Summary

Bugs of task bio

Total bugs: 366

Open bugs: 319

Fixed bugs: 47

Links to other tasks

Tasks overview

Biology 319 (1782)

Biology development 139 (748)

Next generation sequencing 10 (53)

Phylogeny 13 (57)

Cloud 54 (303)

Content management 0 (0)

Covid-19 168 (1426)

Medical data 1 (1)

Dental 1 (3)

Epidemiology 4 (75)

Hospital information systems 1 (9)

Imaging 226 (1020)

Imaging development 82 (589)

Laboratory 1 (9)

Oncology 1 (3)

Pharmacology 1 (9)

Physics 27 (176)

Practice 7 (42)

Psychology 8 (42)

Rehabilitation 0 (0)

Research 0 (0)

Statistics 3 (7)

Tools 38 (241)

Typesetting 63 (508)

Legend

Severity	Dependent	Suggested
critical	0	0
grave	0	1
serious	7	7
important	26	10
normal	57	25
minor	151	11
wishlist	20	4

Summary bugs page of task Biology

Immediately looking into bugs of the dependencies of this task is advised (1782)^*

Open bugs in dependent packages

7 serious, 26 important, 57 normal, 151 minor, 20 wishlist

abyss (1) Homepage: https://github.com/bcgsc/abyss Vcs Debian Med Packaging Team
920282	abyss fails to build on hurd - googletest EXPECT_DEATH
andi (1) Homepage: https://github.com/EvolBioInf/andi Vcs Debian Med Packaging Team
1043772	andi: Fails to build source after successful build	ftbfs, sid, trixie
anfo (1) Homepage: https://bioinf.eva.mpg.de/anfo/ Vcs Debian Med Packaging Team
1012893	anfo: ftbfs with GCC-12	help, bookworm, sid, ftbfs, trixie
arden (2) Homepage: http://sourceforge.net/projects/arden/ Vcs Debian Med Packaging Team
1035113	arden: please add autopkgtests (to add coverage for python3-numpy)
1036488	arden: please add autopkgtests (to add coverage for python3-matplotlib)
art-nextgen-simulation-tools (1) Homepage: https://www.niehs.nih.gov/research/resources/software/biostatistics/art/ Vcs Debian Med Packaging Team
1043622	art-nextgen-simulation-tools: Fails to build source after successful build	ftbfs, sid, trixie
assemblytics (1) Homepage: http://assemblytics.com/ Vcs Debian Med Packaging Team
1035116	assemblytics: please add autopkgtests (to add coverage for python3-numpy)
ataqv (2) Homepage: https://github.com/ParkerLab/ataqv/ Vcs Debian Med Packaging Team
1044021	ataqv: Fails to build source after successful build	ftbfs, sid, trixie
1049553	ataqv: Fails to build binary packages again after successful build	ftbfs, sid, trixie
atropos (1) Homepage: https://github.com/jdidion/atropos Vcs Debian Med Packaging Team
1056788	atropos: ftbfs with cython 3.0.x	sid, trixie
augur (1) Homepage: https://github.com/nextstrain/augur Vcs Debian Med Packaging Team
1044079	augur: FTBFS with pandas 2.0	fixed-upstream, help
autodock-vina (1) Homepage: https://vina.scripps.edu Vcs Debian Med Packaging Team
1056089	autodock-vina: FTBFS: boost1.83 transition
axe-demultiplexer (1) Homepage: https://github.com/kdmurray91/axe Vcs Debian Med Packaging Team
1043648	axe-demultiplexer: Fails to build source after successful build	ftbfs, sid, trixie
baitfisher (1) Homepage: https://github.com/cmayer/BaitFisher-package Vcs Debian Med Packaging Team
1043995	baitfisher: Fails to build source after successful build	ftbfs, sid, trixie
bali-phy (2) Homepage: http://www.bali-phy.org Vcs Debian Med Packaging Team
1043647	bali-phy: Fails to build source after successful build	ftbfs, sid, trixie
1056087	bali-phy: FTBFS: boost1.83 transition
ball (1) Homepage: http://www.ball-project.org/ Vcs Debian Med Packaging Team
1040385	libball1.5-data: broken symlink: /usr/share/BALL-1.5/BALLView/html -> ../../doc/libball1.5-data/BALLView/html
bamtools (2) 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'	upstream, ftbfs
1043881	bamtools: Fails to build source after successful build	ftbfs, sid, trixie
bcftools (1) Homepage: https://samtools.github.io/bcftools/ Vcs Debian Med Packaging Team
870060	bcftools FTBFS on big endian: 107 tests failed	ftbfs, upstream
beads (1) Homepage: http://pappso.inrae.fr/bioinfo/beads Vcs Debian Med Packaging Team
1043686	beads: Fails to build source after successful build	ftbfs, sid, trixie
beagle (2) Homepage: https://faculty.washington.edu/browning/beagle/beagle.html Vcs Debian Med Packaging Team
1032034	beagle: broken package on non arm64/amd64 architectures
1043854	beagle: Fails to build source after successful build	ftbfs, sid, trixie
beast-mcmc (2) Homepage: http://beast.bio.ed.ac.uk/ Vcs Debian Med Packaging Team
1025424	beast-mcmc: please enable autopkgtest	help
1043640	beast-mcmc: Fails to build source after successful build	ftbfs, sid, trixie
beast2-mcmc (1) Homepage: https://www.beast2.org Vcs Debian Med Packaging Team
1025830	beauti2 fails to start	help
bedtools (1) Homepage: https://github.com/arq5x/bedtools2 Vcs Debian Med Packaging Team
1043957	bedtools: Fails to build source after successful build	ftbfs, sid, trixie
bio-tradis (1) Homepage: https://github.com/sanger-pathogens/Bio-Tradis Vcs Debian Med Packaging Team
1043774	bio-tradis: Fails to build source after successful build	ftbfs, sid, trixie
biosyntax (2) Homepage: https://biosyntax.org/ Vcs Debian Med Packaging Team
1043674	biosyntax: Fails to build source after successful build	ftbfs, sid, trixie
1049738	biosyntax: Fails to build binary packages again after successful build	ftbfs, sid, trixie
bitseq (1) Homepage: https://github.com/BitSeq/BitSeq Vcs Debian Med Packaging Team
1035121	bitseq: please add autopkgtests (to add coverage for python3-numpy)
bolt-lmm (2) Homepage: https://data.broadinstitute.org/alkesgroup/BOLT-LMM/ Vcs Debian Med Packaging Team
1043783	bolt-lmm: Fails to build source after successful build	ftbfs, sid, trixie
1049735	bolt-lmm: Fails to build binary packages again after successful build	ftbfs, sid, trixie
bowtie (1) Homepage: http://bowtie-bio.sourceforge.net/ Vcs Debian Med Packaging Team
1043697	bowtie: Fails to build source after successful build	ftbfs, sid, trixie
btllib (2) Homepage: https://github.com/bcgsc/btllib Vcs Debian Med Packaging Team
1022772	btllib: fails to build on 32-bit archs
1032358	btllib: Depends on libsdsl-dev, breaking installability when not needed	patch
busco (1) Homepage: https://gitlab.com/ezlab/busco Vcs Debian Med Packaging Team
1010653	busco: add autopkgtest to check integration with hmmer and prodigal
