Summary

Bugs of task bio-ngs

Total bugs: 26

Open bugs: 16

Fixed bugs: 10

Links to other tasks

Tasks overview

Biology 144 (1426)

Biology development 55 (708)

Next generation sequencing 16 (243)

Phylogeny 9 (75)

Cloud 43 (507)

Content management 0 (0)

Medical data 1 (9)

Dental 0 (0)

Epidemiology 1 (9)

Hospital information systems 2 (18)

Imaging 190 (1158)

Imaging development 96 (1003)

Laboratory 0 (0)

Oncology 2 (30)

Pharmacology 3 (27)

Physics 30 (288)

Practice 2 (9)

Psychology 8 (93)

Rehabilitation 1 (9)

Research 0 (0)

Statistics 2 (6)

Tools 35 (209)

Typesetting 64 (322)

Legend

Severity	Dependent	Suggested
critical	0	0
grave	0	0
serious	4	0
important	7	0
normal	2	0
minor	0	0
wishlist	3	0

Summary bugs page of task Next generation sequencing

Immediately looking into bugs of the dependencies of this task is advised (243)^*

Open bugs in dependent packages

4 serious, 7 important, 2 normal, 3 wishlist

bcftools (4) Homepage: http://samtools.github.io/bcftools/ Vcs Debian Med Packaging Team
819617	FTBFS: any-i386 - floating point idiosyncracies	buster, sid, stretch
860682	bcftools: FTBFS on i386: Test failures	buster, sid, stretch
860704	python-pysam: FTBFS on i386: build-dependency not installable: bcftools (>= 1.3.1)	buster, sid, stretch
868958	bcftools FTBFS on 32bit: test failures
bedtools (1) Homepage: https://github.com/arq5x/bedtools2 Vcs Debian Med Packaging Team
747337	broken autopkgtest: missing dependency, not testing installed package, test failures	upstream
blasr (1) Homepage: https://github.com/PacificBiosciences/blasr Vcs Debian Med Packaging Team
860655	blasr: FTBFS on i386: unsatisfiable build-dependencies: libpbseq-dev (>= 0~20160912), libpbbam-dev	buster, sid, stretch
bowtie (2) Homepage: http://bowtie-bio.sourceforge.net/ Vcs Debian Med Packaging Team
864439	bowtie: FTBFS on mips64el - /usr/bin/ld: .gnu.hash is incompatible with the MIPS ABI
864448	bowtie FTBFS on mips64el: /usr/bin/ld: .gnu.hash is incompatible with the MIPS ABI
fastx-toolkit (1) Homepage: http://hannonlab.cshl.edu/fastx_toolkit/ Vcs Debian Med Packaging Team
853396	fastx-toolkit: ftbfs with GCC-7	buster, sid
filo (1) Homepage: https://github.com/arq5x/filo Vcs Debian Med Packaging Team
848335	Filo should be removed from Debian after Stretch release since it is unmaintained and can be replaced	newcomer
htslib (1) Homepage: https://github.com/samtools/htslib Vcs Debian Med Packaging Team
866137	htslib autopkgtest is broken in 1.4.1-2
last-align (1) Homepage: http://last.cbrc.jp/ Vcs Debian Med Packaging Team
866438	last-align: depends on obsolete python-imaging (replace with python3-pil or python-pil)	buster, sid
mhap (1) Homepage: http://mhap.readthedocs.org/en/stable/ Vcs Debian Med Packaging Team
860672	mhap: FTBFS on i386: build-dependency not installable: libssw-java	buster, sid, stretch
qiime (1) Homepage: http://www.qiime.org/ Vcs Debian Med Packaging Team
820308	qiime: many unsatisfiable dependencies
rna-star (1) Homepage: https://github.com/alexdobin/STAR/ Vcs Debian Med Packaging Team
868742	rna-star should remove s390x from the architecture list
tophat (1) Homepage: http://ccb.jhu.edu/software/tophat Vcs Debian Med Packaging Team
780816	tophat: contains and uses convience copy of samtools 0.1.18

Open bugs in suggested packages

Done bugs

bcftools (2) Homepage: http://samtools.github.io/bcftools/ Vcs Debian Med Packaging Team
865006	bcftools FTBFS with htslib 1.4.1-2: [E::hts_idx_push] Region 536870912..536870913 cannot be stored in a tbi index. Try using a csi index with min_shift = 14, n_lvls >= 6	buster, sid
865060	bcftools FTBFS: Usage: test-regidx [OPTIONS]	patch
bwa (1) Homepage: http://bio-bwa.sourceforge.net/ Vcs Debian Med Packaging Team
853859	bwa: Segmentation fault with specific data set
htslib (6) Homepage: https://github.com/samtools/htslib Vcs Debian Med Packaging Team
749367	htslib FTBFS on testing for mips/mipsel	buster, moreinfo, patch, sid, stretch
774109	htslib: FTBFS on hppa
800469	htslib FTBFS on armhf, bus error.	buster, patch, sid, stretch
849667	htslib: FTBFS on armhf: [test] Bus error	buster, patch, sid, stretch
865010	htslib: use -fPIC to fix FTBFS on s390x	patch
865012	htslib FTBFS on i386: test_vcf_{api,sweep} failed	patch, upstream
samtools (1) Homepage: http://www.htslib.org/ Vcs Debian Med Packaging Team
865008	samtools FTBFS with htslib 1.4.1-2: error: conflicting types for 'errmod_t'	buster, sid

^*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