Summary

Bugs of task bio

Total bugs: 419

Open bugs: 375

Fixed bugs: 44

Links to other tasks

Tasks overview

Biology 375 (4189)

Biology development 170 (1815)

Next generation sequencing 5 (22)

Phylogeny 18 (222)

Cloud 74 (987)

Content management 0 (0)

Covid-19 222 (2451)

Medical data 0 (0)

Dental 1 (3)

Epidemiology 20 (249)

Hospital information systems 3 (48)

Imaging 224 (1142)

Imaging development 95 (852)

Laboratory 1 (9)

Oncology 1 (3)

Pharmacology 1 (9)

Physics 28 (213)

Practice 5 (36)

Psychology 11 (133)

Rehabilitation 0 (0)

Research 0 (0)

Statistics 4 (16)

Tools 35 (254)

Typesetting 74 (629)

Legend

Severity	Dependent	Suggested
critical	0	0
grave	0	0
serious	58	20
important	89	29
normal	59	20
minor	57	7
wishlist	29	7

Summary bugs page of task Biology

Immediately looking into bugs of the dependencies of this task is advised (4189)^*

Open bugs in dependent packages

58 serious, 89 important, 59 normal, 57 minor, 29 wishlist

abyss (1) Homepage: https://github.com/bcgsc/abyss Vcs Debian Med Packaging Team
920282	abyss fails to build on hurd - googletest EXPECT_DEATH
acedb (1) Homepage: http://www.acedb.org/ Vcs Debian Med Packaging Team
1066334	acedb: FTBFS: acein.c:2045:15: error: implicit declaration of function âadd_historyâ [-Werror=implicit-function-declaration]	forky, ftbfs, help, sid, trixie
altree (1) Homepage: https://gitlab.inria.fr/NGS/ALTree Vcs Debian Med Packaging Team
1067631	src:altree: autopkgtest timeouts on armel, armhf and ppc64el	confirmed, help
ampliconnoise (2) Homepage: https://github.com/lanzen/ampliconnoise Vcs Debian Med Packaging Team
1096305	ampliconnoise: ftbfs with GCC-15	forky, ftbfs, sid
1107485	ampliconnoise FTCBFS: misses mpi flags	patch
assembly-stats (1) Homepage: https://github.com/sanger-pathogens/assembly-stats Vcs Debian Med Packaging Team
1112710	assembly-stats: FTBFS with CMake 4	forky, ftbfs, sid
augur (1) Homepage: https://github.com/nextstrain/augur Vcs Debian Med Packaging Team
1094842	augur: Please update to latest upstream 28.0.0, released 2025-01-30
autodock-vina (1) Homepage: https://vina.scripps.edu Vcs Debian Med Packaging Team
1110595	autodock-vina ftbfs with boost1.88	forky, sid
avogadro (1) Homepage: https://avogadro.cc/ Vcs Debichem Team
1110448	avogadro: FTBFS on arm64 with GCC-15 due to GCS warning
axe-demultiplexer (1) Homepage: https://github.com/kdmurray91/axe Vcs Debian Med Packaging Team
1112715	axe-demultiplexer: FTBFS with CMake 4	forky, ftbfs, sid
ball (3) 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
1112717	ball: FTBFS with CMake 4	forky, ftbfs, sid
1114056	ball: FTBFS: /<<PKGBUILDDIR>>/include/BALL/DATATYPE/contourSurface.h:305:80: error: 'const class BALL::TContourSurface<T>' has no member named 'data_' [-Wtemplate-body]	forky, ftbfs, sid
bamtools (1) Homepage: https://github.com/pezmaster31/bamtools/wiki Vcs Debian Med Packaging Team
1112718	bamtools: FTBFS with CMake 4	forky, ftbfs, sid
bcalm (1) Homepage: https://github.com/GATB/bcalm Vcs Debian Med Packaging Team
1112722	bcalm: FTBFS with CMake 4	forky, ftbfs, sid
beads (2) Homepage: http://pappso.inrae.fr/bioinfo/beads Vcs Debian Med Packaging Team
1043686	beads: Fails to build source after successful build	forky, ftbfs, sid, trixie
1112754	beads: FTBFS with CMake 4	forky, ftbfs, sid
beagle (1) Homepage: https://faculty.washington.edu/browning/beagle/beagle.html Vcs Debian Med Packaging Team
1032034	beagle: broken package on non arm64/amd64 architectures	wontfix
beast-mcmc (2) Homepage: http://beast.bio.ed.ac.uk/ Vcs Debian Med Packaging Team
1025424	beast-mcmc: please enable autopkgtest	help
1107598	beast-mcmc: please honor CFLAGS
beast2-mcmc (1) Homepage: https://www.beast2.org Vcs Debian Med Packaging Team
1025830	beauti2 fails to start	help
bedtools (2) Homepage: https://github.com/arq5x/bedtools2 Vcs Debian Med Packaging Team
1104751	bedtools: FTBFS with GNUMAKEFLAGS=--shuffle=random	patch
1105730	bedtools: FTBFS with make --shuffle=random: src/utils/version/version.cpp:2:10: fatal error: version_git.h: No such file or directory	forky, ftbfs, sid, trixie
berkeley-express (2) Homepage: http://bio.math.berkeley.edu/eXpress/index.html Vcs Debian Med Packaging Team
1110628	berkeley-express ftbfs with boost1.88	forky, sid
1112724	berkeley-express: FTBFS with CMake 4	forky, ftbfs, sid
bifrost (2) Homepage: https://github.com/pmelsted/bifrost Vcs Debian Med Packaging Team
1096367	bifrost: ftbfs with GCC-15	forky, ftbfs, sid
1112726	bifrost: FTBFS with CMake 4	forky, ftbfs, sid
bioxtasraw (1) Homepage: https://sourceforge.net/p/bioxtasraw/git/ Vcs Debian Science Maintainers
1085363	bioxtasraw: Python SyntaxWarning
bppphyview (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
1112732	bppphyview: FTBFS with CMake 4	forky, ftbfs, sid
bppsuite (1) Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Vcs Debian Med Packaging Team
1112733	bppsuite: FTBFS with CMake 4	forky, ftbfs, sid
btllib (1) Homepage: https://github.com/bcgsc/btllib Vcs Debian Med Packaging Team
1104172	btlib - breaks autopkgtests for nthash.
bustools (2) Homepage: https://bustools.github.io/ Vcs Debian Med Packaging Team
1104777	bustools: do not hardcode CFLAGS and CXXFLAGS	patch
1112739	bustools: FTBFS with CMake 4	forky, ftbfs, sid
cassiopee (1) Homepage: https://github.com/osallou/cassiopee-c Vcs Debian Med Packaging Team
1112764	cassiopee: FTBFS with CMake 4	forky, ftbfs, sid
chromhmm (1) Homepage: https://compbio.mit.edu/ChromHMM/ Vcs Debian Med Packaging Team
1032036	chromhmm: broken package on non arm64/amd64 architectures	wontfix
cif-tools (1) Homepage: https://github.com/PDB-REDO/cif-tools Vcs Debian Med Packaging Team
1112778	cif-tools: FTBFS with CMake 4	forky, ftbfs, sid
clonalorigin (1) Homepage: https://github.com/xavierdidelot/clonalorigin Vcs Debian Med Packaging Team
1112565	clonalorigin: recommends libxml-parserl-perl which is not in unstable
coils (1) Homepage: http://www.russelllab.org/coils/ Vcs Debian Med Packaging Team
1096450	coils: ftbfs with GCC-15	forky, ftbfs, sid
coot (1) Homepage: https://github.com/pemsley/coot Vcs Debian Science Maintainers
1072286	coot: add autopkgtest for coot executable	patch