cassiopee (1) Homepage: https://github.com/osallou/cassiopee-c Vcs Debian Med Packaging Team
1043792	cassiopee: Fails to build source after successful build	ftbfs, sid, trixie
chromhmm (2) Homepage: http://compbio.mit.edu/ChromHMM/ Vcs Debian Med Packaging Team
1032036	chromhmm: broken package on non arm64/amd64 architectures
1043980	chromhmm: Fails to build source after successful build	ftbfs, sid, trixie
chromimpute (1) Homepage: https://www.biolchem.ucla.edu/labs/ernst/ChromImpute/ Vcs Debian Med Packaging Team
1043645	chromimpute: Fails to build source after successful build	ftbfs, sid, trixie
cif-tools (1) Homepage: https://github.com/PDB-REDO/cif-tools Vcs Debian Med Packaging Team
1043897	cif-tools: Fails to build source after successful build	ftbfs, sid, trixie
clonalframeml (1) Homepage: https://github.com/xavierdidelot/ClonalFrameML Vcs Debian Med Packaging Team
1044020	clonalframeml: Fails to build source after successful build	ftbfs, sid, trixie
clonalorigin (2) Homepage: https://github.com/xavierdidelot/clonalorigin Vcs Debian Med Packaging Team
884475	clonalorigin: FTBFS on alpha: tests time out	upstream, wontfix
1043663	clonalorigin: Fails to build source after successful build	ftbfs, sid, trixie
clustalo (1) Homepage: http://www.clustal.org/omega/ Vcs Debian Med Packaging Team
1043849	clustalo: Fails to build source after successful build	ftbfs, sid, trixie
cnvkit (1) Homepage: http://cnvkit.readthedocs.org Vcs Debian Med Packaging Team
1044078	cnvkit: FTBFS with pandas 2.0
concavity (1) Homepage: https://compbio.cs.princeton.edu/concavity/ Vcs Debian Med Packaging Team
1043837	concavity: Fails to build source after successful build	ftbfs, sid, trixie
cutesv (1) Homepage: https://github.com/tjiangHIT/cuteSV Vcs Debian Med Packaging Team
1035182	cutesv: please add autopkgtests (to add coverage for python3-numpy)
damapper (2) Homepage: https://github.com/thegenemyers/DAMAPPER Vcs Debian Med Packaging Team
1044221	damapper: Fails to build source after successful build	ftbfs, sid, trixie
1049504	damapper: Fails to build binary packages again after successful build	ftbfs, sid, trixie
datamash (2) Homepage: https://savannah.gnu.org/projects/datamash/ Vcs Debian Science Maintainers
982869	datamash FTBFS on !x86 32bit: FAIL: tests/decorate-errors	ftbfs, upstream
1044977	datamash: Fails to build source after successful build	ftbfs, sid, trixie
dawg (1) Homepage: https://github.com/reedacartwright/dawg Vcs Debian Med Packaging Team
903886	dawg: Test suite fails	upstream
dssp (1) Homepage: https://github.com/PDB-REDO/dssp Vcs Debian Med Packaging Team
1045047	dssp: Fails to build source after successful build	ftbfs, sid, trixie
dwgsim (2) Homepage: https://github.com/nh13/DWGSIM/ Vcs Debian Med Packaging Team
1044706	dwgsim: Fails to build source after successful build	ftbfs, sid, trixie
1049717	dwgsim: Fails to build binary packages again after successful build	ftbfs, sid, trixie
ea-utils (1) Homepage: https://expressionanalysis.github.io/ea-utils/ Vcs Debian Med Packaging Team
862118	ea-utils: New upstream version available
eigensoft (1) Homepage: http://www.hsph.harvard.edu/faculty/alkes-price/software/ Vcs Debian Med Packaging Team
1045139	eigensoft: Fails to build source after successful build	ftbfs, sid, trixie
emboss (2) Homepage: https://emboss.sourceforge.net Vcs Debian Med Packaging Team
682042	emboss-data: ships bulky taxonomy and gene ontology data
986043	emboss: uses media types that are not registered
emmax (1) Homepage: http://genome.sph.umich.edu/wiki/EMMAX Vcs Debian Med Packaging Team
1056671	(build-)depends on atlas, which is obsolete and scheduled for removal	sid, help, trixie
emperor (1) Homepage: https://biocore.github.io/emperor/ Vcs Debian Med Packaging Team
1050144	emperor: FTBFS with pandas 2.0
examl (1) Homepage: https://github.com/stamatak/ExaML Vcs Debian Med Packaging Team
1044839	examl: Fails to build source after successful build	ftbfs, sid, trixie
fasta3 (1) Homepage: https://fasta.bioch.virginia.edu Vcs Debian Med Packaging Team
1044536	fasta3: Fails to build source after successful build	ftbfs, sid, trixie
fastaq (1) Homepage: https://github.com/sanger-pathogens/Fastaq Vcs Debian Med Packaging Team
1044289	fastaq: Fails to build source after successful build	ftbfs, sid, trixie
fastlink (1) Homepage: https://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html Vcs Debian Med Packaging Team
1044987	fastlink: Fails to build source after successful build	ftbfs, sid, trixie
fastml (1) Homepage: http://fastml.tau.ac.il/ Vcs Debian Med Packaging Team
1044832	fastml: Fails to build source after successful build	ftbfs, sid, trixie
fastqtl (2) Homepage: http://fastqtl.sourceforge.net/ Vcs Debian Med Packaging Team
1044949	fastqtl: Fails to build source after successful build	ftbfs, sid, trixie
1049574	fastqtl: Fails to build binary packages again after successful build	ftbfs, sid, trixie
fermi-lite (2) Homepage: https://github.com/lh3/fermi-lite Vcs Debian Med Packaging Team
1044647	fermi-lite: Fails to build source after successful build	ftbfs, sid, trixie
1049564	fermi-lite: Fails to build binary packages again after successful build	ftbfs, sid, trixie
freecontact (1) Homepage: https://rostlab.org/ Vcs Debian Med Packaging Team
1049797	freecontact: Fails to build binary packages again after successful build	ftbfs, sid, trixie
gamgi (3) Homepage: http://www.gamgi.org/ Vcs Debichem Team
750139	gamgi: Conflicting return types of function gamgi_engine_iarray_push	upstream
967366	gamgi: depends on deprecated GTK 2
1044244	gamgi: Fails to build source after successful build	ftbfs, sid, trixie
garli (1) Homepage: https://github.com/Ashod/garli Vcs Debian Med Packaging Team
1044308	garli: Fails to build source after successful build	ftbfs, sid, trixie
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
gatb-core (2) Homepage: https://github.com/GATB/gatb-core Vcs Debian Med Packaging Team
929564	gatb-core-testdata: broken symlink: /usr/share/doc/gatb-core/test/gatb-core-cppunit -> ../../../../lib/gatb-core/gatb-core-cppunit
983926	gatb-core: ftbfs with -march=x86-64-v2
gbrowse (3) Homepage: http://gmod.org/wiki/GBrowse Vcs Debian Med Packaging Team
