Summary

Bugs of task bio

Total bugs: 331

Open bugs: 308

Fixed bugs: 23

Links to other tasks

Tasks overview

Biology 308 (2722)

Biology development 142 (1200)

Next generation sequencing 5 (21)

Phylogeny 18 (201)

Cloud 73 (741)

Content management 0 (0)

Covid-19 193 (1849)

Medical data 0 (0)

Dental 2 (12)

Epidemiology 18 (204)

Hospital information systems 3 (33)

Imaging 206 (867)

Imaging development 80 (502)

Laboratory 1 (9)

Oncology 1 (3)

Pharmacology 1 (9)

Physics 24 (159)

Practice 6 (45)

Psychology 11 (133)

Rehabilitation 0 (0)

Research 0 (0)

Statistics 4 (16)

Tools 35 (227)

Typesetting 81 (632)

Legend

Severity	Dependent	Suggested
critical	0	0
grave	0	0
serious	19	12
important	76	24
normal	61	20
minor	52	7
wishlist	30	7

Summary bugs page of task Biology

Immediately looking into bugs of the dependencies of this task is advised (2722)^*

Open bugs in dependent packages

19 serious, 76 important, 61 normal, 52 minor, 30 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]	ftbfs, help, sid, trixie
aegean (1) Homepage: https://standage.github.io/AEGeAn Vcs Debian Med Packaging Team
1096281	aegean: ftbfs with GCC-15	forky, sid
altree (3) Homepage: https://gitlab.inria.fr/NGS/ALTree Vcs Debian Med Packaging Team
1067631	src:altree: autopkgtest timeouts on armel, armhf and ppc64el
1096300	altree: ftbfs with GCC-15	forky, sid
1102872	altree: add perl-xs-dev to Build-Depends
ampliconnoise (2) Homepage: https://github.com/lanzen/ampliconnoise Vcs Debian Med Packaging Team
1096305	ampliconnoise: ftbfs with GCC-15	forky, sid
1107485	ampliconnoise FTCBFS: misses mpi flags	patch
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
ball (2) 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
1060741	ball: Please port from sip4 to sip6	confirmed, help, sid, trixie, upstream
bamtools (1) Homepage: https://github.com/pezmaster31/bamtools/wiki Vcs Debian Med Packaging Team
865130	reapr FTBFS on big endian: Error sampling from files '00.Sample/fragCov.gz', '00.assembly.fa.gc.gz'	ftbfs, upstream
beads (2) Homepage: http://pappso.inrae.fr/bioinfo/beads Vcs Debian Med Packaging Team
1043686	beads: Fails to build source after successful build	ftbfs, sid, trixie
1096362	beads: ftbfs with GCC-15	forky, 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	ftbfs, sid, trixie
bifrost (1) Homepage: https://github.com/pmelsted/bifrost Vcs Debian Med Packaging Team
1096367	bifrost: ftbfs with GCC-15	forky, sid
bioxtasraw (1) Homepage: https://sourceforge.net/p/bioxtasraw/git/ Vcs Debian Science Maintainers
1085363	bioxtasraw: Python SyntaxWarning
bitseq (1) Homepage: https://github.com/BitSeq/BitSeq Vcs Debian Med Packaging Team
1035121	bitseq: please add autopkgtests (to add coverage for python3-numpy)
btllib (1) Homepage: https://github.com/bcgsc/btllib Vcs Debian Med Packaging Team
1104172	btlib - breaks autopkgtests for nthash.
bustools (1) Homepage: https://bustools.github.io/ Vcs Debian Med Packaging Team
1104777	bustools: do not hardcode CFLAGS and CXXFLAGS	patch
chromhmm (1) Homepage: https://compbio.mit.edu/ChromHMM/ Vcs Debian Med Packaging Team
1032036	chromhmm: broken package on non arm64/amd64 architectures	wontfix
coils (1) Homepage: http://www.russelllab.org/coils/ Vcs Debian Med Packaging Team
1096450	coils: ftbfs with GCC-15	forky, 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	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 (3) 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
1096504	datamash: ftbfs with GCC-15	forky, sid
dawg (1) Homepage: https://github.com/reedacartwright/dawg Vcs Debian Med Packaging Team
903886	dawg: Test suite fails	upstream
dwgsim (1) Homepage: https://github.com/nh13/DWGSIM/ Vcs Debian Med Packaging Team
1096554	dwgsim: ftbfs with GCC-15	forky, sid
ea-utils (1) Homepage: https://expressionanalysis.github.io/ea-utils/ Vcs Debian Med Packaging Team
862118	ea-utils: New upstream version available
emboss (6) 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, sid, trixie
1069142	emboss: build time testsuite is failing silently
1096578	emboss: ftbfs with GCC-15	forky, sid
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	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	ftbfs, sid, trixie
fasta3 (1) Homepage: https://fasta.bioch.virginia.edu Vcs Debian Med Packaging Team
1096607	fasta3: ftbfs with GCC-15	forky, 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, sid
freecontact (1) Homepage: https://rostlab.org/ Vcs Debian Med Packaging Team
1096651	freecontact: ftbfs with GCC-15	forky, sid
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
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	ftbfs, sid, trixie
genometools (1) Homepage: http://genometools.org Vcs Debian Med Packaging Team
1105339	genometools: FTBFS with make --shuffle=reverse: ./obj/gt_config.h:1: error: unterminated #ifndef	ftbfs, sid, trixie
genomicsdb (2) Homepage: https://www.genomicsdb.org/ Vcs Debian Med Packaging Team
1092841	genomicsdb: FTBFS with fmtlib 11.1	ftbfs
1103009	genomicsdb: FTBFS in testing/arm64: tests failed	ftbfs, sid, trixie, upstream
