Summary

Bugs of task bio-ngs

Total bugs: 19

Open bugs: 10

Fixed bugs: 9

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	0	0
serious	3	0
important	4	0
normal	3	0
minor	0	0
wishlist	0	0

Summary bugs page of task Next generation sequencing

Immediately looking into bugs of the dependencies of this task is advised (177)^*

Open bugs in dependent packages

3 serious, 4 important, 3 normal

bcftools (4) Homepage: http://samtools.github.io/bcftools/ Vcs Debian Med Packaging Team
819617	FTBFS: any-i386 - floating point idiosyncracies	buster, ftbfs, sid, stretch
860682	bcftools: FTBFS on i386: Test failures	buster, ftbfs, sid, stretch
860704	python-pysam: FTBFS on i386: build-dependency not installable: bcftools (>= 1.3.1)	buster, ftbfs, sid, stretch
870060	bcftools FTBFS on big endian: 107 tests failed	ftbfs
bedtools (2) Homepage: https://github.com/arq5x/bedtools2 Vcs Debian Med Packaging Team
890116	bedtools FTBFS on 32bit: Tools failing: coverage intersect negativecontrol reldist shuffle split	ftbfs
890117	bedtools FTBFS on big endian: Tools failing: bamtobed bamtofastq coverage genomecov groupby intersect jaccard map merge multicov negativecontrol	ftbfs
blasr (1) Homepage: https://github.com/PacificBiosciences/blasr Vcs Debian Med Packaging Team
906811	FTBFS: libconfig.h: No such file or directory	ftbfs, pending
picard-tools (2) Homepage: http://broadinstitute.github.io/picard/ Vcs Debian Med Packaging Team
880258	picard-tools: FTBFS: CollectRrbsMetricsTest.java:29: error: package org.testng does not exist	buster, sid
905645	picard-tools: autopkgtest regression: Option 'ALIGNMENT_STATUS' is required.
tophat (1) Homepage: http://ccb.jhu.edu/software/tophat Vcs Debian Med Packaging Team
873866	tophat: Please add arm64

Open bugs in suggested packages

Done bugs

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
picard-tools (1) Homepage: http://broadinstitute.github.io/picard/ Vcs Debian Med Packaging Team
905706	libpicard-java-doc: ships /usr/share/javascript/jquery/jquery.min.js
sra-sdk (1) Homepage: https://github.com/ncbi/sra-tools/ Vcs Debian Med Packaging Team
906509	sra-sdk: FTBFS in buster (unknown type name 'HttpProxy')	ftbfs
ssake (1) Homepage: http://www.bcgsc.ca/platform/bioinfo/software/ssake Vcs Debian Med Packaging Team
910414	ssake-examples: broken symlink: /usr/share/doc/ssake/examples/runSSAKE.sh -> ../tools/runSSAKE.sh
vcftools (1) Homepage: https://vcftools.github.io/ Vcs Debian Med Packaging Team
902190	vcftools: CVE-2018-11099 CVE-2018-11129 CVE-2018-11130	fixed-upstream, security

^*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