Summary

Bugs of task bio

Total bugs: 143

Open bugs: 102

Fixed bugs: 41

Links to other tasks

Tasks overview

Biology 102 (1265)

Biology development 39 (574)

Next generation sequencing 11 (207)

Phylogeny 6 (57)

Cloud 35 (441)

Content management 0 (0)

Medical data 1 (0)

Dental 2 (39)

Epidemiology 3 (48)

Hospital information systems 0 (0)

Imaging 219 (1259)

Imaging development 97 (1034)

Laboratory 0 (0)

Oncology 0 (0)

Pharmacology 0 (0)

Physics 26 (219)

Practice 4 (39)

Psychology 12 (152)

Rehabilitation 2 (39)

Research 0 (0)

Statistics 3 (7)

Tools 38 (249)

Typesetting 81 (601)

Legend

Severity	Dependent	Suggested
critical	0	0
grave	0	2
serious	21	2
important	14	0
normal	38	7
minor	7	1
wishlist	9	1

Summary bugs page of task Biology

Immediately looking into bugs of the dependencies of this task is advised (1265)^*

Open bugs in dependent packages

21 serious, 14 important, 38 normal, 7 minor, 9 wishlist

abyss (1) Homepage: http://www.bcgsc.ca/platform/bioinfo/software/abyss Vcs Debian Med Packaging Team
889147	abyss: PairedDBG_LoadAlgorithm test fails on sparc64 due to strict alignment violation	patch, upstream
avogadro (3) Homepage: http://avogadro.cc/ Vcs Debichem Team
712789	Fwd: avogadro crashes	patch
731226	avogadro crashes on export image	upstream
874834	[avogadro] Future Qt4 removal from Buster	help
baitfisher (1) Homepage: https://github.com/cmayer/BaitFisher-package Vcs Debian Med Packaging Team
852839	baitfisher: FTBFS (32-bit): mixes ::size_t and faststring::size_t	fixed-upstream, ftbfs, help
ball (3) Homepage: http://www.ball-project.org/ Vcs Debian Med Packaging Team
784451	[ball] Qt4's WebKit removal	buster, fixed-upstream, sid, upstream
874837	[ball] Future Qt4 removal from Buster	fixed-upstream
905443	ball: FTBFS - test failures	ftbfs
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
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
beast2-mcmc (1) Homepage: http://www.beast2.org Vcs Debian Med Packaging Team
894359	beast2-mcmc build depends on openjdk-8-jdk	buster, help, sid
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
clonalframe (1) Homepage: http://www.xavierdidelot.xtreemhost.com/clonalframe.htm Vcs Debian Med Packaging Team
891730	clonalframe: Please provide autopkgtest
clonalorigin (1) Homepage: https://github.com/xavierdidelot/clonalorigin Vcs Debian Med Packaging Team
884475	clonalorigin: FTBFS on alpha: tests time out	upstream, wontfix
concavity (1) Homepage: http://compbio.cs.princeton.edu/concavity/ Vcs Debian Med Packaging Team
904145	concavity FTCBFS: uses a C compiler for C++ sources	patch, upstream
datamash (1) Homepage: https://savannah.gnu.org/projects/datamash/ Vcs Debian Science Maintainers
896487	datamash FTBFS on !x86/ia64: FAIL: tests/datamash-output-format	ftbfs
dawg (1) Homepage: https://github.com/reedacartwright/dawg Vcs Debian Med Packaging Team
903886	dawg: Test suite fails	upstream
ea-utils (2) Homepage: https://expressionanalysis.github.io/ea-utils/ Vcs Debian Med Packaging Team
846858	src:ea-utils: New version available
862118	ea-utils: New upstream version available
emboss (1) Homepage: http://emboss.sourceforge.net Vcs Debian Med Packaging Team
682042	emboss-data: ships bulky taxonomy and gene ontology data
examl (1) Homepage: https://github.com/stamatak/ExaML Vcs Debian Med Packaging Team
896492	examl: autopkgtest started failing for unclear reasons, but old test logs contain error code 255 as well
falcon (1) Homepage: https://github.com/PacificBiosciences/FALCON Vcs Debian Med Packaging Team
902132	falcon: FTBFS since python-networkx version 2.1-1; fails in test suite	ftbfs
fastqc (1) Homepage: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Vcs Debian Med Packaging Team
897109	fastqc: autopkgtest fails with new version while succeeded in the past; htsjdk.samtools.util.RuntimeIOException: java.io.IOException: Stream closed
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
gamgi (2) Homepage: http://www.gamgi.org/ Vcs Debichem Team
750139	gamgi: Conflicting return types of function gamgi_engine_iarray_push	upstream
903048	gamgi: Please do not depend on transitional dummy pkg ttf-dejavu
garli (1) Homepage: https://github.com/Ashod/garli Vcs Debian Med Packaging Team
907905	garli: FTBFS randomly (failing tests)	ftbfs, upstream
garlic (2) Homepage: http://www.zucic.org/garlic/ Vcs Debichem Team
715937	[Mayhem] Bug report on garlic: garlic crashes with exit status 139
749656	garlic: Conflicting declarations of function BlurMainWindow_ to cause undefined behaviour
gentle (1) Homepage: http://gentle.magnusmanske.de Vcs Debian Med Packaging Team
732691	Pressing "alignment or Ctrl+G" only results in a dialog with a cancel button
gff2aplot (1) Homepage: http://genome.imim.es/software/gfftools/GFF2APLOT.html Vcs Debian Med Packaging Team
890789	gff2aplot: Please provide autopkgtest	newcomer
ghemical (1) Homepage: http://bioinformatics.org/ghemical/ghemical/ Vcs Debichem Team
826069	ghemical: does not display color or allow building	help
gromacs (1) Homepage: http://www.gromacs.org/ Vcs Debichem Team
644397	Provide runtime detection for CPU SIMD capabilities	upstream
htslib (1) Homepage: https://github.com/samtools/htslib Vcs Debian Med Packaging Team
905438	htslib: FTBFS on i386: 2 tests fail	ftbfs