1037272	gbrowse: reproducible builds: random value in /etc/gbrowse/ConfigData.pm	patch
1039206	gbrowse: ships sysv-init script without systemd unit
1044196	gbrowse: Fails to build source after successful build	ftbfs, sid, trixie
gdpc (2) Homepage: https://web.archive.org/web/20180212152753/http://www.frantz.fi/software/gdpc.php Vcs Debian Med Packaging Team
967379	gdpc: depends on deprecated GTK 2	wontfix
982103	gdpc: autopkgtest failure on s390x
gemma (1) Homepage: https://www.xzlab.org/software.html Vcs Debian Med Packaging Team
1044789	gemma: Fails to build source after successful build	ftbfs, sid, trixie
genomethreader (2) Homepage: http://genomethreader.org Vcs Debian Med Packaging Team
1044585	genomethreader: Fails to build source after successful build	ftbfs, sid, trixie
1049675	genomethreader: Fails to build binary packages again after successful build	ftbfs, sid, trixie
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	upstream
gff2aplot (1) Homepage: https://genome.crg.es/software/gfftools/GFF2APLOT.html Vcs Debian Med Packaging Team
1044834	gff2aplot: Fails to build source after successful build	ftbfs, sid, trixie
ghemical (3) Homepage: http://bioinformatics.org/ghemical/ghemical/ Vcs Debichem Team
967392	ghemical: depends on deprecated GTK 2
967865	ghemical: depends on deprecated libglade2
996006	ghemical: Segmentation fault when starting
ghmm (2) Homepage: https://sourceforge.net/p/ghmm/wiki/Home/ Vcs Debian Med Packaging Team
1044649	ghmm: Fails to build source after successful build	ftbfs, sid, trixie
1056673	build-depends on atlas, which is obsolete and scheduled for removal	sid, trixie
grabix (1) Homepage: https://github.com/arq5x/grabix Vcs Debian Med Packaging Team
1045023	grabix: Fails to build source after successful build	ftbfs, sid, trixie
gromacs (2) Homepage: https://www.gromacs.org/ Vcs Debichem Team
644397	Provide runtime detection for CPU SIMD capabilities	upstream
983942	gromacs: ftbfs with -march=x86-64-v3
gwama (1) Homepage: https://www.geenivaramu.ee/en/tools/gwama Vcs Debian Med Packaging Team
1044305	gwama: Fails to build source after successful build	ftbfs, sid, trixie
hilive (1) Homepage: https://gitlab.com/rki_bioinformatics/HiLive2 Vcs Debian Med Packaging Team
1053499	hilive: flaky autopkgtest on several archs: segfault	upstream
hinge (4) Homepage: https://github.com/HingeAssembler/HINGE Vcs Debian Med Packaging Team
958244	Use system libinih-dev
986193	hinge: no autopkgtest available yet	newcomer
1035178	hinge: please add autopkgtests (to add coverage for python3-numpy)
1036500	hinge: please add autopkgtests (to add coverage for python3-matplotlib)
hisat2 (1) Homepage: https://daehwankimlab.github.io/hisat2/ Vcs Debian Med Packaging Team
1048028	hisat2: Fails to build source after successful build	ftbfs, sid, trixie
hmmer2 (2) Homepage: http://hmmer.janelia.org/ Vcs Debian Med Packaging Team
1046065	hmmer2: Fails to build source after successful build	ftbfs, sid, trixie
1049476	hmmer2: Fails to build binary packages again after successful build	ftbfs, sid, trixie
igdiscover (1) Homepage: http://docs.igdiscover.se/en/stable/ Vcs Debian Med Packaging Team
1032975	igdiscover -- Broken, unusable package due to incomplete code in the binary package
igor (1) Homepage: https://github.com/qmarcou/IGoR/ Vcs Debian Med Packaging Team
1049535	igor: Fails to build binary packages again after successful build	ftbfs, sid, trixie
infernal (1) Homepage: http://eddylab.org/infernal/ Vcs Debian Med Packaging Team
1045517	infernal: Fails to build source after successful build	ftbfs, sid, trixie
ipig (1) Homepage: http://sourceforge.net/projects/ipig/ Vcs Debian Med Packaging Team
1045547	ipig: Fails to build source after successful build	ftbfs, sid, trixie
iva (1) Homepage: https://github.com/sanger-pathogens/iva Vcs Debian Med Packaging Team
1045886	iva: Fails to build source after successful build	ftbfs, sid, trixie
jellyfish (2) Homepage: https://github.com/gmarcais/Jellyfish Vcs Debian Med Packaging Team
1021557	jellyfish: Performance regression in 2.3.0 (orders of magnitude for some inputs)	upstream
1046793	jellyfish: Fails to build source after successful build	ftbfs, sid, trixie
jellyfish1 (2) Homepage: https://www.cbcb.umd.edu/software/jellyfish/ Vcs Debian Med Packaging Team
875328	jellyfish1: FTBFS: __sync_val_compare_and_swap_8 undefined	wontfix, upstream
1045535	jellyfish1: Fails to build source after successful build	ftbfs, sid, trixie
jmol (1) Homepage: https://jmol.sourceforge.net/ Vcs Debichem Team
872418	jmol: Weblinks in Help do not work
kallisto (2) Homepage: https://pachterlab.github.io/kallisto Vcs Debian Med Packaging Team
1047324	kallisto: Fails to build source after successful build	ftbfs, sid, trixie
1057131	kallisto: add support for loongarch64 in d/control	patch, pending
kmc (1) Homepage: https://sun.aei.polsl.pl/kmc Vcs Debian Med Packaging Team
1049134	kmc: Fails to build source after successful build	ftbfs, sid, trixie
kmerresistance (1) Homepage: https://bitbucket.org/genomicepidemiology/kmerresistance Vcs Debian Med Packaging Team
1009159	kmerresistance: Add autopkgtest	newcomer
last-align (1) Homepage: https://gitlab.com/mcfrith/last Vcs Debian Med Packaging Team
1048396	last-align: Fails to build source after successful build	ftbfs, sid, trixie
libfastahack (1) Homepage: https://github.com/ekg/fastahack Vcs Debian Med Packaging Team
1015486	libfastahack: ftbfs with LTO (link time optimization) enabled	sid, trixie
libncl (1) Homepage: https://github.com/mtholder/ncl Vcs Debian Med Packaging Team
1015505	libncl: ftbfs with LTO (link time optimization) enabled	sid, trixie
librg-utils-perl (2) Homepage: https://predictprotein.org/ Vcs Debian Med Packaging Team
1045341	librg-utils-perl: Fails to build source after successful build	ftbfs, sid, trixie
1049488	librg-utils-perl: Fails to build binary packages again after successful build	ftbfs, sid, trixie
libssw (1) Homepage: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library Vcs Debian Med Packaging Team
1015525	libssw: ftbfs with LTO (link time optimization) enabled	sid, trixie, experimental
libvcflib (1) Homepage: https://github.com/vcflib/vcflib Vcs Debian Med Packaging Team