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
ghemical (5) Homepage: http://bioinformatics.org/ghemical/ghemical/ Vcs Debichem Team
967392	ghemical: depends on deprecated GTK 2
967865	ghemical: depends on deprecated libglade2	sid, trixie
996006	ghemical: Segmentation fault when starting
1066986	ghemical: FTBFS: /usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/libghemical.so: undefined reference to `sc::RenderedBallMolecule::RenderedBallMolecule(sc::Ref<sc::KeyVal> const&)'	ftbfs, sid, trixie
1089786	ghemical: uninstallable since transition to openmpi version 5
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, sid
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
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 (2) Homepage: https://daehwankimlab.github.io/hisat2/ Vcs Debian Med Packaging Team
1048028	hisat2: Fails to build source after successful build	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	ftbfs, sid, trixie
iqtree (1) Homepage: http://www.cibiv.at/software/iqtree/ Vcs Debian Med Packaging Team
1096850	iqtree: ftbfs with GCC-15	forky, sid
jalview (1) Homepage: https://www.jalview.org Vcs Debian Java Maintainers
1104128	jalview: Update/add debconf template translation [INTL:ca]	l10n, patch
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	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	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
kineticstools (1) Homepage: https://github.com/PacificBiosciences/kineticsTools Vcs Debian Med Packaging Team
1103315	kineticstools: FTBFS with the nocheck build profile	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.	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
lastz (1) Homepage: https://github.com/lastz/lastz Vcs Debian Med Packaging Team
1097151	lastz: ftbfs with GCC-15	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	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	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
mafft (1) Homepage: https://mafft.cbrc.jp/alignment/software/ Vcs Debian Med Packaging Team
1097352	mafft: ftbfs with GCC-15	forky, sid
massxpert (2) Homepage: http://www.msxpertsuite.org/ Vcs The Debichem Group
1045227	massxpert: Fails to build source after successful build	ftbfs, sid, trixie
1084296	massxpert: FTBFS: rror: static assertion failed: No Q_OBJECT in the class passed to QObject::findChildren	ftbfs, sid, trixie
massxpert2 (1) Homepage: http://www.msxpertsuite.org/ Vcs The Debichem Group
1097365	massxpert2: ftbfs with GCC-15	forky, sid
megahit (1) Homepage: https://github.com/voutcn/megahit Vcs Debian Med Packaging Team
1088028	megahit: consider unembedding parallel-hashmap
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
microbegps (1) Homepage: http://sourceforge.net/projects/microbegps/ Vcs Debian Med Packaging Team
1035188	microbegps: please add autopkgtests (to add coverage for python3-numpy)
minexpert2 (1) Homepage: http://www.msxpertsuite.org/ Vcs The Debichem Group
1097402	minexpert2: ftbfs with GCC-15	forky, 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	ftbfs, sid, trixie
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	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
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	ftbfs, sid, trixie
nanopolish (1) Homepage: https://github.com/jts/nanopolish Vcs Debian Med Packaging Team
1097430	nanopolish: ftbfs with GCC-15	forky, 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 (2) Homepage: https://ncbi.github.io/igblast/ Vcs Debian Med Packaging Team
1048966	ncbi-igblast: Fails to build source after successful build	ftbfs, sid, trixie
1097435	ncbi-igblast: ftbfs with GCC-15	forky, sid
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, sid
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 (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	ftbfs, sid, trixie
openms (1) 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
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, 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	ftbfs, sid, trixie
phast (1) Homepage: http://compgen.cshl.edu/phast/ Vcs Debian Med Packaging Team
1097575	phast: ftbfs with GCC-15	forky, sid
phyml (1) Homepage: http://www.atgc-montpellier.fr/phyml Vcs Debian Med Packaging Team
1106652	phyml FTCBFS: cross compilation support reverted	patch, upstream
plast (2) Homepage: https://plast.inria.fr/ Vcs Debian Med Packaging Team
1047303	plast: Fails to build source after successful build	ftbfs, sid, trixie
1097619	plast: ftbfs with GCC-15	forky, sid
plink (1) Homepage: http://zzz.bwh.harvard.edu/plink/ Vcs Debian Med Packaging Team
1107047	plink: add libcrypt-dev to Build-Depends
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 (2) 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, sid
primer3 (1) Homepage: http://primer3.sourceforge.net Vcs Debian Med Packaging Team
1097649	primer3: ftbfs with GCC-15	forky, 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	ftbfs, sid, trixie
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	ftbfs, sid, trixie
psortb (2) Homepage: https://www.psort.org/ Vcs Debian Med Packaging Team
