Summary

Bugs of task bio-dev

Total bugs: 57

Open bugs: 38

Fixed bugs: 19

Links to other tasks

Tasks overview

Biology 114 (1337)

Biology development 38 (544)

Next generation sequencing 10 (177)

Phylogeny 9 (93)

Cloud 43 (411)

Content management 0 (0)

Medical data 1 (0)

Dental 1 (30)

Epidemiology 3 (69)

Hospital information systems 0 (0)

Imaging 227 (1359)

Imaging development 101 (1082)

Laboratory 0 (0)

Oncology 0 (0)

Pharmacology 0 (0)

Physics 26 (219)

Practice 3 (30)

Psychology 11 (122)

Rehabilitation 2 (39)

Research 0 (0)

Statistics 3 (7)

Tools 37 (246)

Typesetting 81 (601)

Legend

Severity	Dependent	Suggested
critical	0	0
grave	1	0
serious	11	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 (544)^*

Open bugs in dependent packages

1 grave, 11 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
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	ftbfs
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	fixed-upstream, 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

fast5 (1) Homepage: https://github.com/mateidavid/fast5 Vcs Debian Med Packaging Team
910655	fast5: please make the build reproducible	patch
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 (5) 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
905438	htslib: FTBFS on i386: 2 tests fail	ftbfs
908501	Does not depend on zlib1g-dev
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-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-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 (1) 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
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
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
pbbam (1) Homepage: http://pbbam.readthedocs.org/en/latest/index.html Vcs Debian Med Packaging Team
910206	libpbbam-dev: missing Breaks+Replaces: libpbbam (<< 0.18)
python-cogent (1) Homepage: http://pycogent.org/ Vcs Debian Med Packaging Team
730515	cd-hit-est is cdhit-est in Debian [Why?]

^*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