1057253	libvcflib: add support for loongarch64	patch
ltrsift (2) Homepage: https://www.zbh.uni-hamburg.de/en/forschung/gi/software/ltrsift.html Vcs Debian Med Packaging Team
967603	ltrsift: depends on deprecated GTK 2	upstream, wontfix
1048669	ltrsift: Fails to build source after successful build	ftbfs, sid, trixie
lucy (1) Homepage: https://lucy.sourceforge.net Vcs Debian Med Packaging Team
1047296	lucy: Fails to build source after successful build	ftbfs, sid, trixie
lumpy-sv (1) Homepage: https://github.com/arq5x/lumpy-sv Vcs Debian Med Packaging Team
1047978	lumpy-sv: Fails to build source after successful build	ftbfs, sid, trixie
macs (3) Homepage: https://github.com/taoliu/MACS/ Vcs Debian Med Packaging Team
1047612	macs: Fails to build source after successful build	ftbfs, sid, trixie
1055692	macs ftbfs with Python 3.12
1056813	macs: ftbfs with cython 3.0.x	sid, trixie
macsyfinder (1) Homepage: https://github.com/gem-pasteur/macsyfinder Vcs Debian Med Packaging Team
1048586	macsyfinder: Fails to build source after successful build	ftbfs, sid, trixie
mash (1) Homepage: https://mash.readthedocs.io Vcs Debian Med Packaging Team
1046553	mash: Fails to build source after successful build	ftbfs, sid, trixie
massxpert (1) Homepage: http://www.msxpertsuite.org/ Vcs The Debichem Group
1045227	massxpert: Fails to build source after successful build	ftbfs, sid, trixie
melting (1) Homepage: https://www.ebi.ac.uk/compneur-srv/melting/ Vcs Debian Med Packaging Team
1048833	melting: Fails to build source after successful build	ftbfs, sid, trixie
metaphlan (1) Homepage: https://github.com/biobakery/MetaPhlAn Vcs Debian Med Packaging Team
1035175	metaphlan: please add autopkgtests (to add coverage for python3-numpy)
microbegps (2) Homepage: http://sourceforge.net/projects/microbegps/ Vcs Debian Med Packaging Team
1035188	microbegps: please add autopkgtests (to add coverage for python3-numpy)
1036480	microbegps: please add autopkgtests (to add coverage for python3-matplotlib)
minimap (1) Homepage: https://github.com/lh3/minimap Vcs Debian Med Packaging Team
1049859	minimap: Fails to build binary packages again after successful build	ftbfs, sid, trixie
minimap2 (1) Homepage: https://github.com/lh3/minimap2 Vcs Debian Med Packaging Team
1046060	minimap2: Fails to build source after successful build	ftbfs, sid, trixie
mira (2) Homepage: https://sourceforge.net/p/mira-assembler/wiki/Home/ Vcs Debian Med Packaging Team
1045311	mira: Fails to build source after successful build	ftbfs, sid, trixie
1049789	mira: Fails to build binary packages again after successful build	ftbfs, sid, trixie
mirtop (1) Homepage: https://github.com/miRTop/mirtop Vcs Debian Med Packaging Team
1044055	mirtop: test failure with pandas 2.0
mosdepth (1) Homepage: https://github.com/brentp/mosdepth Vcs Debian Med Packaging Team
1054602	mosdepth: Needs "libhts.so" as a dependency, avaialbe in package "libhts-dev"
mptp (1) Homepage: https://github.com/Pas-Kapli/mptp Vcs Debian Med Packaging Team
1048555	mptp: Fails to build source after successful build	ftbfs, sid, trixie
mrbayes (2) Homepage: http://mrbayes.csit.fsu.edu/ Vcs Debian Med Packaging Team
1045400	mrbayes: Fails to build source after successful build	ftbfs, sid, trixie
1049739	mrbayes: Fails to build binary packages again after successful build	ftbfs, sid, trixie
multiqc (1) Homepage: https://multiqc.info/ Vcs Debian Med Packaging Team
996981	multiqc: Link to jquery missing
muscle3 (1) Homepage: https://www.drive5.com/muscle/ Vcs Debian Med Packaging Team
1048044	muscle3: Fails to build source after successful build	ftbfs, sid, trixie
nanook (1) Homepage: https://documentation.tgac.ac.uk/display/NANOOK/NanoOK Vcs Debian Med Packaging Team
1045898	nanook: Fails to build source after successful build	ftbfs, sid, trixie
ncbi-blast+ (4) Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/ Vcs Debian Med Packaging Team
891197	Please switch to pcre2	sid, trixie
956850	ncbi-blast+: Please provide /usr/bin/legacy_blast.pl
984871	ncbi-blast+: Missing headers for shared libraries
1010110	ncbi-blast+: terminate called after throwing an instance of 'ncbi::CIO_Exception'	wontfix
ncbi-igblast (1) Homepage: https://ncbi.github.io/igblast/ Vcs Debian Med Packaging Team
1048966	ncbi-igblast: Fails to build source after successful build	ftbfs, sid, trixie
ncbi-tools6 (1) Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/ Vcs Debian Med Packaging Team
225651	ncbi-tools-x11: want Cn3D++
norsnet (1) Homepage: https://www.rostlab.org/owiki/index.php/Norsnet Vcs Debian Med Packaging Team
1049529	norsnet: Fails to build binary packages again after successful build	ftbfs, sid, trixie
ntcard (3) Homepage: https://github.com/bcgsc/ntCard Vcs Debian Med Packaging Team
1025370	ntcard: ftbfs with nthash 2.3.0	ftbfs, upstream
1047206	ntcard: Fails to build source after successful build	ftbfs, sid, trixie
1049666	ntcard: Fails to build binary packages again after successful build	ftbfs, sid, trixie
nxtrim (1) Homepage: https://github.com/sequencing/NxTrim Vcs Debian Med Packaging Team
1045354	nxtrim: Fails to build source after successful build	ftbfs, sid, trixie
obitools (2) Homepage: https://pypi.python.org/pypi/OBITools Vcs Debian Med Packaging Team
1047870	obitools: Fails to build source after successful build	ftbfs, sid, trixie
1056824	obitools: ftbfs with cython 3.0.x	sid, trixie
phast (1) Homepage: http://compgen.cshl.edu/phast/ Vcs Debian Med Packaging Team
1056681	build-depends on atlas, which is obsolete and scheduled for removal	help, trixie, sid
piler (1) Homepage: https://www.drive5.com/piler/ Vcs Debian Med Packaging Team
1047737	piler: Fails to build source after successful build	ftbfs, sid, trixie
pinfish (1) Homepage: https://github.com/nanoporetech/pinfish Vcs Debian Med Packaging Team
1048260	pinfish: Fails to build source after successful build	ftbfs, sid, trixie
pique (1) Homepage: https://github.com/tony-travis/PIQUE/ Vcs Debian Med Packaging Team
986194	pique: no autopkgtest available yet	newcomer
pirs (2) Homepage: https://github.com/galaxy001/pirs Vcs Debian Med Packaging Team
1048393	pirs: Fails to build source after successful build	ftbfs, sid, trixie
