Summary

Bugs of task cloud

Total bugs: 59

Open bugs: 41

Fixed bugs: 18

Links to other tasks

Tasks overview

Biology 243 (2340)

Biology development 138 (1464)

Next generation sequencing 2 (18)

Phylogeny 10 (120)

Cloud 41 (455)

Content management 0 (0)

Covid-19 197 (2151)

Medical data 0 (0)

Dental 3 (21)

Epidemiology 21 (292)

Hospital information systems 0 (0)

Imaging 205 (879)

Imaging development 102 (1002)

Laboratory 1 (30)

Oncology 0 (0)

Pharmacology 1 (30)

Physics 27 (195)

Practice 8 (54)

Psychology 16 (150)

Rehabilitation 0 (0)

Research 0 (0)

Statistics 8 (12)

Tools 35 (230)

Typesetting 72 (599)

Legend

Severity	Dependent	Suggested
critical	0	0
grave	0	0
serious	6	1
important	12	2
normal	6	0
minor	7	0
wishlist	7	0

Summary bugs page of task Cloud

Immediately looking into bugs of the dependencies of this task is advised (455)^*

Open bugs in dependent packages

6 serious, 12 important, 6 normal, 7 minor, 7 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 (2) 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
1134595	control Homepage seems not existent
aevol (1) Homepage: https://www.aevol.fr/ Vcs Debian Med Packaging Team
1131937	aevol: autopkgtest failure in testing: workflow/wild_type: No such file or directory
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
cassiopee (1) Homepage: https://github.com/osallou/cassiopee-c Vcs Debian Med Packaging Team
1133438	cassiopee: ftbfs with GCC-16	forky, ftbfs, sid
datamash (1) Homepage: https://savannah.gnu.org/projects/datamash/ Vcs Debian Science Maintainers
1044977	datamash: Fails to build source after successful build	forky, ftbfs, sid, trixie
dssp (1) Homepage: https://github.com/PDB-REDO/dssp Vcs Debian Med Packaging Team
1045047	dssp: Fails to build source after successful build	ftbfs, sid, trixie
emboss (4) 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
1069142	emboss: build time testsuite is failing silently
1131851	emboss: consider namespecing binaries
freecontact (1) Homepage: https://rostlab.org/ Vcs Debian Med Packaging Team
1129505	freecontact build-depends on legacy GCC 14	forky, sid
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
hisat2 (1) Homepage: https://daehwankimlab.github.io/hisat2/ Vcs Debian Med Packaging Team
1076524	hisat2: autopkgtest uses absurd amount of memory on s390x
hmmer (1) Homepage: http://hmmer.org/ Vcs Debian Med Packaging Team
1120150	hmmer: Ship easel miniapps instead of easel source code.
htslib (1) Homepage: https://github.com/samtools/htslib Vcs Debian Med Packaging Team
1131493	htslib: CVE-2026-31962 CVE-2026-31963 CVE-2026-31964 CVE-2026-31965 CVE-2026-31966 CVE-2026-31967 CVE-2026-31968 CVE-2026-31969 CVE-2026-31970 CVE-2026-31971	security, upstream
idba (1) Homepage: https://github.com/loneknightpy/idba Vcs Debian Med Packaging Team
1133503	idba: ftbfs with GCC-16	forky, ftbfs, sid
jellyfish (2) 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
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
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
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
ncbi-tools6 (2) Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/ Vcs Debian Med Packaging Team
225651	ncbi-tools-x11: want Cn3D++
1117994	vecscreen: UniVec is not packaged, UniVec_Core should be default + default path issue
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
prime-phylo (1) 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
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
python-biopython (3) Homepage: https://biopython.org Vcs Debian Med Packaging Team
1123673	python-biopython: CVE-2025-68463	fixed-upstream, security, upstream
1131072	python-biopython: autopkgtest regression with NumPy 2.4
1135451	python-biopython: FTBFS: build finished with problems, 6 warnings (with warnings treated as errors).	forky, ftbfs, sid
python-cogent (3) 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
1123705	Should python-cogent be removed from unstable?	wontfix
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
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	forky, ftbfs, sid, trixie

Open bugs in suggested packages

1 serious, 2 important

cufflinks (3) 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
1127186	cufflinks: libboost-system-dev package is obsolete with boost 1.89 and newer	forky, pending, sid

Done bugs

bedtools (1) Homepage: https://github.com/arq5x/bedtools2 Vcs Debian Med Packaging Team
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
bioperl-run (1) Homepage: https://metacpan.org/release/BioPerl-Run Vcs Debian Med Packaging Team
1133180	src:bioperl-run: fails to migrate to testing for too long	forky, sid
emboss (1) Homepage: https://emboss.sourceforge.net Vcs Debian Med Packaging Team
1069098	emboss: all executables segfault on s390x	bookworm, bullseye, forky, pending, sid, trixie
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
flexbar (1) Homepage: https://github.com/seqan/flexbar Vcs Debian Med Packaging Team
1125731	flexbar: FTBFS: /<<PKGBUILDDIR>>/src/FlexbarTypes.h:96:17: error: 'seqan' does not name a type	forky, ftbfs, sid
jellyfish (1) Homepage: https://www.genome.umd.edu/jellyfish.html Vcs Debian Med Packaging Team
1133507	jellyfish: ftbfs with GCC-16	forky, ftbfs, sid
kalign (1) Homepage: https://msa.sbc.su.se/ Vcs Debian Med Packaging Team
1132348	src:kalign: fails to migrate to testing for too long	forky, 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
macs (1) Homepage: https://github.com/taoliu/MACS/ Vcs Debian Med Packaging Team
1047612	macs: Fails to build source after successful build	ftbfs, sid, trixie
mapsembler2 (1) Homepage: http://colibread.inria.fr/mapsembler2/ Vcs Debian Med Packaging Team
1125550	mapsembler2: FTBFS with CMake 4.2	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
mira (1) Homepage: https://sourceforge.net/p/mira-assembler/wiki/Home/ Vcs Debian Med Packaging Team
1045311	mira: Fails to build source after successful build	ftbfs, sid, trixie
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
r-cran-vegan (1) Homepage: https://cran.r-project.org/package=vegan Vcs Debian R Packages Maintainers
1134233	src:r-cran-vegan: fails to migrate to testing for too long	forky, sid
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, patch, sid, trixie
theseus (1) Homepage: http://www.theseus3d.org Vcs Debian Med Packaging Team
1133649	theseus: ftbfs with GCC-16	forky, ftbfs, sid
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

^*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