1048520	psortb: Fails to build source after successful build	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	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	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	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'	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, sid
rambo-k (1) Homepage: http://rambok.sourceforge.net/ Vcs Debian Med Packaging Team
1047092	rambo-k: Fails to build source after successful build	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, ftbfs, sid, trixie
1097770	rapmap: ftbfs with GCC-15	forky, sid
rasmol (1) Homepage: http://rasmol.org Vcs Debian Science Maintainers
1097771	rasmol: ftbfs with GCC-15	forky, sid
raster3d (2) Homepage: http://www.bmsc.washington.edu/raster3d/raster3d.html Vcs Debian Med Packaging Team
1097773	raster3d: ftbfs with GCC-15	forky, 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	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	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, 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, sid
relion (1) 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, sid
roguenarok (1) Homepage: https://github.com/aberer/RogueNaRok Vcs Debian Med Packaging Team
1097803	roguenarok: ftbfs with GCC-15	forky, 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	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, sid
1103327	salmon: FTBFS with the nocheck build profile	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	sid, trixie
1095434	sambamba: rare segmentation fault makes nanosv autopkgtest flaky
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
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
sim4 (1) Homepage: https://globin.bx.psu.edu/html/docs/sim4.html Vcs Debian Med Packaging Team
1097885	sim4: ftbfs with GCC-15	forky, sid
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, sid
soapdenovo (1) Homepage: http://soap.genomics.org.cn/soapdenovo.html Vcs Debian Med Packaging Team
1097907	soapdenovo: ftbfs with GCC-15	forky, sid
soapdenovo2 (2) Homepage: http://soap.genomics.org.cn/soapdenovo.html Vcs Debian Med Packaging Team
1097909	soapdenovo2: ftbfs with GCC-15	forky, sid
1105578	soapdenovo2: FTBFS with make --shuffle=reverse: ld: cannot find sparsePregraph/*.o: No such file or directory	ftbfs, sid, trixie
sortmerna (2) Homepage: https://github.com/sortmerna/sortmerna Vcs Debian Med Packaging Team
1072346	sortmerna: please update autopkgtest	newcomer
1097910	sortmerna: ftbfs with GCC-15	forky, sid
spades (3) 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, sid
spoa (1) Homepage: https://github.com/rvaser/spoa Vcs Debian Med Packaging Team
1097922	spoa: ftbfs with GCC-15	forky, sid
sra-sdk (1) Homepage: https://github.com/ncbi/sra-tools/ Vcs Debian Med Packaging Team
1106622	sra-sdk ftbfs with libxml 2.14.x from experimental	forky, ftbfs, patch, sid
staden (1) Homepage: https://sourceforge.net/projects/staden/ Vcs Debian Med Packaging Team
1097934	staden: ftbfs with GCC-15	forky, sid
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
sweed (1) Homepage: https://sco.h-its.org/exelixis/web/software/sweed/ Vcs Debian Med Packaging Team
1097956	sweed: ftbfs with GCC-15	forky, 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
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	ftbfs, sid, trixie
thesias (1) Homepage: https://github.com/daissi/thesias Vcs Debian Med Packaging Team
1097993	thesias: ftbfs with GCC-15	forky, sid
tnseq-transit (1) Homepage: http://saclab.tamu.edu/essentiality/transit/ Vcs Debian Med Packaging Team
1098008	tnseq-transit: ftbfs with GCC-15	forky, sid
toil (1) Homepage: https://github.com/BD2KGenomics/toil Vcs Debian Med Packaging Team
1108056	toil: FTBFS: Some tests fail on single-cpu systems	ftbfs, help, sid, trixie
tracetuner (1) Homepage: https://sourceforge.net/projects/tracetuner/ Vcs Debian Med Packaging Team
1098011	tracetuner: ftbfs with GCC-15	forky, 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 (1) Homepage: https://github.com/trinityrnaseq/trinityrnaseq Vcs Debian Med Packaging Team
981874	trinityrnaseq: flaky autopkgtest	bookworm, bullseye, sid, trixie
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
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'	ftbfs, sid, trixie
ugene (1) Homepage: https://ugene.unipro.ru Vcs Debian Med Packaging Team
1098031	ugene: ftbfs with GCC-15	forky, sid
umap-learn (3) 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
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	ftbfs, sid, trixie
vg (4) 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, ftbfs, sid, trixie
987184	vg -- excessive variants built, and not tested
1015699	vg: ftbfs with LTO (link time optimization) enabled	sid, trixie
1089275	vg: FTBFS with make 4.4.1	ftbfs, sid, trixie
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	ftbfs, sid, trixie
wise (1) Homepage: https://www.ebi.ac.uk/~birney/wise2/ Vcs Debian Med Packaging Team
1098098	wise: ftbfs with GCC-15	forky, sid
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	ftbfs, sid, trixie