1056023	pirs:FTBFS: boost1.83 transition
plast (1) Homepage: https://plast.inria.fr/ Vcs Debian Med Packaging Team
1047303	plast: Fails to build source after successful build	ftbfs, sid, trixie
plink1.9 (1) Homepage: https://www.cog-genomics.org/plink/1.9/ Vcs Debian Med Packaging Team
1056682	build-depends on atlas, which is obsolete and scheduled for removal	sid, trixie
plink2 (1) Homepage: https://www.cog-genomics.org/plink/2.0/ Vcs Debian Med Packaging Team
1048822	plink2: Fails to build source after successful build	ftbfs, sid, trixie
porechop (1) Homepage: https://rrwick.github.io/Porechop Vcs Debian Med Packaging Team
1047456	porechop: Fails to build source after successful build	ftbfs, sid, trixie
pplacer (2) Homepage: https://github.com/matsen/pplacer Vcs Debian Med Packaging Team
1009156	pplacer: Add autopkgtest
1024889	pplacer: build-depends on dropped package
primer3 (1) Homepage: http://primer3.sourceforge.net Vcs Debian Med Packaging Team
1045454	primer3: Fails to build source after successful build	ftbfs, sid, trixie
proalign (1) Homepage: http://loytynojalab.biocenter.helsinki.fi/software/proalign/ Vcs Debian Med Packaging Team
1046067	proalign: Fails to build source after successful build	ftbfs, sid, trixie
proda (1) Homepage: http://proda.stanford.edu/ Vcs Debian Med Packaging Team
1048254	proda: Fails to build source after successful build	ftbfs, sid, trixie
proteinortho (1) Homepage: https://gitlab.com/paulklemm_PHD/proteinortho Vcs Debian Med Packaging Team
1046514	proteinortho: Fails to build source after successful build	ftbfs, sid, trixie
provean (1) Homepage: http://provean.jcvi.org Vcs Debian Med Packaging Team
1042769	provean: incompatible with cd-hit >= 4.8.1-4	trixie, sid
psortb (1) Homepage: https://www.psort.org/ Vcs Debian Med Packaging Team
1048520	psortb: Fails to build source after successful build	ftbfs, sid, trixie
pymol (4) Homepage: https://www.pymol.org Vcs Debichem Team
602610	Package freemol.mengine for full modeling capabilities
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
python-csb (1) Homepage: https://github.com/csb-toolbox/CSB Vcs Debian Med Packaging Team
1056464	python-csb's autopkg tests fail with Python 3.12	sid, trixie
python-pyvcf (1) Homepage: https://github.com/jamescasbon/PyVCF Vcs Debian Med Packaging Team
1046140	python-pyvcf: Fails to build source after successful build	ftbfs, sid, trixie
python-sqt (1) Homepage: https://bitbucket.org/marcelm/sqt Vcs Debian Med Packaging Team
1049145	python-sqt: Fails to build source after successful build	ftbfs, sid, trixie
qcumber (3) Homepage: https://gitlab.com/RKIBioinformaticsPipelines/QCumber Vcs Debian Med Packaging Team
1036374	[INTL:es] Spanish translation of qcumber debconf template	l10n, patch
1036506	qcumber: please add autopkgtests (to add coverage for python3-matplotlib)
1049117	qcumber: Fails to build source after successful build	ftbfs, sid, trixie
qutemol (2) Homepage: http://qutemol.sourceforge.net/ Vcs Debichem Team
642084	qutemol: Cannot start the program
939033	qutemol: Uses GifQuantizeBuffer - stops working with newer giflib
rambo-k (1) Homepage: http://rambok.sourceforge.net/ Vcs Debian Med Packaging Team
1047092	rambo-k: Fails to build source after successful build	ftbfs, sid, trixie
rapmap (2) Homepage: https://github.com/COMBINE-lab/RapMap Vcs Debian Med Packaging Team
909766	Use Debian packaged spdlog instead of code copy of old version	help, upstream
976588	rapmap: FTBFS on arm64 (when trying to build arch:all)	trixie, bullseye, ftbfs, sid, bookworm
ray (1) Homepage: http://denovoassembler.sourceforge.net/ Vcs Debian Med Packaging Team
1047580	ray: Fails to build source after successful build	ftbfs, sid, trixie
rdp-classifier (1) Homepage: https://github.com/rdpstaff/classifier Vcs Debian Med Packaging Team
1040587	rdp-classifier-doc: broken symlink: /usr/share/doc/rdp-classifier-doc/api/jquery/jquery-3.5.1.js -> ../../../../javascript/jquery/query.js
reapr (1) Homepage: https://www.sanger.ac.uk/science/tools/reapr Vcs Debian Med Packaging Team
1045461	reapr: Fails to build source after successful build	ftbfs, sid, trixie
reprof (2) Homepage: https://rostlab.org/ Vcs Debian Med Packaging Team
1045897	reprof: Fails to build source after successful build	ftbfs, sid, trixie
1049597	reprof: Fails to build binary packages again after successful build	ftbfs, sid, trixie
rna-star (1) Homepage: https://github.com/alexdobin/STAR/ Vcs Debian Med Packaging Team
1045634	rna-star: Fails to build source after successful build	ftbfs, sid, trixie
roary (2) Homepage: http://sanger-pathogens.github.io/Roary/ Vcs Debian Med Packaging Team
1047005	roary: Fails to build source after successful build	ftbfs, sid, trixie
1049576	roary: Fails to build binary packages again after successful build	ftbfs, sid, trixie
rsem (2) Homepage: https://deweylab.github.io/RSEM/ Vcs Debian Med Packaging Team
1056010	rsem: FTBFS: boost1.83 transition
1056011	rsem: FTBFS: boost1.83 transition
sambamba (1) Homepage: https://github.com/lomereiter/sambamba Vcs Debian Med Packaging Team
1015654	sambamba: ftbfs with LTO (link time optimization) enabled	sid, trixie
scythe (1) Homepage: https://github.com/vsbuffalo/scythe Vcs Debian Med Packaging Team
1048084	scythe: Fails to build source after successful build	ftbfs, sid, trixie
seqan-needle (1) Homepage: https://github.com/seqan/needle Vcs Debian Med Packaging Team
1048377	seqan-needle: Fails to build source after successful build	pending, ftbfs, sid, trixie
seqan2 (2) Homepage: https://www.seqan.de/ Vcs Debian Med Packaging Team
917851	seqan2 2.4.0+dfsg-9: FTBFS, alignment problem	ftbfs
1047218	seqan2: Fails to build source after successful build	ftbfs, sid, trixie
seqkit (1) Homepage: https://github.com/shenwei356/seqkit Vcs Debian Med Packaging Team
1046668	seqkit: Fails to build source after successful build	ftbfs, sid, trixie
seqprep (1) Homepage: http://seqanswers.com/wiki/SeqPrep Vcs Debian Med Packaging Team
1049489	seqprep: Fails to build binary packages again after successful build	ftbfs, sid, trixie
seqtools (2) Homepage: https://www.sanger.ac.uk/science/tools/seqtools Vcs Debian Med Packaging Team
