Summary

Bugs of task cloud

Total bugs: 88

Open bugs: 74

Fixed bugs: 14

Links to other tasks

Tasks overview

Biology 372 (4153)

Biology development 170 (1800)

Next generation sequencing 5 (22)

Phylogeny 18 (222)

Cloud 74 (987)

Content management 0 (0)

Covid-19 222 (2436)

Medical data 0 (0)

Dental 1 (3)

Epidemiology 20 (234)

Hospital information systems 3 (48)

Imaging 224 (1142)

Imaging development 94 (822)

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	17	1
important	20	1
normal	12	0
minor	18	0
wishlist	5	0

Summary bugs page of task Cloud

Immediately looking into bugs of the dependencies of this task is advised (987)^*

Open bugs in dependent packages

17 serious, 20 important, 12 normal, 18 minor, 5 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
autodock-vina (1) Homepage: https://vina.scripps.edu Vcs Debian Med Packaging Team
1110595	autodock-vina ftbfs with boost1.88	forky, sid
bamtools (1) Homepage: https://github.com/pezmaster31/bamtools/wiki Vcs Debian Med Packaging Team
1112718	bamtools: FTBFS with CMake 4	forky, ftbfs, sid
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
cassiopee (1) Homepage: https://github.com/osallou/cassiopee-c Vcs Debian Med Packaging Team
1112764	cassiopee: FTBFS with CMake 4	forky, ftbfs, sid
coils (1) Homepage: http://www.russelllab.org/coils/ Vcs Debian Med Packaging Team
1096450	coils: ftbfs with GCC-15	forky, ftbfs, sid
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
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
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
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
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
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
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
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
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
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
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
mapsembler2 (1) Homepage: http://colibread.inria.fr/mapsembler2/ Vcs Debian Med Packaging Team
1113267	mapsembler2: 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
minia (1) Homepage: http://minia.genouest.org/ Vcs Debian Med Packaging Team
1113290	minia: FTBFS with CMake 4	forky, ftbfs, sid
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 (1) Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/ Vcs Debian Med Packaging Team
225651	ncbi-tools-x11: want Cn3D++
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
phyml (1) Homepage: http://www.atgc-montpellier.fr/phyml Vcs Debian Med Packaging Team
1106652	phyml FTCBFS: cross compilation support reverted	patch, upstream
plink (1) Homepage: http://zzz.bwh.harvard.edu/plink/ Vcs Debian Med Packaging Team
1107047	plink: add libcrypt-dev to Build-Depends
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
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
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
r-cran-pvclust (1) Homepage: http://www.is.titech.ac.jp/~shimo/prog/pvclust/ Vcs Debian R Packages Maintainers
1081769	r-cran-pvclust: homepage defunct
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
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
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
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
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
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
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
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

Open bugs in suggested packages

1 serious, 1 important

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

Done bugs

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
bioperl (1) Homepage: http://www.bioperl.org/ Vcs Debian Med Packaging Team
1113735	libbio-perl-perl: warns with Perl 5.42: Possible precedence problem between ! and numeric eq (==)	forky, 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
htslib (1) Homepage: https://github.com/samtools/htslib Vcs Debian Med Packaging Team
1111788	htslib: autopkgtest regression
mafft (1) Homepage: https://mafft.cbrc.jp/alignment/software/ Vcs Debian Med Packaging Team
1097352	mafft: ftbfs with GCC-15	forky, ftbfs, 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
probcons (1) Homepage: http://probcons.stanford.edu/ Vcs Debian Med Packaging Team
1111708	probcons: Uses deprecated BSD file reference	patch
python-biopython (2) Homepage: https://biopython.org Vcs Debian Med Packaging Team
1103472	python-biopython: FTBFS with the nocheck build profile	forky, ftbfs, sid, trixie
1114298	python-biopython: FTBFS: dh_auto_test: error: pybuild --test -i python{version} -p 3.13 --test --system=custom "--test-args= \\	forky, ftbfs, patch, sid, upstream
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