jalview (1) Homepage: http://www.jalview.org Vcs Debian Java Maintainers
849025	jalview: FTBFS: error: cannot find symbol EnumCallback	ftbfs
jellyfish (1) Homepage: http://www.cbcb.umd.edu/software/jellyfish/ Vcs Debian Med Packaging Team
907819	jellyfish: Does not build on paths containing "-L" resulting in random FTBFS when built by sbuild	ftbfs
jmodeltest (1) Homepage: https://github.com//ddarriba/jmodeltest2 Vcs Debian Med Packaging Team
906371	jmodeltest: FTBFS in buster/sid	ftbfs, help
jmol (2) Homepage: http://jmol.sourceforge.net/ Vcs Debichem Team
712791	jmol - exporting the image as PDF saves only partial image	patch
872418	jmol: Weblinks in Help do not work
khmer (1) Homepage: http://khmer.readthedocs.org Vcs Debian Med Packaging Team
851830	arm64 has flaky tests
kineticstools (1) Homepage: https://github.com/PacificBiosciences/kineticsTools Vcs Debian Med Packaging Team
902591	kineticstools: autopkgtest failure with NumPy 1.14
mipe (1) Homepage: http://mipe.sourceforge.net Vcs Debian Med Packaging Team
890788	mipe: Please provide autopkgtest	newcomer
ncbi-blast+ (1) Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/ Vcs Debian Med Packaging Team
891197	Please switch to pcre2
ncbi-entrez-direct (1) Homepage: http://www.ncbi.nlm.nih.gov/books/NBK179288 Vcs Debian Med Packaging Team
901028	ncbi-entrez-direct: New upstream version available
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
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
pdb2pqr (1) Homepage: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html Vcs Debian Med Packaging Team
903759	pdb2pqr: autopkgtest regression
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.
primer3 (1) Homepage: http://primer3.sourceforge.net Vcs Debian Med Packaging Team
895243	primer3: autopkgtest fails since 2.4.0-1 while it succeeded in the past
profnet (1) Homepage: http://www.predictprotein.org/ Vcs Debian Med Packaging Team
905206	profnet: autopkgtest regression
profphd (1) Homepage: http://predictprotein.org/ Vcs Debian Med Packaging Team
897605	profphd failure in stretch
pymol (7) Homepage: http://www.pymol.org Vcs Debichem Team
602610	Package freemol.mengine for full modeling capabilities
651609	pymol: Setting-Error: type read mismatch (int) 667
703782	pymol: Unable to launch the Menu
709306	pymol: Crashes when running within xrdp/vnc (no 3D support)
765794	Race condition when running scripts in "stdin" mode
783653	pymol: Segmentation fault immediately after loading pdb
897431	pymol: Public modules must be in the python-pymol package
pyscanfcs (1) Homepage: https://fcs-analysis.github.io/PyScanFCS/ Vcs Debian Med Packaging Team
886634	pyscanfcs: Please migrate to Python 3	fixed-upstream
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-treetime (1) Homepage: https://github.com/neherlab/treetime Vcs Debian Med Packaging Team
905055	python-treetime: broken symlinks: /usr/bin/* -> ../share/treetime/*.py
qcumber (1) Homepage: https://gitlab.com/RKIBioinformaticsPipelines/QCumber Vcs Debian Med Packaging Team
883260	qcumber: [INLT:ru] Russian translation of debconf template	l10n, patch
qiime (1) Homepage: http://www.qiime.org/ Vcs Debian Med Packaging Team
820308	qiime: many unsatisfiable dependencies
rapmap (1) Homepage: https://github.com/COMBINE-lab/RapMap Vcs Debian Med Packaging Team
887943	rapmap: FTBFS on mips64el: both tests fail	help, upstream
rasmol (1) Homepage: http://rasmol.org Vcs Debian Science Maintainers
790196	rasmol: depends on vte which is deprecated	buster, help, patch, sid
sambamba (1) Homepage: https://github.com/lomereiter/sambamba Vcs Debian Med Packaging Team
907489	sambamba FTBFS	fixed-upstream, ftbfs, help, upstream
seqan2 (3) Homepage: http://www.seqan.de/ Vcs Debian Med Packaging Team
890185	seqan2: FTBFS on ia64
892222	seqan2: FTBFS on hppa: app_test_seqan_tcoffee fails on 2trx.mlcs.fasta	upstream
892223	seqan2: FTBFS on sparc64: 39 tests failed out of 403	upstream
snap-aligner (1) Homepage: http://snap.cs.berkeley.edu/ Vcs Debian Med Packaging Team
848589	snap-aligner: Build requires 188 GB of memory (fortunately not used, just allocated)
spades (1) Homepage: http://cab.spbu.ru/software/spades/ Vcs Debian Med Packaging Team
853113	spades: Fails to build with unhelpful error message in a "low" memory machine
t-coffee (1) Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html Vcs Debian Med Packaging Team
716373	[Mayhem] Bug report on t-coffee: t_coffee crashes with exit status 139	help
theseus (1) Homepage: http://www.theseus3d.org Vcs Debian Med Packaging Team
908459	theseus FTBFS with gcc 8	ftbfs
tophat (1) Homepage: http://ccb.jhu.edu/software/tophat Vcs Debian Med Packaging Team
873866	tophat: Please add arm64
tree-puzzle (2) Homepage: http://www.tree-puzzle.de Vcs Debian Med Packaging Team
806214	tree-puzzle: Package fails test suite
890790	tree-puzzle: Please provide autopkgtest	newcomer
treeviewx (1) Homepage: http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/ Vcs Debian Med Packaging Team
846481	src:treeviewx: Please remove statically linked code copy of libncl
trinityrnaseq (1) Homepage: http://trinityrnaseq.github.io/ Vcs Debian Med Packaging Team
897877	trinityrnaseq: ftbfs with GCC-8	buster, fixed-upstream, ftbfs, sid