crac (1) Homepage: https://crac.gforge.inria.fr/ Vcs Debian Med Packaging Team
1105260	crac: FTBFS with make --shuffle=reverse: dh_auto_test: error: make -j1 check "TESTSUITEFLAGS=-j1 --verbose" VERBOSE=1 returned exit code 2	forky, 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)
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	forky, ftbfs, sid, trixie
dawg (2) Homepage: https://github.com/reedacartwright/dawg Vcs Debian Med Packaging Team
903886	dawg: Test suite fails	upstream
1112828	dawg: FTBFS with CMake 4	forky, ftbfs, sid
delly (1) Homepage: https://github.com/dellytools/delly Vcs Debian Med Packaging Team
1110577	delly ftbfs with boost1.88	forky, sid
diamond-aligner (1) Homepage: https://github.com/bbuchfink/diamond Vcs Debian Med Packaging Team
1112842	diamond-aligner: FTBFS with CMake 4	forky, ftbfs, sid
discosnp (1) Homepage: http://colibread.inria.fr/discosnp/ Vcs Debian Med Packaging Team
1112847	discosnp: FTBFS with CMake 4	forky, ftbfs, sid
disulfinder (1) Homepage: https://disulfind.dsi.unifi.it/ Vcs Debian Med Packaging Team
1114089	disulfinder: FTBFS: /usr/include/f2c.h:135:9: error: reference to 'complex' is ambiguous	forky, ftbfs, sid
dnaclust (1) Homepage: http://dnaclust.sourceforge.net/ Vcs Debian Med Packaging Team
1110576	dnaclust ftbfs with boost1.88	forky, sid
dssp (1) Homepage: https://github.com/PDB-REDO/dssp Vcs Debian Med Packaging Team
1112859	dssp: FTBFS with CMake 4	forky, ftbfs, sid
dwgsim (1) Homepage: https://github.com/nh13/DWGSIM/ Vcs Debian Med Packaging Team
1096554	dwgsim: ftbfs with GCC-15	forky, ftbfs, sid
ea-utils (1) Homepage: https://expressionanalysis.github.io/ea-utils/ Vcs Debian Med Packaging Team
862118	ea-utils: New upstream version available
emboss (5) 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
1069098	emboss: all executables segfault on s390x	bookworm, bullseye, forky, sid, trixie
1069142	emboss: build time testsuite is failing silently
1106974	emboss: add libcrypt-dev to Build-Depends
emperor (1) Homepage: https://biocore.github.io/emperor/ Vcs Debian Med Packaging Team
1088492	python3-emperor-doc: move from twitter-bootstrap{3,4} to bootstrap-html (v5)	upstream
epcr (1) Homepage: https://www.ncbi.nlm.nih.gov/tools/epcr/ Vcs Debian Med Packaging Team
1105316	epcr: FTBFS with make --shuffle=reverse: fahash_lookup.cpp:30:10: fatal error: epcr/fahash.hpp: No such file or directory	forky, ftbfs, sid, trixie
examl (2) Homepage: https://github.com/stamatak/ExaML Vcs Debian Med Packaging Team
1087184	examl: fails to run with tight cores count
1105362	examl: FTBFS with make --shuffle=reverse: dh_install: error: missing files, aborting	forky, ftbfs, sid, trixie
fasta3 (1) Homepage: https://fasta.bioch.virginia.edu Vcs Debian Med Packaging Team
1096607	fasta3: ftbfs with GCC-15	forky, ftbfs, sid
fastlink (1) Homepage: https://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html Vcs Debian Med Packaging Team
1096612	fastlink: ftbfs with GCC-15	forky, ftbfs, sid
fastqtl (2) Homepage: http://fastqtl.sourceforge.net/ Vcs Debian Med Packaging Team
1113830	submit@bugs.debian.org
1113845	fastqtl: recommends r-cran-qvalue which is not in unstable
flexbar (1) Homepage: https://github.com/seqan/flexbar Vcs Debian Med Packaging Team
1112919	flexbar: FTBFS with CMake 4	forky, ftbfs, sid
freecontact (1) Homepage: https://rostlab.org/ Vcs Debian Med Packaging Team
1096651	freecontact: ftbfs with GCC-15	forky, ftbfs, sid
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 (2) Homepage: http://gmod.org/wiki/GBrowse Vcs Debian Med Packaging Team
1039206	gbrowse: ships sysv-init script without systemd unit
1102804	gbrowse: add perl-xs-dev to Build-Depends
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
genometester (1) Homepage: https://github.com/bioinfo-ut/GenomeTester4 Vcs Debian Med Packaging Team
1107684	genometester FTCBFS: C vs C++ confusion	patch, upstream
genomethreader (1) Homepage: https://genomethreader.org Vcs Debian Med Packaging Team
1105366	genomethreader: FTBFS with make --shuffle=reverse: src/libgenomethreader/gthversionfunc.c:3:10: fatal error: gth_config.h: No such file or directory	forky, ftbfs, sid, trixie
genometools (2) Homepage: http://genometools.org Vcs Debian Med Packaging Team
1105339	genometools: FTBFS with make --shuffle=reverse: ./obj/gt_config.h:1: error: unterminated #ifndef	forky, ftbfs, sid, trixie
1114122	genometools: FTBFS: src/extended/md5set.c:32:3: error: conflicting types for 'md5_t'; have 'struct <anonymous>'	forky, ftbfs, sid
genomicsdb (1) Homepage: https://www.genomicsdb.org/ Vcs Debian Med Packaging Team
1092841	genomicsdb: FTBFS with fmtlib 11.1	ftbfs
gentle (2) 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
1107615	gentle FTCBFS: uses mysql_config and the build architecture pkg-config	patch, upstream
gmap (1) Homepage: http://research-pub.gene.com/gmap Vcs Debian Med Packaging Team
1107772	gmap inlining failed in call to âalways_inlineâ â_mm_alignr_epi8â: target specific option mismatch	confirmed, ftbfs
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
hhsuite (1) Homepage: https://toolkit.tuebingen.mpg.de/ Vcs Debian Med Packaging Team
1112991	hhsuite: FTBFS with CMake 4	forky, ftbfs, sid
hilive (2) Homepage: https://gitlab.com/rki_bioinformatics/HiLive2 Vcs Debian Med Packaging Team
1053499	hilive: flaky autopkgtest on several archs: segfault	upstream
1113687	Should hilive be removed from unstable?
hinge (5) 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)
1112992	hinge: FTBFS with CMake 4	forky, ftbfs, sid
hisat2 (2) Homepage: https://daehwankimlab.github.io/hisat2/ Vcs Debian Med Packaging Team
1048028	hisat2: Fails to build source after successful build	forky, ftbfs, sid, trixie
1076524	hisat2: autopkgtest uses absurd amount of memory on s390x
hmmer (1) Homepage: http://hmmer.org/ Vcs Debian Med Packaging Team
1103312	hmmer: FTBFS with the nocheck build profile	forky, ftbfs, sid, trixie
iqtree (2) Homepage: http://www.cibiv.at/software/iqtree/ Vcs Debian Med Packaging Team
1096850	iqtree: ftbfs with GCC-15	forky, ftbfs, sid
1113054	iqtree: FTBFS with CMake 4	forky, ftbfs, sid