967743	seqtools: depends on deprecated GTK 2
1047310	seqtools: Fails to build source after successful build	ftbfs, sid, trixie
shasta (1) Homepage: https://github.com/chanzuckerberg/shasta Vcs Debian Med Packaging Team
1053509	shasta: autopkgtest regression on arm64: is memory suddenly not enough?
ska (1) Homepage: https://github.com/simonrharris/SKA Vcs Debian Med Packaging Team
1048122	ska: Fails to build source after successful build	ftbfs, sid, trixie
smalt (1) Homepage: https://www.sanger.ac.uk/science/tools/smalt-0 Vcs Debian Med Packaging Team
1047681	smalt: Fails to build source after successful build	ftbfs, sid, trixie
snap-aligner (2) Homepage: https://snap.cs.berkeley.edu/ Vcs Debian Med Packaging Team
848589	snap-aligner: Build requires 188 GB of memory (fortunately not used, just allocated)
1050330	snap-aligner: Please add loong64 to architectures list
snippy (1) Homepage: https://github.com/tseemann/snippy/ Vcs Debian Med Packaging Team
1031465	snippy: FTBFS: make[2]: *** [Makefile:32: S1/snps.tab] Error 2	bookworm, sid, ftbfs, trixie
snpeff (1) Homepage: https://pcingola.github.io/SnpEff/ Vcs Debian Med Packaging Team
1029202	snippy: Error when using snpeff 5.1	upstream
snpomatic (1) Homepage: https://github.com/magnusmanske/snpomatic Vcs Debian Med Packaging Team
1046157	snpomatic: Fails to build source after successful build	ftbfs, sid, trixie
snpsift (1) Homepage: https://pcingola.github.io/SnpEff/ss_introduction/ Vcs Debian Med Packaging Team
1046827	snpsift: Fails to build source after successful build	sid, ftbfs, trixie, pending
spades (1) Homepage: http://cab.spbu.ru/software/spades/ Vcs Debian Med Packaging Team
1015668	spades: ftbfs with LTO (link time optimization) enabled	sid, trixie
spoa (1) Homepage: https://github.com/rvaser/spoa Vcs Debian Med Packaging Team
1015667	spoa: ftbfs with LTO (link time optimization) enabled	trixie, sid, experimental
sprai (1) Homepage: https://web.archive.org/web/20180316202959/http://zombie.cb.k.u-tokyo.ac.jp/sprai/ Vcs Debian Med Packaging Team
1047125	sprai: Fails to build source after successful build	ftbfs, sid, trixie
sra-sdk (2) Homepage: https://github.com/ncbi/sra-tools/ Vcs Debian Med Packaging Team
1040391	sra-toolkit: broken symlink: /usr/lib/debian-med/bin/kget -> ../../../bin/vdb-get
1053411	sra-sdk: FTBFS with re2 >= 20230601 (which requires abseil)	upstream
srst2 (1) Homepage: https://katholt.github.io/srst2/ Vcs Debian Med Packaging Team
1046135	srst2: Fails to build source after successful build	ftbfs, sid, trixie
subread (1) Homepage: http://sourceforge.net/projects/subread/ Vcs Debian Med Packaging Team
1049300	subread: Fails to build source after successful build	ftbfs, sid, trixie
surankco (1) Homepage: https://sourceforge.net/projects/surankco/ Vcs Debian Med Packaging Team
1048111	surankco: Fails to build source after successful build	ftbfs, sid, trixie
t-coffee (1) Homepage: https://www.tcoffee.org/Projects/tcoffee/index.html Vcs Debian Med Packaging Team
956848	t-coffee: should use "example" blastpgp.pl
tantan (1) Homepage: https://gitlab.com/mcfrith/tantan Vcs Debian Med Packaging Team
1045561	tantan: Fails to build source after successful build	ftbfs, sid, trixie
terraphast (1) Homepage: https://github.com/amkozlov/terraphast-one Vcs Debian Med Packaging Team
1049550	terraphast: Fails to build binary packages again after successful build	ftbfs, sid, trixie
tombo (3) Homepage: https://github.com/nanoporetech/tombo Vcs Debian Med Packaging Team
1049071	tombo: Fails to build source after successful build	ftbfs, sid, trixie
1056041	tombo ftbfs with Python 3.12 (and cython 3.0.5)	sid, trixie
1056892	tombo: ftbfs with cython 3.0.x	sid, trixie
tortoize (1) Homepage: https://github.com/PDB-REDO/tortoize Vcs Debian Med Packaging Team
1045986	tortoize: Fails to build source after successful build	ftbfs, sid, trixie
tree-puzzle (1) Homepage: http://www.tree-puzzle.de Vcs Debian Med Packaging Team
1049170	tree-puzzle: Fails to build source after successful build	ftbfs, sid, trixie
treeview (1) Homepage: http://jtreeview.sourceforge.net Vcs Debian Med Packaging Team
1046737	treeview: Fails to build source after successful build	ftbfs, sid, trixie
treeviewx (1) Homepage: https://github.com/rdmpage/treeviewx Vcs Debian Med Packaging Team
846481	src:treeviewx: Please remove statically linked code copy of libncl
trinityrnaseq (1) Homepage: https://github.com/trinityrnaseq/trinityrnaseq Vcs Debian Med Packaging Team
981874	trinityrnaseq: flaky autopkgtest	bookworm, sid, trixie, bullseye
twopaco (1) Homepage: https://github.com/medvedevgroup/TwoPaCo Vcs Debian Med Packaging Team
1047488	twopaco: Fails to build source after successful build	ftbfs, sid, trixie
umap-learn (1) Homepage: https://github.com/lmcinnes/umap Vcs Debian Med Packaging Team
980509	umap-learn: Binary package name should be python3-umap-learn	pending
unicycler (1) Homepage: https://github.com/rrwick/Unicycler Vcs Debian Med Packaging Team
1048635	unicycler: Fails to build source after successful build	ftbfs, sid, trixie
varna (1) Homepage: https://varna.lri.fr/ Vcs Debian Med Packaging Team
1048125	varna: Fails to build source after successful build	ftbfs, sid, trixie
vcfanno (2) Homepage: https://github.com/brentp/vcfanno Vcs Debian Med Packaging Team
1049212	vcfanno: Fails to build source after successful build	ftbfs, sid, trixie
1049762	vcfanno: Fails to build binary packages again after successful build	ftbfs, sid, trixie
vg (5) Homepage: https://github.com/vgteam/vg#vg Vcs Debian Med Packaging Team
976511	vg: FTBFS on arm64: configure: error: Could not find a version of the library!	bullseye, trixie, ftbfs, bookworm, sid
987184	vg -- excessive variants built, and not tested
1013061	vg: ftbfs with GCC-12	bookworm, sid, trixie, ftbfs
1015699	vg: ftbfs with LTO (link time optimization) enabled	sid, trixie
1043312	vg: Replace transitional bsdmainutils
vmatch (1) Homepage: http://www.vmatch.de Vcs Debian Med Packaging Team
1045627	vmatch: Fails to build source after successful build	ftbfs, sid, trixie
xpore (1) Homepage: https://github.com/GoekeLab/xpore/ Vcs Debian Med Packaging Team
1035276	xpore: please add autopkgtests (to add coverage for python3-numpy)