Open bugs in suggested packages

2 grave, 2 serious, 7 normal, 1 minor, 1 wishlist

autodocktools (1) Homepage: http://autodock.scripps.edu/ Vcs Debian Med Packaging Team
580670	autodocktools: Please split out non-gui/biochemistry-oriented python bits
cain (2) Homepage: http://cain.sourceforge.net Vcs Debian Med Packaging Team
715587	[Mayhem] Bug report on cain-solvers: HomogeneousHistogramsAverage crashes with exit status 139	help
715588	[Mayhem] Bug report on cain-solvers: HomogeneousHistogramsAverageAps crashes with exit status 139	help
debian-science (3) Homepage: http://wiki.debian.org/DebianScience/ Vcs Debian Science Team
772407	science-config: bashism in /bin/sh script
881612	debian-science: s/libalberta2-dev/libalberta-dev/
901047	debian-science: s/spglib/libsymspg-dev/
gmap (1) Homepage: http://research-pub.gene.com/gmap Vcs Debian Med Packaging Team
907898	gmap: autopkgtest regression
igv (1) Homepage: http://www.broadinstitute.org/igv/ Vcs Debian Med Packaging Team
895765	igv: FTBFS with java 9
mgltools-pmv (3) Homepage: http://mgltools.scripps.edu/ Vcs Debian Med Packaging Team
855485	runPmv script does not work
855494	mgltools-pmv: runPmv does not start
855701	runPmv script does not work
ugene (2) Homepage: http://ugene.unipro.ru Vcs Debian Med Packaging Team
868885	ugene wont find translate
887305	ugene: FTBFS ucontext_reader.cc:92:12: error: invalid use of incomplete type 'const struct google_breakpad::ucontext'	buster, sid