jellyfish (3) Homepage: https://www.genome.umd.edu/jellyfish.html Vcs Debian Med Packaging Team
1021557	jellyfish: Performance regression in 2.3.0 (orders of magnitude for some inputs)	upstream
1102846	jellyfish: add perl-xs-dev to Build-Depends
1105388	jellyfish: FTBFS with make --shuffle=reverse: jellyfish/fastq2sam.cc:12:10: fatal error: jellyfish/fastq2sam_cmdline.hpp: No such file or directory	forky, ftbfs, sid, trixie
jellyfish1 (1) Homepage: https://www.cbcb.umd.edu/software/jellyfish/ Vcs Debian Med Packaging Team
875328	jellyfish1: FTBFS: __sync_val_compare_and_swap_8 undefined	upstream, wontfix
jmodeltest (2) Homepage: https://github.com//ddarriba/jmodeltest2 Vcs Debian Med Packaging Team
1095078	jmodeltest: reduce the permissions on /var/log/jmodeltest
1099239	jmodeltest: FTBFS: rc/main/java/es/uvigo/darwin/jmodeltest/io/HtmlReporter.java:38: error: cannot find symbol	forky, ftbfs, sid, trixie
jmol (1) Homepage: https://jmol.sourceforge.net/ Vcs Debichem Team
872418	jmol: Weblinks in Help do not work
kallisto (3) Homepage: https://pachterlab.github.io/kallisto Vcs Debian Med Packaging Team
1047324	kallisto: Fails to build source after successful build	forky, ftbfs, sid, trixie
1057131	kallisto: add support for loongarch64 in d/control	patch, pending
1113067	kallisto: FTBFS with CMake 4	forky, ftbfs, sid
kineticstools (1) Homepage: https://github.com/PacificBiosciences/kineticsTools Vcs Debian Med Packaging Team
1103315	kineticstools: FTBFS with the nocheck build profile	forky, ftbfs, sid, trixie
kmer (2) Homepage: http://kmer.sourceforge.net Vcs Debian Med Packaging Team
1081273	meryl: Meryl should be packaged separately from new upstream location
1105422	kmer: FTBFS with make --shuffle=reverse: make[2]: *** No rule to make target '/build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a', needed by 'atac-driver/chimera/happy-clones-span-clumps'. Stop.	forky, ftbfs, sid, trixie
kmerresistance (1) Homepage: https://bitbucket.org/genomicepidemiology/kmerresistance Vcs Debian Med Packaging Team
1009159	kmerresistance: Add autopkgtest	newcomer
lambda-align (1) Homepage: https://seqan.github.io/lambda Vcs Debian Med Packaging Team
1113092	lambda-align: FTBFS with CMake 4	forky, ftbfs, sid
lambda-align2 (1) Homepage: https://seqan.github.io/lambda Vcs Debian Med Packaging Team
1113093	lambda-align2: FTBFS with CMake 4	forky, ftbfs, sid
last-align (1) Homepage: https://gitlab.com/mcfrith/last Vcs Debian Med Packaging Team
1048396	last-align: Fails to build source after successful build	forky, ftbfs, sid, trixie
lastz (1) Homepage: https://github.com/lastz/lastz Vcs Debian Med Packaging Team
1097151	lastz: ftbfs with GCC-15	forky, ftbfs, sid
libpwiz (1) Homepage: http://proteowizard.sourceforge.net/downloads.shtml Vcs The Debichem Group
1110624	libpwiz ftbfs with boost 1.88	forky, sid
ltrsift (3) 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	forky, ftbfs, sid, trixie
1105470	ltrsift: FTBFS with make --shuffle=reverse: Fatal error: can't create obj/src/ltrsift_encode.o: No such file or directory	forky, 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	forky, ftbfs, sid, trixie
macromoleculebuilder (2) Homepage: https://simtk.org/projects/rnatoolbox Vcs Debichem Team
1113261	macromoleculebuilder: FTBFS with CMake 4	forky, ftbfs, sid
1114196	macromoleculebuilder: FTBFS: dh_auto_configure: err [too-long-redacted] on -O0" .. returned exit code 1	experimental, forky, ftbfs, sid
maffilter (1) Homepage: https://jydu.github.io/maffilter/ Vcs Debian Med Packaging Team
1113263	maffilter: FTBFS with CMake 4	forky, ftbfs, sid
mapsembler2 (1) Homepage: http://colibread.inria.fr/mapsembler2/ Vcs Debian Med Packaging Team
1113267	mapsembler2: FTBFS with CMake 4	forky, ftbfs, sid
massxpert (2) Homepage: http://www.msxpertsuite.org/ Vcs The Debichem Group
1045227	massxpert: Fails to build source after successful build	forky, ftbfs, sid, trixie
1084296	massxpert: FTBFS: rror: static assertion failed: No Q_OBJECT in the class passed to QObject::findChildren	forky, ftbfs, sid, trixie
megadepth (1) Homepage: https://github.com/ChristopherWilks/megadepth Vcs Debian Med Packaging Team
1113273	megadepth: FTBFS with CMake 4	forky, ftbfs, sid
megahit (2) Homepage: https://github.com/voutcn/megahit Vcs Debian Med Packaging Team
1088028	megahit: consider unembedding parallel-hashmap
1113276	megahit: FTBFS with CMake 4	forky, ftbfs, sid
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	forky, ftbfs, sid, trixie
metabat (1) Homepage: https://bitbucket.org/berkeleylab/metabat/wiki/Home Vcs Debian Med Packaging Team
1113279	metabat: FTBFS with CMake 4	forky, ftbfs, sid
metaeuk (1) Homepage: https://github.com/soedinglab/metaeuk Vcs Debian Med Packaging Team
1113280	metaeuk: FTBFS with CMake 4	forky, ftbfs, sid
microbegps (1) Homepage: http://sourceforge.net/projects/microbegps/ Vcs Debian Med Packaging Team
1035188	microbegps: please add autopkgtests (to add coverage for python3-numpy)
mindthegap (1) Homepage: https://github.com/GATB/MindTheGap Vcs Debian Med Packaging Team
1113288	mindthegap: FTBFS with CMake 4	forky, ftbfs, sid
minia (1) Homepage: http://minia.genouest.org/ Vcs Debian Med Packaging Team
1113290	minia: FTBFS with CMake 4	forky, ftbfs, sid
minimap2 (1) Homepage: https://github.com/lh3/minimap2 Vcs Debian Med Packaging Team
1099518	minimap2: error: type mismatch in conditional expression on loong64	patch
mlv-smile (1) Homepage: http://www-igm.univ-mlv.fr/~marsan/smile_english.html Vcs Debian Med Packaging Team
1105480	mlv-smile: FTBFS with make --shuffle=reverse: ld: cannot find grep+/obj/global_fonctions.o: No such file or directory	forky, ftbfs, sid, trixie
mmseqs2 (1) Homepage: https://github.com/soedinglab/MMseqs2 Vcs Debian Med Packaging Team
1113291	mmseqs2: FTBFS with CMake 4	forky, ftbfs, sid
mosdepth (1) Homepage: https://github.com/brentp/mosdepth Vcs Debian Med Packaging Team
1112654	mosdepth: FTBFS: /usr/share/nimble/regex/regex.nim(859, 18) Error: Exception can raise an unlisted exception: Exception	forky, ftbfs, sid
mptp (1) Homepage: https://github.com/Pas-Kapli/mptp Vcs Debian Med Packaging Team
1105502	mptp: FTBFS with make --shuffle=reverse: lex_rtree.l:22:10: fatal error: parse_rtree.h: No such file or directory	forky, ftbfs, sid, trixie