Open bugs in suggested packages

1 grave, 7 serious, 10 important, 25 normal, 11 minor, 4 wishlist

arb (1) Homepage: http://www.arb-home.de/ Vcs Debian Med Packaging Team
916406	libarb-dev: Missing symbols in static libraries
bcbio (2) Homepage: https://github.com/bcbio/bcbio-nextgen Vcs Debian Med Packaging Team
928076	bcbio: Workflows not ready for non-developers to depend on.
1018312	bcbio: build-depends on python3-nose or uses it for autopkgtest
conda-package-handling (2) Homepage: https://github.com/conda/conda-package-handling Vcs Debian Med Packaging Team
976506	conda-package-handling: FTBFS in bullseye (failing tests)	sid, ftbfs, pending, bullseye, trixie, patch
1052523	conda-package-handling: please remove extraneous dependency on python3-six
cyvcf2 (1) Homepage: https://github.com/brentp/cyvcf2 Vcs Debian Med Packaging Team
1056799	cyvcf2: ftbfs with cython 3.0.x	sid, trixie
debian-science (3) Homepage: https://wiki.debian.org/DebianScience/ Vcs Debian Science Team
1030327	science-numericalcomputation: please stop recommending python3-theano as it is being removed
1032638	please drop transitional package science-electronics from src:debian-science
1055339	debian-science: please replace recommendation of src:dolfin by src:fenics-dolfinx
emboss-explorer (2) Homepage: http://embossgui.sourceforge.net/ Vcs Debian Med Packaging Team
1044407	emboss-explorer: Fails to build source after successful build	ftbfs, sid, trixie
1049733	emboss-explorer: Fails to build binary packages again after successful build	ftbfs, sid, trixie
epigrass (2) Homepage: https://github.com/fccoelho/epigrass Vcs Debian Med Packaging Team
995966	epigrass: epirunner and epidash fail to run due to missing dash modules	pending
998265	epigrass: autopkgtest regression: The 'panel' distribution was not found
hdf5 (19) Homepage: http://hdfgroup.org/HDF5/ Vcs Gilles Filippini
638753	libhdf5-serial-1.8.7: threadsafe memory leaks	moreinfo
715959	[Mayhem] Bug report on hdf5-tools: gif2h5 crashes with exit status 139
716008	[Mayhem] Bug report on hdf5-tools: h5copy crashes with exit status 139
716010	[Mayhem] Bug report on hdf5-tools: h5diff crashes with exit status 139
716011	[Mayhem] Bug report on hdf5-tools: h5dump crashes with exit status 139
716012	[Mayhem] Bug report on hdf5-tools: h5import crashes with exit status 139
740613	libhdf5-7: Please include support for compression with libaec
748587	Duplicate and conflicting definitions of variable FILENAME	upstream
839784	libhdf5-dev: pkg-config file references ONLY the C library
915807	hdf5: CVE-2017-17507	security, upstream
958174	hdf5: please add the hdf5plugins
968559	libhdf5-openmpi-dev: hdf5-mpi.pc alternative sometimes goes missing	moreinfo
1023446	libhdf5-openmpi-dev: h5pcc configured as static build
1023820	hdf5: Dependencies not tight enough
1031726	hdf5: CVE-2022-26061 CVE-2022-25972 CVE-2022-25942	upstream, security
1034807	hdf5: CVE-2018-11205	upstream, security
1034838	hdf5: CVE-2019-8396 CVE-2019-8398	security
1040862	hdf5: S3 VFD pulls in networking dependencies (libcurl), please package it as a VFD plugin
1052250	pkg-config file incorrect for static linking
htseq (1) Homepage: https://www-huber.embl.de/users/anders/HTSeq/doc/overview.html Vcs Debian Med Packaging Team
1046620	htseq: Fails to build source after successful build	ftbfs, sid, trixie
intake (2) Homepage: https://github.com/intake/intake Vcs Debian Med Packaging Team
1044050	intake: FTBFS with pandas 2.0
1050623	intake: autopkgtest needs update for dask 2023.8.0	trixie, sid, ftbfs
pychopper (1) Homepage: https://github.com/epi2me-labs/pychopper Vcs Debian Med Packaging Team
1048644	pychopper: Fails to build source after successful build	ftbfs, sid, trixie
pyranges (1) Homepage: https://github.com/biocore-ntnu/pyranges Vcs Debian Med Packaging Team
1044064	pyranges: FTBFS with pandas 2.0
pyrle (1) Homepage: https://github.com/pyranges/pyrle Vcs Debian Python Team
1047039	pyrle: Fails to build source after successful build	ftbfs, sid, trixie
python-anndata (2) Homepage: https://github.com/theislab/anndata Vcs Debian Med Packaging Team
1044072	python-anndata: FTBFS with pandas 2.0
1056455	python-anndata's autopkg tests fail with Python 3.12	sid, trixie
python-nanoget (1) Homepage: https://github.com/wdecoster/nanoget Vcs Debian Med Packaging Team
1044056	python-nanoget: test failure with pandas 2.0
python-ncls (1) Homepage: https://github.com/biocore-ntnu/ncls Vcs Debian Python Team
1046648	python-ncls: Fails to build source after successful build	ftbfs, sid, trixie
python-seqcluster (1) Homepage: https://github.com/lpantano/seqcluster Vcs Debian Med Packaging Team
1035277	python-seqcluster: please add autopkgtests (to add coverage for python3-numpy)
q2-demux (2) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1045829	q2-demux: Fails to build source after successful build	ftbfs, sid, trixie
1053942	q2-demux: test failure with pandas 2.1
q2-quality-control (1) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1044060	q2-quality-control: test failure with pandas 2.0
q2-taxa (2) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1048362	q2-taxa: Fails to build source after successful build	ftbfs, sid, trixie
1053943	q2-taxa: test failure with pandas 2.1
q2-types (1) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1053944	q2-types: test failure with pandas 2.1
q2templates (1) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1044068	q2templates: FTBFS with pandas 2.0
relion-cuda (2) Homepage: https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page Vcs Debian Med Packaging Team
1036681	relion-cuda: FTBFS with CUDA 12: nvcc fatal : Value 'sm_35' is not defined for option 'gpu-architecture'	sid, ftbfs, trixie
1040128	relion-cuda: FTBFS with cub 2.0.1: error: function "cub::Debug" has already been defined	ftbfs, sid, trixie
resfinder-db (1) Homepage: https://bitbucket.org/genomicepidemiology/resfinder Vcs Debian Med Packaging Team
1049268	resfinder-db: Fails to build source after successful build	ftbfs, sid, trixie
sift (2) Homepage: http://sift.bii.a-star.edu.sg/ Vcs Debian Med Packaging Team
986200	sift: Please provide autopkgtest	newcomer
987606	sift: does not autobuild on buildds
ugene (3) Homepage: https://ugene.unipro.ru Vcs Debian Med Packaging Team
1010358	ugene: Fix for non-constant SIGSTKSZ	pending, ftbfs, patch
1018252	Is ugene still non-free?
1032688	ugene: unused build-dependency on removed libprocps-dev	patch

