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)	sid, stretch
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
860704	python-pysam: FTBFS on i386: build-dependency not installable: bcftools (>= 1.3.1)	sid, stretch
python-ruffus (1) Homepage: http://www.ruffus.org.uk/ Vcs Debian Med Packaging Team
841073	python-ruffus: Needs 18 GB of RAM to build
rdkit (1) Homepage: http://www.rdkit.org Vcs Debichem Team
751414	rdkit: postgresql cartridge not built
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)
swissknife (1) Homepage: http://swissknife.sourceforge.net Not maintained in Vcs Steffen Moeller
826505	swissknife: Unescaped left brace in regex is deprecated

Open bugs in suggested packages

1 serious, 1 important, 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
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

Done bugs

genometools (1) Homepage: http://genometools.org Vcs Debian Med Packaging Team
836230	FTBFS in a low memory machine with poor error message
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
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
861496	python-pysam: accesses network during build

^*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:

critical	10
grave	10
serious	10
important	5
normal	3
minor	1
wishlist	0