multiqc (1) Homepage: https://multiqc.info/ Vcs Debian Med Packaging Team
1088472	multiqc: move from twitter-bootstrap{3,4} to bootstrap-html (v5)	upstream
murasaki (1) Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/ Vcs Debian Med Packaging Team
1110615	murasaki ftbfs with boost 1.88	forky, sid
muscle (1) Homepage: https://www.drive5.com/muscle/ Vcs Debian Med Packaging Team
1105460	muscle: FTBFS with make --shuffle=reverse: Fatal error: can't create Linux/usage.o: No such file or directory	forky, ftbfs, sid, trixie
nanopolish (1) Homepage: https://github.com/jts/nanopolish Vcs Debian Med Packaging Team
1097430	nanopolish: ftbfs with GCC-15	forky, ftbfs, sid
nanostat (1) Homepage: https://github.com/wdecoster/nanostat Vcs Debian Med Packaging Team
1103286	Autopkgtest not working in s390x architecture
ncbi-blast+ (5) Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/ Vcs Debian Med Packaging Team
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
1077777	ncbi-blast+: makeblastdb yields broken DBs on s390x (BE generally?)	upstream
1080479	ncbi-blast+: failure to create blastdb v5 on riscv64
ncbi-igblast (3) Homepage: https://ncbi.github.io/igblast/ Vcs Debian Med Packaging Team
1048966	ncbi-igblast: Fails to build source after successful build	forky, ftbfs, sid, trixie
1097435	ncbi-igblast: ftbfs with GCC-15	forky, ftbfs, sid
1113797	ncbi-igblast FTCBFS: does not pass --host to configure	patch
ncbi-seg (1) Homepage: https://ftp.ncbi.nih.gov/pub/seg/seg/ Vcs Debian Med Packaging Team
1097436	ncbi-seg: ftbfs with GCC-15	forky, ftbfs, sid
ncbi-tools6 (1) Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/ Vcs Debian Med Packaging Team
225651	ncbi-tools-x11: want Cn3D++
ngmlr (1) Homepage: https://github.com/philres/ngmlr Vcs Debian Med Packaging Team
1113324	ngmlr: FTBFS with CMake 4	forky, ftbfs, sid
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	forky, ftbfs, sid, trixie
norsp (1) Homepage: https://rostlab.org/owiki/index.php/NORSp_-_predictor_of_NOn-Regular_Secondary_Structure Vcs Debian Med Packaging Team
1115455	norsp: recommends blast2 and profphd which are not in unstable
ntcard (1) Homepage: https://github.com/bcgsc/ntCard Vcs Debian Med Packaging Team
1025370	ntcard: ftbfs with nthash 2.3.0	ftbfs, upstream
obitools (1) Homepage: https://metabarcoding.org/obitools3 Vcs Debian Med Packaging Team
1047870	obitools: Fails to build source after successful build	forky, ftbfs, sid, trixie
openms (3) Homepage: http://www.openms.de Vcs The Debichem Group
1068052	openms: FTBFS on armel,armhf (error: âQOpenGLFunctions_2_0â does not name a type)	ftbfs
1112634	openms FTBFS: error from pdflatex	forky, ftbfs, sid
1113360	openms: FTBFS with CMake 4	forky, ftbfs, sid
parsinsert (1) Homepage: http://sourceforge.net/projects/parsinsert/ Vcs Debian Med Packaging Team
1069488	parsinsert: FTBFS on armhf: make[1]: *** [debian/rules:30: override_dh_auto_test] Error 1	confirmed, forky, ftbfs, sid, trixie
pbsuite (1) Homepage: http://sourceforge.net/projects/pb-jelly Vcs Debian Med Packaging Team
1091721	pbsuite: autopkgtest regression in testing	confirmed
pftools (1) Homepage: https://github.com/sib-swiss/pftools3 Vcs Debian Med Packaging Team
1103318	pftools: FTBFS with the nocheck build profile	forky, ftbfs, sid, trixie
phast (1) Homepage: http://compgen.cshl.edu/phast/ Vcs Debian Med Packaging Team
1097575	phast: ftbfs with GCC-15	forky, ftbfs, sid
phyml (1) Homepage: http://www.atgc-montpellier.fr/phyml Vcs Debian Med Packaging Team
1106652	phyml FTCBFS: cross compilation support reverted	patch, upstream
physamp (1) Homepage: https://jydu.github.io/physamp/ Vcs Debian Med Packaging Team
1113404	physamp: FTBFS with CMake 4	forky, ftbfs, sid
pigx-rnaseq (1) Homepage: https://github.com/BIMSBbioinfo/pigx_rnaseq Vcs Debian Med Packaging Team
1114262	pigx-rnaseq: FTBFS: dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2	forky, ftbfs, sid
pizzly (1) Homepage: https://github.com/pmelsted/pizzly Vcs Debian Med Packaging Team
1113407	pizzly: FTBFS with CMake 4	forky, ftbfs, sid
plast (3) Homepage: https://plast.inria.fr/ Vcs Debian Med Packaging Team
1047303	plast: Fails to build source after successful build	forky, ftbfs, sid, trixie
1097619	plast: ftbfs with GCC-15	forky, ftbfs, sid
1113412	plast: FTBFS with CMake 4	forky, ftbfs, sid
plink (1) Homepage: http://zzz.bwh.harvard.edu/plink/ Vcs Debian Med Packaging Team
1107047	plink: add libcrypt-dev to Build-Depends
populations (1) Homepage: https://www.bioinformatics.org/~tryphon/populations/ Vcs Debian Med Packaging Team
1113418	populations: FTBFS with CMake 4	forky, ftbfs, sid
pplacer (2) Homepage: https://github.com/matsen/pplacer Vcs Debian Med Packaging Team
1074546	FTBFS with OCaml 5.2.0 (Uses C functions without caml_ prefix)	ftbfs
1093109	pplacer: FTBFS with OCaml 5.3.0 (error in C stubs)	ftbfs
prime-phylo (3) Homepage: http://prime.sbc.su.se Vcs Debian Med Packaging Team
1078584	prime-phylo fails to build with mpi-defaults 1.17 on armhf	wontfix
1097647	prime-phylo: ftbfs with GCC-15	forky, ftbfs, sid
1113421	prime-phylo: FTBFS with CMake 4	forky, ftbfs, sid
primer3 (1) Homepage: http://primer3.sourceforge.net Vcs Debian Med Packaging Team
1097649	primer3: ftbfs with GCC-15	forky, ftbfs, sid
probabel (1) Homepage: http://www.genabel.org Vcs Debian Med Packaging Team
1091575	probabel: FTBFS on i386: dh_auto_test: error: make -j8 check "TESTSUITEFLAGS=-j8 --verbose" VERBOSE=1 returned exit code 2	forky, ftbfs, sid, trixie
profbval (1) Homepage: https://www.rostlab.org/owiki/index.php/PROFbval Vcs Debian Med Packaging Team
1115675	profbval: recommends blast2 and profphd which are not in unstable
profphd-utils (1) Homepage: https://www.rostlab.org/ Vcs Debian Med Packaging Team
1115676	profphd-utils: recommends profphd which is not in unstable
proteinortho (1) Homepage: https://gitlab.com/paulklemm_PHD/proteinortho Vcs Debian Med Packaging Team
1105698	proteinortho: FTBFS with make --shuffle=reverse: rm: cannot remove 'remove.*': No such file or directory	forky, ftbfs, sid, trixie
psortb (2) Homepage: https://www.psort.org/ Vcs Debian Med Packaging Team