Open bugs in suggested packages

12 serious, 24 important, 20 normal, 7 minor, 7 wishlist

arb (4) 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
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.
catfishq (1) Homepage: https://github.com/philres/catfishq Vcs Steffen Moeller
1085412	catfishq: Python SyntaxWarning
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 (29) 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	security, upstream
1103538	hdf5: CVE-2025-2913	security, upstream
1103539	hdf5: CVE-2025-2912	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	ftbfs, sid, trixie
1108155	hdf5: CVE-2025-6269	security, upstream
1108156	hdf5: CVE-2025-6270	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
intake (5) Homepage: https://github.com/intake/intake Vcs Debian Med Packaging Team
1063953	intake: autopkgtest regression with pytest 8
1064752	intake: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12 3.11" returned exit code 13	ftbfs, sid, trixie
1067969	python3-intake: Please replace python3-appdirs dependency with platformdirs	patch, pending, sid, trixie
1088416	intake: move from twitter-bootstrap{3,4} to bootstrap-html (v5)	upstream
1094915	intake commatibility with zarr3
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	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	ftbfs, sid, trixie
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	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	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	sid, trixie
q2-feature-classifier (1) Homepage: https://qiime2.org/ Vcs Debian Med Packaging Team
1071882	q2-feature-classifier: FTBFS: unsatisfiable build-dependencies	ftbfs
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	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'	ftbfs, sid, 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 (3) 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	ftbfs, sid, trixie
vienna-rna (1) Homepage: https://www.tbi.univie.ac.at/RNA/ Vcs Debian Med Packaging Team
1102852	vienna-rna: add perl-xs-dev to Build-Depends

Done bugs

beast-mcmc (1) Homepage: http://beast.bio.ed.ac.uk/ Vcs Debian Med Packaging Team
1103836	Depends on an EOLed version of libitext
cluster3 (1) Homepage: http://bonsai.hgc.jp/~mdehoon/software/cluster/ Vcs Debian Med Packaging Team
1092364	cluster3: needs rebuild for Python 3.13 as default	ftbfs
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
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
915807	hdf5: CVE-2017-17507	security, upstream
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
metaphlan (1) Homepage: https://github.com/biobakery/MetaPhlAn Vcs Debian Med Packaging Team
1035175	metaphlan: please add autopkgtests (to add coverage for python3-numpy)
ncbi-tools6 (1) Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/ Vcs Debian Med Packaging Team
1105544	ncbi-tools6: FTBFS with make --shuffle=reverse: mv: cannot stat 'algorend.o': No such file or directory	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, bullseye, sid, trixie
porechop (1) Homepage: https://rrwick.github.io/Porechop Vcs Debian Med Packaging Team
1085786	porechop: Python SyntaxWarning
pyranges (1) Homepage: https://github.com/biocore-ntnu/pyranges Vcs Debian Med Packaging Team
1104599	pyranges: FTBFS randomly: failing tests	ftbfs, sid, trixie
python-anndata (3) Homepage: https://github.com/theislab/anndata Vcs Debian Med Packaging Team
1075928	python-anndata: tests fail with scipy 1.13
1094924	python-anndata compatibility with zarr3	fixed-upstream, ftbfs, sid, trixie
1100261	python-anndata: FTBFS: E AttributeError: module 'zarr' has no attribute 'DirectoryStore'	fixed-upstream, ftbfs, sid, trixie
python-pyflow (2) 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
1081243	python3-pyflow: helloWorld and other examples not runnable, possibly since python2 dropped	upstream, wontfix
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
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

^*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