Done bugs

acedb (1) Homepage: http://www.acedb.org/ Vcs Debian Med Packaging Team
1056591	acedb FTBFS against glibc 2.38	patch
aegean (1) Homepage: https://standage.github.io/AEGeAn Vcs Debian Med Packaging Team
1043943	aegean: Fails to build source after successful build	ftbfs, sid, trixie
aragorn (1) Homepage: http://mbio-serv2.mbioekol.lu.se/ARAGORN/ Vcs Debian Med Packaging Team
1043665	aragorn: Fails to build source after successful build	ftbfs, sid, trixie
atropos (1) Homepage: https://github.com/jdidion/atropos Vcs Debian Med Packaging Team
1055730	atropos ftbfs with Python 3.12	sid, trixie
augustus (1) Homepage: https://bioinf.uni-greifswald.de/augustus/ Vcs Debian Med Packaging Team
1043915	augustus: Fails to build source after successful build	ftbfs, sid, trixie
bcftools (2) Homepage: https://samtools.github.io/bcftools/ Vcs Debian Med Packaging Team
1043668	bcftools: Fails to build source after successful build	ftbfs, sid, trixie
1055669	bcftools: test_vcf_merge failures on armhf: Bus error	ftbfs
beast2-mcmc (2) Homepage: https://www.beast2.org Vcs Debian Med Packaging Team
1043696	beast2-mcmc: Fails to build source after successful build	ftbfs, sid, trixie
1049745	beast2-mcmc: Fails to build binary packages again after successful build	trixie, ftbfs, sid
bedtools (1) Homepage: https://github.com/arq5x/bedtools2 Vcs Debian Med Packaging Team
1055414	bedtools: FTBFS on i386: "intersect" tool failure	patch, ftbfs
canu (1) Homepage: https://canu.readthedocs.org/en/latest/ Vcs Debian Med Packaging Team
1052347	src:canu: fails to migrate to testing for too long: unresolved RC issue	sid, upstream, trixie
circlator (1) Homepage: https://sanger-pathogens.github.io/circlator/ Vcs Debian Med Packaging Team
1056234	circulator's autopkg tests fail with Python 3.12	trixie, sid
comet-ms (1) Homepage: http://comet-ms.sourceforge.net Vcs The Debichem Group
1043799	comet-ms: Fails to build source after successful build	ftbfs, sid, trixie
emperor (1) Homepage: https://biocore.github.io/emperor/ Vcs Debian Med Packaging Team
1029689	emperor: tests fail with scipy 1.10
gffread (1) Homepage: https://ccb.jhu.edu/software/stringtie/gff.shtml Vcs Debian Med Packaging Team
1033703	gffread: autopkgtest regression: test dependency not in testing	bookworm-ignore
hdf5 (1) Homepage: http://hdfgroup.org/HDF5/ Vcs Gilles Filippini
972537	please add --enable-ros3-vfd to the build options to allow RO access to HDF5 on S3
jellyfish1 (1) Homepage: https://www.cbcb.umd.edu/software/jellyfish/ Vcs Debian Med Packaging Team
1057127	jellyfish1: add support for loongarch64 in d/control	patch
khmer (2) Homepage: https://khmer.readthedocs.org Vcs Debian Med Packaging Team
1055687	khmer ftbfs with Python 3.12	patch, sid, trixie
1056809	khmer: ftbfs with cython 3.0.x	sid, trixie
kma (1) Homepage: https://bitbucket.org/genomicepidemiology/kma Vcs Debian Med Packaging Team
1057132	kma: add support for loongarch64 in d/control	patch
malt (1) Homepage: https://github.com/danielhuson/malt Vcs Debian Med Packaging Team
1046315	malt: Fails to build source after successful build	sid, ftbfs, trixie
mecat2 (1) Homepage: https://github.com/xiaochuanle/MECAT2 Vcs Debian Med Packaging Team
1054708	mecat2: FTBFS: app/fsa/simple_align.hpp:12:45: error: âuint8_tâ has not been declared	ftbfs, sid, trixie
megahit (1) Homepage: https://github.com/voutcn/megahit Vcs Debian Med Packaging Team
1054672	megahit: FTBFS: local_assemble.h:31:3: error: âuint32_tâ does not name a type	sid, trixie, ftbfs
megan-ce (1) Homepage: https://github.com/danielhuson/megan-ce Vcs Debian Med Packaging Team
1046802	megan-ce: Fails to build source after successful build	trixie, sid, ftbfs
minexpert2 (1) Homepage: http://www.msxpertsuite.org/ Vcs The Debichem Group
1046641	minexpert2: Fails to build source after successful build	ftbfs, sid, trixie
parsinsert (1) Homepage: http://sourceforge.net/projects/parsinsert/ Vcs Debian Med Packaging Team
964082	parsinsert fails it's tests when built with -O2	bookworm, trixie, sid, bullseye
pilon (1) Homepage: https://github.com/broadinstitute/pilon/wiki Vcs Debian Med Packaging Team
1047000	pilon: Fails to build source after successful build	ftbfs, sid, trixie
plink2 (1) Homepage: https://www.cog-genomics.org/plink/2.0/ Vcs Debian Med Packaging Team
1056683	build-depends on atlas, which is obsolete and scheduled for removal	sid, trixie
python-cogent (1) Homepage: https://github.com/cogent3/cogent3 Vcs Debian Med Packaging Team
1030885	python-cogent: FTBFS (some tests require more than one CPU)	ftbfs, patch
python-gffutils (1) Homepage: https://daler.github.io/gffutils Vcs Debian Med Packaging Team
1054738	python-gffutils: FTBFS: make: *** [debian/rules:14: clean] Error 25	trixie, sid, ftbfs
python-pybedtools (2) Homepage: https://daler.github.io/pybedtools/ Vcs Debian Med Packaging Team
1042651	python-pybedtools: FTBFS with Sphinx 7.1, docutils 0.20: error: invalid command 'build_sphinx'	trixie, ftbfs, sid
1048006	python-pybedtools: Fails to build source after successful build	ftbfs, trixie, sid
python-pyflow (1) Homepage: https://illumina.github.io/pyflow/ Vcs Debian Med Packaging Team
1054591	python3-pyflow: ${VERSION} not expanded in package metadata, causing PEP-440 validation failures
python-pysam (2) Homepage: https://pysam.readthedocs.org/en/latest Vcs Debian Med Packaging Team
1047165	python-pysam: Fails to build source after successful build	ftbfs, sid, trixie
1055505	python-pysam new upstream needed to build with Python 3.12	trixie, upstream, sid
python-sqt (1) Homepage: https://bitbucket.org/marcelm/sqt Vcs Debian Med Packaging Team
1056037	python-sqt ftbfs with Python 3.12	sid, trixie
q2-quality-control (1) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1029700	q2-quality-control: tests fail with scipy 1.10
quorum (1) Homepage: https://github.com/gmarcais/Quorum Vcs Debian Med Packaging Team
1040588	quorum: broken symlink: /usr/share/doc/quorum/README -> README.md
r-bioc-annotationhub (1) Homepage: https://bioconductor.org/packages/AnnotationHub/ Vcs Debian R Packages Maintainers
1034852	r-bioc-annotationhub: autopkgtest regression: download failed	bookworm-ignore
r-bioc-megadepth (1) Homepage: https://bioconductor.org/packages/megadepth/ Vcs Debian R Packages Maintainers
1033853	r-bioc-megadepth: autopkgtest regression: different output	bookworm-ignore
r-bioc-structuralvariantannotation (1) Homepage: https://bioconductor.org/packages/StructuralVariantAnnotation/ Vcs Debian R Packages Maintainers
1025045	r-bioc-structuralvariantannotation: Test failures in autopkgtest	bookworm-ignore, upstream
rockhopper (1) Homepage: https://cs.wellesley.edu/~btjaden/Rockhopper/ Vcs Debian Med Packaging Team
1048408	rockhopper: Fails to build source after successful build	ftbfs, trixie, sid
spades (1) Homepage: http://cab.spbu.ru/software/spades/ Vcs Debian Med Packaging Team
976523	spades: FTBFS: jemalloc_internal.h:292:6: error: #error "No LG_QUANTUM definition for architecture; specify via CPPFLAGS"	sid, bookworm, trixie, bullseye, ftbfs
tnseq-transit (2) Homepage: http://saclab.tamu.edu/essentiality/transit/ Vcs Debian Med Packaging Team
1047512	tnseq-transit: Fails to build source after successful build	trixie, sid, ftbfs
1049672	tnseq-transit: Fails to build binary packages again after successful build	sid, trixie, ftbfs
toil (1) Homepage: https://github.com/BD2KGenomics/toil Vcs Debian Med Packaging Team
1031192	toil: FTBFS (The job JobClass is requesting 2.0 cores)	ftbfs
umap-learn (1) Homepage: https://github.com/lmcinnes/umap Vcs Debian Med Packaging Team
1055871	umap-learn: requires tbb, which is not installed ?

^*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