1048520	psortb: Fails to build source after successful build	forky, ftbfs, sid, trixie
1102847	psortb: add perl-xs-dev to Build-Depends
pymol (3) Homepage: https://www.pymol.org Vcs Debichem Team
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-cogent (2) Homepage: https://github.com/cogent3/cogent3 Vcs Debian Med Packaging Team
1058479	python-cogent: please (temporarily) drop python3-numba dependencies	wontfix
1090269	python-cogent: FTBFS: E ImportError: Numba could not be imported.	ftbfs
python-csb (1) Homepage: https://github.com/csb-toolbox/CSB Vcs Debian Med Packaging Team
1085900	python-csb: Python SyntaxWarning	pending
qcat (1) Homepage: https://github.com/nanoporetech/qcat Vcs Debian Med Packaging Team
1103326	qcat: FTBFS with the nocheck build profile	forky, ftbfs, sid, trixie
qcumber (6) 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	forky, ftbfs, sid, trixie
1068856	[INTL:sv] Swedish strings for qcumber debconf	l10n, patch
1088515	qcumber: move from twitter-bootstrap{3,4} to bootstrap-html (v5)	upstream
1103459	qcumber: [INTL:pt_BR] Brazilian Portuguese debconf templates translation	l10n, patch
qiime (2) Homepage: https://qiime2.org Vcs Debian Med Packaging Team
1076314	qiime hard-codes python 3.11 without depending on it	forky, pending, sid, trixie
1084668	qiime: removal of Python standard libraries in Python 3.13	fixed-upstream, pending
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
r-bioc-mofa (1) Homepage: https://bioconductor.org/packages/MOFA/ Vcs Debian R Packages Maintainers
1085689	r-bioc-mofa: Python SyntaxWarning
r-cran-genabel (1) Homepage: https://cran.r-project.org/package=GenABEL Vcs Debian R Packages Maintainers
1103201	r-cran-genabel: FTBFS: fexact.c:181:37: error: implicit declaration of function 'Calloc'	forky, ftbfs, sid, trixie
r-cran-sdmtools (1) Homepage: https://cran.r-project.org/package=SDMTools Vcs Debian R Packages Maintainers
1081161	r-cran-sdmtools: removed from CRAN repository
r-cran-spp (1) Homepage: https://cran.r-project.org/package=spp Vcs Debian R Packages Maintainers
1084108	r-cran-spp: removed from CRAN repository
r-cran-tcr (1) Homepage: https://cran.r-project.org/package=tcR Vcs Debian R Packages Maintainers
1081175	r-cran-tcr: removed from CRAN repository
racon (1) Homepage: https://github.com/lbcb-sci/racon Vcs Debian Med Packaging Team
1097767	racon: ftbfs with GCC-15	forky, ftbfs, sid
rambo-k (1) Homepage: http://rambok.sourceforge.net/ Vcs Debian Med Packaging Team
1047092	rambo-k: Fails to build source after successful build	forky, ftbfs, pending, sid, trixie
rapmap (3) 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)	bookworm, bullseye, forky, ftbfs, sid, trixie
1097770	rapmap: ftbfs with GCC-15	forky, ftbfs, sid
rasmol (1) Homepage: http://rasmol.org Vcs Debian Science Maintainers
1097771	rasmol: ftbfs with GCC-15	forky, ftbfs, sid
raster3d (2) Homepage: http://www.bmsc.washington.edu/raster3d/raster3d.html Vcs Debian Med Packaging Team
1097773	raster3d: ftbfs with GCC-15	forky, ftbfs, sid
1105671	raster3d: FTBFS with make --shuffle=reverse: Fatal Error: Cannot open module file âlists.modâ for reading at (1): No such file or directory	forky, ftbfs, sid, trixie
raxml (1) Homepage: https://cme.h-its.org/exelixis/web/software/raxml/index.html Vcs Debian Med Packaging Team
1105678	raxml: FTBFS with make --shuffle=reverse: ld: cannot find multiple.o: No such file or directory	forky, ftbfs, sid, trixie
rdp-classifier (2) Homepage: https://github.com/rdpstaff/classifier Vcs Debian Med Packaging Team
1099282	rdp-classifier: FTBFS: src/edu/msu/cme/rdp/classifier/train/validation/distance/BoxPlotUtils.java:28: error: cannot find symbol	confirmed, forky, ftbfs, help, sid, trixie
1108589	rdp-classifier: FTBFS with default Java 25	ftbfs
readseq (1) Homepage: http://iubio.bio.indiana.edu/soft/molbio/readseq/ Vcs Debian Med Packaging Team
1097779	readseq: ftbfs with GCC-15	forky, ftbfs, sid
relion (2) Homepage: https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page Vcs Debian Med Packaging Team
1097784	relion: ftbfs with GCC-15	forky, ftbfs, sid
1113466	relion: FTBFS with CMake 4	forky, ftbfs, sid
roguenarok (1) Homepage: https://github.com/aberer/RogueNaRok Vcs Debian Med Packaging Team
1097803	roguenarok: ftbfs with GCC-15	forky, ftbfs, sid
saint (1) Homepage: http://saint-apms.sourceforge.net/Main.html Vcs Debian Med Packaging Team
1105603	saint: FTBFS with make --shuffle=reverse: mv: target '/build/reproducible-path/saint-2.5.0+dfsg/build': No such file or directory	forky, ftbfs, sid, trixie
salmon (3) Homepage: https://github.com/COMBINE-lab/salmon Vcs Debian Med Packaging Team
1088027	salmon: consider unembedding parallel-hashmap
1097838	salmon: ftbfs with GCC-15	forky, ftbfs, sid
1103327	salmon: FTBFS with the nocheck build profile	forky, ftbfs, sid, trixie
sambamba (2) Homepage: https://github.com/lomereiter/sambamba Vcs Debian Med Packaging Team
1015654	sambamba: ftbfs with LTO (link time optimization) enabled	forky, sid, trixie
1095434	sambamba: rare segmentation fault makes nanosv autopkgtest flaky
savvy (1) Homepage: https://github.com/statgen/savvy Vcs Debian Med Packaging Team
1113483	savvy: FTBFS with CMake 4	forky, ftbfs, sid
scrappie (1) Homepage: https://github.com/nanoporetech/scrappie Vcs Debian Med Packaging Team
1113489	scrappie: FTBFS with CMake 4	forky, ftbfs, sid
seqan-raptor (1) Homepage: https://github.com/seqan/raptor Vcs Debian Med Packaging Team
1111716	seqan-raptor: FTBFS pdflatex refman	ftbfs
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	forky, 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	forky, 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	forky, ftbfs, sid, trixie
shasta (1) Homepage: https://github.com/chanzuckerberg/shasta Vcs Debian Med Packaging Team
1110602	shasta ftbfs with boost 1.88	forky, sid
sibelia (1) Homepage: http://bioinf.spbau.ru/sibelia Vcs Debian Med Packaging Team
1113499	sibelia: FTBFS with CMake 4	forky, ftbfs, sid
sim4 (1) Homepage: https://globin.bx.psu.edu/html/docs/sim4.html Vcs Debian Med Packaging Team
1097885	sim4: ftbfs with GCC-15	forky, ftbfs, sid