Done bugs

adun.app (1) Homepage: http://diana.imim.es/Adun Vcs Debian Med Packaging Team
749733	adun.app: GCC warnings that may lead to runtime issues with new GNUstep libraries	buster, jessie, sid, stretch
alter-sequence-alignment (1) Homepage: http://sing.ei.uvigo.es/ALTER/ Vcs Debian Med Packaging Team
909103	consider switching alter-sequence-alignment to Architecture: all
bowtie (1) Homepage: http://bowtie-bio.sourceforge.net/ Vcs Debian Med Packaging Team
906341	bowtie: FTBFS in buster/sid	ftbfs
bppphyview (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
874835	[bppphyview] Future Qt4 removal from Buster
cgview (1) Homepage: http://wishart.biology.ualberta.ca/cgview/ Vcs Debian Med Packaging Team
907559	cgview: Does not start
diamond-aligner (1) Homepage: https://github.com/bbuchfink/diamond Vcs Debian Med Packaging Team
906615	diamond-aligner builds with -march=native
fastqc (1) Homepage: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Vcs Debian Med Packaging Team
896931	fastqc: If the package libfindbin-libs-perl is not installed, fastqc exits with an error immediately.
ffindex (1) Homepage: http://www.splashground.de/~andy/programs/FFindex/ Vcs Debian Med Packaging Team
905334	ffindex: missing build dependency on cmake	ftbfs
figtree (1) Homepage: http://tree.bio.ed.ac.uk/software/figtree/ Vcs Debian Med Packaging Team
908039	figtree: Crashes with NoClassDefFoundError
gasic (1) Homepage: http://sourceforge.net/projects/gasic/ Vcs Debian Med Packaging Team
873859	gasic: Please add arm64
gbrowse (2) Homepage: http://www.gbrowse.org/ Vcs Debian Med Packaging Team
826458	gbrowse: Unescaped left brace in regex is deprecated
833885	gbrowse: ships a deterministic/predictable OpenID consumer secret	security
gmap (2) Homepage: http://research-pub.gene.com/gmap Vcs Debian Med Packaging Team
902820	gmap: FTBFS on stretch/amd64 if CPU has SSE2 and nothing more	ftbfs
908386	gmap: please limit to Architecture: amd64	ftbfs
gromacs (1) Homepage: http://www.gromacs.org/ Vcs Debichem Team
887340	gromacs: FTBFS on x32: tests 2 and 13 time out	upstream
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
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)
metaphlan2 (1) Homepage: https://bitbucket.org/biobakery/metaphlan2 Vcs Debian Med Packaging Team
908426	metaphlan2 depends on libjs-twitter-bootstrap that will not be in buster
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
mobyle (1) Homepage: https://projets.pasteur.fr/projects/mobyle Vcs Debian Med Packaging Team
884525	mobyle: Mobyle javascript includes Google analytics beacon	security, upstream
mothur (1) Homepage: http://www.mothur.org Vcs Debian Med Packaging Team
908786	mothur-mpi contains the same binary as mothur
mrs (1) Homepage: http://mrs.cmbi.ru.nl/ Vcs Debian Med Packaging Team
906712	mrs fails on several architectures: undefined reference to __atomic_*	ftbfs, patch
msxpertsuite (1) Homepage: https://www.msxpertsuite.org/ Vcs The Debichem Group
907388	test
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
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
pyscanfcs (1) Homepage: https://fcs-analysis.github.io/PyScanFCS/ Vcs Debian Med Packaging Team
879617	pyscanfcs: Please provide autopkgtest
python-cogent (1) Homepage: http://pycogent.org/ Vcs Debian Med Packaging Team
730515	cd-hit-est is cdhit-est in Debian [Why?]
snap-aligner (1) Homepage: http://snap.cs.berkeley.edu/ Vcs Debian Med Packaging Team
860652	snap-aligner: FTBFS on i386: SNAPLib/SortedDataWriter.cpp:338:70: error: no matching function for call to 'max(long unsigned int, _int64)'	buster, ftbfs, sid, stretch
spades (1) Homepage: http://cab.spbu.ru/software/spades/ Vcs Debian Med Packaging Team
897867	spades: ftbfs with GCC-8	buster, ftbfs, help, sid
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
stacks (1) Homepage: http://creskolab.uoregon.edu/stacks/ Vcs Debian Med Packaging Team
848464	stacks-web: Should Depends/Recommends the metapackage default-mysql-*
trinityrnaseq (1) Homepage: http://trinityrnaseq.github.io/ Vcs Debian Med Packaging Team
860645	trinityrnaseq: FTBFS on i386: unsatisfiable build-dependencies: jellyfish (>= 2.1.4), parafly	buster, sid, stretch
trnascan-se (1) Homepage: http://lowelab.ucsc.edu/tRNAscan-SE Vcs Debian Med Packaging Team
904444	trnascan-se: FTBFS during arch-indep build
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