simka (1) Homepage: https://github.com/GATB/simka Vcs Debian Med Packaging Team
1113504	simka: FTBFS with CMake 4	forky, ftbfs, sid
skesa (1) Homepage: https://github.com/ncbi/SKESA Vcs Debian Med Packaging Team
1112688	skesa FTCBFS: uses variable CC for the C++ compiler	patch, upstream
snap-aligner (1) 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)
soapaligner (1) Homepage: https://web.archive.org/web/20190127081222/http://soap.genomics.org.cn/soapaligner.html Vcs Debian Med Packaging Team
1097906	soapaligner: ftbfs with GCC-15	forky, ftbfs, sid
soapdenovo (1) Homepage: http://soap.genomics.org.cn/soapdenovo.html Vcs Debian Med Packaging Team
1097907	soapdenovo: ftbfs with GCC-15	forky, ftbfs, sid
soapdenovo2 (2) Homepage: http://soap.genomics.org.cn/soapdenovo.html Vcs Debian Med Packaging Team
1097909	soapdenovo2: ftbfs with GCC-15	forky, ftbfs, sid
1105578	soapdenovo2: FTBFS with make --shuffle=reverse: ld: cannot find sparsePregraph/*.o: No such file or directory	forky, ftbfs, sid, trixie
sortmerna (3) Homepage: https://github.com/sortmerna/sortmerna Vcs Debian Med Packaging Team
1072346	sortmerna: please update autopkgtest	newcomer
1097910	sortmerna: ftbfs with GCC-15	forky, ftbfs, sid
1113530	sortmerna: FTBFS with CMake 4	forky, ftbfs, sid
sourmash (1) Homepage: https://github.com/dib-lab/sourmash Vcs Debian Med Packaging Team
1115589	sourmash FTBFS with liblzma 0.4	ftbfs
spades (4) Homepage: https://github.com/ablab/spades Vcs Debian Med Packaging Team
1086015	build for all supported python3
1088026	spades: consider unembedding parallel-hashmap
1097913	spades: ftbfs with GCC-15	forky, ftbfs, sid
1113531	spades: FTBFS with CMake 4	forky, ftbfs, sid
spaln (1) Homepage: https://github.com/ogotoh/spaln Vcs Debian Med Packaging Team
1112687	spaln FTCBFS: uses -l flags in Makefile dependencies	patch, upstream
spoa (1) Homepage: https://github.com/rvaser/spoa Vcs Debian Med Packaging Team
1097922	spoa: ftbfs with GCC-15	forky, ftbfs, sid
staden (1) Homepage: https://sourceforge.net/projects/staden/ Vcs Debian Med Packaging Team
1097934	staden: ftbfs with GCC-15	experimental, forky, ftbfs, sid
surankco (1) Homepage: https://sourceforge.net/projects/surankco/ Vcs Debian Med Packaging Team
1048111	surankco: Fails to build source after successful build	forky, ftbfs, sid, trixie
sweed (1) Homepage: https://sco.h-its.org/exelixis/web/software/sweed/ Vcs Debian Med Packaging Team
1097956	sweed: ftbfs with GCC-15	forky, ftbfs, sid
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
terraphast (1) Homepage: https://github.com/amkozlov/terraphast-one Vcs Debian Med Packaging Team
1113569	terraphast: FTBFS with CMake 4	forky, ftbfs, sid
theseus (1) Homepage: http://www.theseus3d.org Vcs Debian Med Packaging Team
1105687	theseus: FTBFS with make --shuffle=reverse: ld: cannot find -ltheseus: No such file or directory	forky, ftbfs, sid, trixie
thesias (1) Homepage: https://github.com/daissi/thesias Vcs Debian Med Packaging Team
1097993	thesias: ftbfs with GCC-15	forky, ftbfs, sid
toil (1) Homepage: https://github.com/BD2KGenomics/toil Vcs Debian Med Packaging Team
1108056	toil: FTBFS: Some tests fail on single-cpu systems	forky, ftbfs, help, sid, trixie
tracetuner (1) Homepage: https://sourceforge.net/projects/tracetuner/ Vcs Debian Med Packaging Team
1098011	tracetuner: ftbfs with GCC-15	forky, ftbfs, sid
transrate-tools (1) Homepage: https://hibberdlab.com/transrate/ Vcs Debian Med Packaging Team
1113584	transrate-tools: FTBFS with CMake 4	forky, ftbfs, sid
tree-puzzle (2) Homepage: http://www.tree-puzzle.de Vcs Debian Med Packaging Team
1106704	tree-puzzle FTCBFS: uses mpicc	patch, upstream
1108273	tree-puzzle: please make the build reproducible	patch
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 (2) Homepage: https://github.com/trinityrnaseq/trinityrnaseq Vcs Debian Med Packaging Team
981874	trinityrnaseq: flaky autopkgtest	bookworm, bullseye, forky, sid, trixie
1113587	trinityrnaseq: FTBFS with CMake 4	forky, ftbfs, sid
twopaco (1) Homepage: https://github.com/medvedevgroup/TwoPaCo Vcs Debian Med Packaging Team
1047488	twopaco: Fails to build source after successful build	forky, ftbfs, sid, trixie
uc-echo (1) Homepage: https://uc-echo.sourceforge.net/ Vcs Debian Med Packaging Team
1105670	uc-echo: FTBFS with make --shuffle=reverse: ././NeighborSet.hpp:200:(.text.startup+0x801): undefined reference to `NeighborSetLoader::CacheSize'	forky, ftbfs, sid, trixie
ugene (1) Homepage: https://ugene.unipro.ru Vcs Debian Med Packaging Team
1114673	ugene FTCBFS: enables sse2 on non-x86
umap-learn (4) Homepage: https://github.com/lmcinnes/umap Vcs Debian Med Packaging Team
980509	umap-learn: Binary package name should be python3-umap-learn	pending
1058489	umap-learn: please (temporarily) drop python3-numba dependencies
1071816	umap-learn: FTBFS: E TypeError: exceptions must be derived from Warning, not <class 'NoneType'>	ftbfs
1112612	Should umap-learn be removed from unstable?	wontfix
umis (1) Homepage: https://github.com/vals/umis Vcs Debian Med Packaging Team
1089115	umis: tracebacks normally fatal during autopkgtest runs	upstream
velvet (1) Homepage: https://github.com/dzerbino/velvet Vcs Debian Med Packaging Team
1105569	velvet: FTBFS with make --shuffle=reverse: Fatal error: can't create obj/autoOpen.o: No such file or directory	forky, 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!	bookworm, bullseye, forky, ftbfs, sid, trixie
987184	vg -- excessive variants built, and not tested
1015699	vg: ftbfs with LTO (link time optimization) enabled	forky, sid, trixie
1089275	vg: FTBFS with make 4.4.1	forky, ftbfs, sid, trixie
1113618	vg: FTBFS with CMake 4	forky, ftbfs, sid
vmatch (1) Homepage: http://www.vmatch.de Vcs Debian Med Packaging Team
1105602	vmatch: FTBFS with make --shuffle=reverse: Fatal error: can't create ../lib/libfiles/kurtz-basic/verbosealpha.dbg.o: No such file or directory	forky, ftbfs, sid, trixie
yaha (1) Homepage: https://github.com/GregoryFaust/yaha Vcs Debian Med Packaging Team
1105561	yaha: FTBFS with make --shuffle=reverse: src/Math.c:343:1: fatal error: opening dependency file obj/Math.d: No such file or directory	forky, ftbfs, sid, trixie

Open bugs in suggested packages

20 serious, 29 important, 20 normal, 7 minor, 7 wishlist

arb (5) Homepage: http://www.arb-home.de/ Vcs Debian Med Packaging Team
1089541	override_dh_auto_build Error
1100471	[INTL:es] Spanish translation of arb debconf template	l10n, patch
1102185	arb: Update/add debconf template translation [INTL:ca]	l10n, patch
1102816	arb: add perl-xs-dev to Build-Depends
1114476	arb: FTBFS: CAP2.c:317:14: error: too many arguments to function 'ckopen'; expected 0, have 2	forky, ftbfs, sid
bcbio (1) Homepage: https://github.com/bcbio/bcbio-nextgen Vcs Debian Med Packaging Team
928076	bcbio: Workflows not ready for non-developers to depend on.
blimps (1) Homepage: https://web.archive.org/web/20170606235903/http://blocks.fhcrc.org/blocks/uploads/blimps/ Vcs Debian Med Packaging Team
1114069	blimps: FTBFS: blksort.c:228:19: error: too many arguments to function 'read_config'; expected 0, have 3	forky, ftbfs, sid
catfishq (1) Homepage: https://github.com/philres/catfishq Vcs Steffen Moeller
1085412	catfishq: Python SyntaxWarning
cufflinks (2) Homepage: https://cufflinks.cbcb.umd.edu Vcs Debian Med Packaging Team
1110578	cufflinks ftbfs with boost1.88	forky, sid
1114084	cufflinks: FTBFS: locfit/adap.c:32:3: error: too many arguments to function 'wdiag'; expected 0, have 6	forky, ftbfs, sid
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
getdata (1) Homepage: http://debian-med.alioth.debian.org Vcs Debian Med Packaging Team
1081508	getdata: homepage defunct
hdf5 (32) Homepage: http://hdfgroup.org/HDF5/ Vcs Gilles Filippini
638753	libhdf5-serial-1.8.7: threadsafe memory leaks	moreinfo
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
839784	libhdf5-dev: pkg-config file references ONLY the C library
968559	libhdf5-openmpi-dev: hdf5-mpi.pc alternative sometimes goes missing	moreinfo
1023446	libhdf5-openmpi-dev: h5pcc configured as static build	wontfix
1040862	hdf5: S3 VFD pulls in networking dependencies (libcurl), please package it as a VFD plugin	moreinfo
1052250	pkg-config file incorrect for static linking
1100440	hdf5: CVE-2025-2153	security, upstream
1103531	hdf5: CVE-2025-2926	security, upstream
1103532	hdf5: CVE-2025-2925	security, upstream
1103533	hdf5: CVE-2025-2924	security, upstream
1103534	hdf5: CVE-2025-2923	security, upstream
1103536	hdf5: CVE-2025-2915	security, upstream
1103537	hdf5: CVE-2025-2914	fixed-upstream, security, upstream
1103538	hdf5: CVE-2025-2913	fixed-upstream, security, upstream
1103539	hdf5: CVE-2025-2912	fixed-upstream, security, upstream
1103540	hdf5: CVE-2025-2310	security, upstream
1103541	hdf5: CVE-2025-2309	security, upstream
1103542	hdf5: CVE-2025-2308	security, upstream
1105370	hdf5: FTBFS with make --shuffle=reverse: ln: failed to create symbolic link 'hdf5/serial/libhdf5.settings': File exists	forky, ftbfs, sid, trixie
1108155	hdf5: CVE-2025-6269	security, upstream
1108156	hdf5: CVE-2025-6270	fixed-upstream, security, upstream
1108409	hdf5: CVE-2025-6750	security, upstream
1108480	hdf5: CVE-2025-6818	security, upstream
1108481	hdf5: CVE-2025-6817	security, upstream
1108482	hdf5: CVE-2025-6816	security, upstream
1108884	hdf5: CVE-2025-7069	fixed-upstream, security, upstream
1108885	hdf5: CVE-2025-7068	security, upstream
1108886	hdf5: CVE-2025-7067	security, upstream
hts-nim-tools (1) Homepage: https://github.com/brentp/hts-nim-tools Vcs Debian Med Packaging Team
1112653	hts-nim-tools: FTBFS: /usr/share/nimble/regex/regex.nim(859, 18) Error: Exception can raise an unlisted exception: Exception	forky, ftbfs, sid
intake (4) Homepage: https://github.com/intake/intake Vcs Debian Med Packaging Team
1063953	intake: autopkgtest regression with pytest 8
1088416	intake: move from twitter-bootstrap{3,4} to bootstrap-html (v5)	upstream
1094915	intake commatibility with zarr3
1112615	Should intake be removed from unstable?
maude (1) Homepage: http://maude.cs.uiuc.edu Vcs Debian Med Packaging Team
1067957	FTBFS: error: call of overloaded â__gmp_expr(__time64_t&)â is ambiguous	forky, ftbfs, sid, trixie
pybel (1) Homepage: https://pybel.readthedocs.io Vcs Debian Med Packaging Team
1108456	pybel: Drop python3-click (build) dependency	forky, patch, sid, upstream
pychopper (1) Homepage: https://github.com/epi2me-labs/pychopper Vcs Debian Med Packaging Team
1082368	FTBFS: TestIntegration.testIntegration: AssertionError: 1 != 0	confirmed, ftbfs
pyrle (1) Homepage: https://github.com/pyranges/pyrle Vcs Debian Python Team
1047039	pyrle: Fails to build source after successful build	forky, ftbfs, sid, trixie
python-anndata (1) Homepage: https://github.com/theislab/anndata Vcs Debian Med Packaging Team
1114293	python-anndata: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.13 returned exit code 13	forky, ftbfs, sid
python-loompy (1) Homepage: https://github.com/linnarsson-lab/loompy Vcs Debian Med Packaging Team
1058482	python-loompy: please (temporarily) drop python3-numba dependencies
python-ncls (1) Homepage: https://github.com/biocore-ntnu/ncls Vcs Debian Python Team
1046648	python-ncls: Fails to build source after successful build	forky, 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-alignment (1) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1076318	q2-alignment hard-codes python 3.11 without depending on it	forky, sid, trixie
q2-cutadapt (1) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1104285	q2-cutadapt: Fix unstable/amd64 debci failure
q2-demux (1) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1076315	q2-demux hard-codes python 3.11 without depending on it	forky, sid, trixie
q2-feature-classifier (2) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1071882	q2-feature-classifier: FTBFS: unsatisfiable build-dependencies	ftbfs
1114504	Should q2-feature-classifier be removed from unstable?
q2-phylogeny (1) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1076317	q2-phylogeny hard-codes python 3.11 without depending on it
q2-quality-control (1) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1076914	q2-quality-control: FTBFS with the nocheck build profile	ftbfs
q2-types (3) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1065333	q2-types: test data heavily outweighs actual code
1076316	q2-types hard-codes python 3.11 without depending on it	forky, sid, trixie
1104050	q2-types: Fix unstable/amd64 debci failure	patch
q2cli (1) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1076080	q2cli: FTBFS in sid (python3.12)	ftbfs
q2templates (1) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1088514	q2templates: move from twitter-bootstrap{3,4} to bootstrap-html (v5)	upstream
r-bioc-org.hs.eg.db (1) Homepage: https://bioconductor.org/packages/org.Hs.eg.db/ Vcs Debian R Packages Maintainers
1083247	r-bioc-org.hs.eg.db: homepage defunct, standardize
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'	forky, ftbfs, sid, trixie
1040128	relion-cuda: FTBFS with cub 2.0.1: error: function "cub::Debug" has already been defined	forky, 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	forky, ftbfs, sid, trixie
seq-gen (1) Homepage: http://tree.bio.ed.ac.uk/software/seqgen/ Vcs Debian Med Packaging Team
1114370	seq-gen: FTBFS: seq-gen.c:143:6: error: conflicting types for 'ReadParams'; have 'void(int, char **)'	forky, ftbfs, sid
sift (4) Homepage: https://sift.bii.a-star.edu.sg/ Vcs Debian Med Packaging Team
986200	sift: Please provide autopkgtest	newcomer
987606	sift: does not autobuild on buildds
1103329	sift: FTBFS with the nocheck build profile	forky, ftbfs, sid, trixie
1114377	sift: FTBFS: Matrix_Info.c:822:1: error: number of arguments doesn't match prototype	forky, ftbfs, sid
trnascan-se (1) Homepage: http://lowelab.ucsc.edu/tRNAscan-SE Vcs Debian Med Packaging Team
1114419	trnascan-se: FTBFS: src/gnuregex.c:1175:20: error: too many arguments to function 'at_begline_loc_p'; expected 0, have 3	forky, ftbfs, sid
vienna-rna (2) Homepage: https://www.tbi.univie.ac.at/RNA/ Vcs Debian Med Packaging Team
1102852	vienna-rna: add perl-xs-dev to Build-Depends
1114434	vienna-rna: FTBFS: subopt.c:618:28: error: passing argument 2 of 'lst_kill' from incompatible pointer type [-Wincompatible-pointer-types]	forky, ftbfs, sid

Done bugs

aegean (2) Homepage: https://standage.github.io/AEGeAn Vcs Debian Med Packaging Team
1096281	aegean: ftbfs with GCC-15	experimental, forky, ftbfs, sid
1109688	aegean: please enable build for loong64	patch
altree (3) Homepage: https://gitlab.inria.fr/NGS/ALTree Vcs Debian Med Packaging Team
1096300	altree: ftbfs with GCC-15	forky, ftbfs, sid
1102872	altree: add perl-xs-dev to Build-Depends
1115489	altree: binary-all FTBFS	ftbfs, patch
augur (1) Homepage: https://github.com/nextstrain/augur Vcs Debian Med Packaging Team
1115122	augur: FTBFS: augur/io/shell_command_runner.py:11: error: Cannot assign to final name "SIGKILL" [misc]	forky, ftbfs, sid
beads (1) Homepage: http://pappso.inrae.fr/bioinfo/beads Vcs Debian Med Packaging Team
1096362	beads: ftbfs with GCC-15	forky, sid
bitseq (2) Homepage: https://github.com/BitSeq/BitSeq Vcs Debian Med Packaging Team
1035121	bitseq: please add autopkgtests (to add coverage for python3-numpy)
1111394	src:bitseq: fails to migrate to testing for too long	forky, sid
cif-tools (1) Homepage: https://github.com/PDB-REDO/cif-tools Vcs Debian Med Packaging Team
1110806	cif-tools: FTBFS: make[1]: *** [debian/rules:9: override_dh_auto_configure] Error 2	forky, ftbfs, sid
datamash (1) Homepage: https://savannah.gnu.org/projects/datamash/ Vcs Debian Science Maintainers
1096504	datamash: ftbfs with GCC-15	forky, sid
dssp (1) Homepage: https://github.com/PDB-REDO/dssp Vcs Debian Med Packaging Team
1110795	dssp: FTBFS: make: *** [debian/rules:15: binary] Error 2	forky, ftbfs, sid
emboss (1) Homepage: https://emboss.sourceforge.net Vcs Debian Med Packaging Team
1096578	emboss: ftbfs with GCC-15	forky, ftbfs, sid
freebayes (1) Homepage: https://github.com/ekg/freebayes Vcs Debian Med Packaging Team
1067271	freebayes: FTBFS: dh_auto_test: error: cd build && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 MESON_TESTTHREADS=8 meson test -v --timeout-multiplier 100 returned exit code 5	ftbfs
genomicsdb (1) Homepage: https://www.genomicsdb.org/ Vcs Debian Med Packaging Team
1103009	genomicsdb: FTBFS in testing/arm64: tests failed	ftbfs, sid, trixie, upstream
ghmm (1) Homepage: https://sourceforge.net/p/ghmm/wiki/Home/ Vcs Debian Med Packaging Team
1106611	ghmm ftbfs with libxml 2.14.x from experimental	forky, ftbfs, patch, sid
hdf5 (3) Homepage: http://hdfgroup.org/HDF5/ Vcs Gilles Filippini
915807	hdf5: CVE-2017-17507	security, upstream
1114023	hdf5 ftbfs in unstable	forky, ftbfs, sid
1114923	libhdf5-dev: undefined reference to symbol 'H5check_version@@HDF5_SERIAL_1.14.3'
htslib (1) Homepage: https://github.com/samtools/htslib Vcs Debian Med Packaging Team
1111788	htslib: autopkgtest regression
intake (2) Homepage: https://github.com/intake/intake Vcs Debian Med Packaging Team
1064752	intake: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12 3.11" returned exit code 13	forky, ftbfs, sid, trixie
1067969	python3-intake: Please replace python3-appdirs dependency with platformdirs	fixed-upstream, forky, patch, sid, trixie
jalview (1) Homepage: https://www.jalview.org Vcs Debian Java Maintainers
1104128	jalview: Update/add debconf template translation [INTL:ca]	l10n, patch
khmer (2) Homepage: https://khmer.readthedocs.org Vcs Debian Med Packaging Team
1082721	khmer: FTBFS: failing tests	ftbfs
1085660	khmer: Python SyntaxWarning
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	experimental, sid, trixie
mafft (1) Homepage: https://mafft.cbrc.jp/alignment/software/ Vcs Debian Med Packaging Team
1097352	mafft: ftbfs with GCC-15	forky, ftbfs, sid
massxpert2 (1) Homepage: http://www.msxpertsuite.org/ Vcs The Debichem Group
1097365	massxpert2: ftbfs with GCC-15	forky, sid
minexpert2 (1) Homepage: http://www.msxpertsuite.org/ Vcs The Debichem Group
1097402	minexpert2: ftbfs with GCC-15	forky, sid
parsinsert (1) Homepage: http://sourceforge.net/projects/parsinsert/ Vcs Debian Med Packaging Team
964082	parsinsert fails it's tests when built with -O2	bookworm, bullseye, sid, trixie
porechop (1) Homepage: https://rrwick.github.io/Porechop Vcs Debian Med Packaging Team
1085786	porechop: Python SyntaxWarning
probcons (1) Homepage: http://probcons.stanford.edu/ Vcs Debian Med Packaging Team
1111708	probcons: Uses deprecated BSD file reference	patch
r-bioc-beachmat (1) Homepage: https://bioconductor.org/packages/beachmat/ Vcs Debian R Packages Maintainers
1111758	r-bioc-beachmat: autopkgtest regression: isNamespaceLoaded("beachmat.hdf5") is not TRUE
seqan-raptor (1) Homepage: https://github.com/seqan/raptor Vcs Debian Med Packaging Team
1114369	seqan-raptor: FTBFS: dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2	forky, ftbfs, sid
ska (1) Homepage: https://github.com/simonrharris/SKA Vcs Debian Med Packaging Team
1111412	ska: autopkgtest fails due to googletest 1.17 no longer supporting C++ prior to C++17
sourmash (2) Homepage: https://github.com/dib-lab/sourmash Vcs Debian Med Packaging Team
1114393	sourmash: FTBFS: error: failed to select a version for the requirement `typed-builder = "^0.20"`	forky, ftbfs, sid
1115342	sourmash: FTBFS: error: failed to select a version for the requirement `needletail = "^0.5"`	ftbfs
spades (2) Homepage: https://github.com/ablab/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"	bookworm, bullseye, ftbfs, sid, trixie
1087093	spades: Python SyntaxWarning
tnseq-transit (1) Homepage: http://saclab.tamu.edu/essentiality/transit/ Vcs Debian Med Packaging Team
1098008	tnseq-transit: ftbfs with GCC-15	forky, sid
tvc (1) Homepage: http://ioncommunity.thermofisher.com Vcs Debian Med Packaging Team
1113589	tvc: FTBFS with CMake 4	forky, ftbfs, sid
ugene (1) Homepage: https://ugene.unipro.ru Vcs Debian Med Packaging Team
1098031	ugene: ftbfs with GCC-15	forky, sid
vcfanno (1) Homepage: https://github.com/brentp/vcfanno Vcs Debian Med Packaging Team
1114433	vcfanno: FTBFS: dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2	forky, ftbfs, sid
wise (1) Homepage: https://www.ebi.ac.uk/~birney/wise2/ Vcs Debian Med Packaging Team
1098098	wise: ftbfs with GCC-15	forky, 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