Summary

Bugs of task cloud

Total bugs: 67

Open bugs: 50

Fixed bugs: 17

Links to other tasks

Tasks overview

Biology 258 (2699)

Biology development 126 (1245)

Next generation sequencing 8 (150)

Phylogeny 9 (72)

Cloud 50 (714)

Content management 0 (0)

Covid-19 150 (1631)

Medical data 1 (1)

Dental 1 (3)

Epidemiology 13 (224)

Hospital information systems 1 (9)

Imaging 207 (1075)

Imaging development 82 (821)

Laboratory 1 (9)

Oncology 1 (3)

Pharmacology 1 (9)

Physics 29 (273)

Practice 6 (33)

Psychology 6 (46)

Rehabilitation 0 (0)

Research 0 (0)

Statistics 3 (7)

Tools 38 (243)

Typesetting 66 (529)

Legend

Severity	Dependent	Suggested
critical	0	0
grave	0	0
serious	16	0
important	8	0
normal	8	0
minor	14	0
wishlist	4	0

Summary bugs page of task Cloud

Immediately looking into bugs of the dependencies of this task is advised (714)^*

Open bugs in dependent packages

16 serious, 8 important, 8 normal, 14 minor, 4 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
altree (1) Homepage: https://gitlab.inria.fr/NGS/ALTree Vcs Debian Med Packaging Team
1067631	src:altree: autopkgtest timeouts on armel, armhf and ppc64el
ampliconnoise (1) Homepage: https://github.com/lanzen/ampliconnoise Vcs Debian Med Packaging Team
1077153	ampliconnoise FTBFS with gcc 14	ftbfs
anfo (2) Homepage: https://bioinf.eva.mpg.de/anfo/ Vcs Debian Med Packaging Team
1012893	anfo: ftbfs with GCC-12	help, bookworm, sid, ftbfs, trixie
1061888	anfo: NMU diff for 64-bit time_t transition	patch
arden (2) Homepage: http://sourceforge.net/projects/arden/ Vcs Debian Med Packaging Team
1035113	arden: please add autopkgtests (to add coverage for python3-numpy)
1036488	arden: please add autopkgtests (to add coverage for python3-matplotlib)
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'	upstream, ftbfs
concavity (1) Homepage: https://compbio.cs.princeton.edu/concavity/ Vcs Debian Med Packaging Team
1043837	concavity: Fails to build source after successful build	ftbfs, sid, trixie
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
1057439	datamash: "antimode" returns lowest, instead of least common, value
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
1069098	emboss: all executables segfault on s390x	bookworm, bullseye, sid, trixie
1069142	emboss: build time testsuite is failing silently
freecontact (2) Homepage: https://rostlab.org/ Vcs Debian Med Packaging Team
1049797	freecontact: Fails to build binary packages again after successful build	ftbfs, sid, trixie
1069552	freecontact: FTBFS on armel: make[1]: *** [Makefile:469: all-recursive] Error 1	ftbfs, sid, trixie
gromacs (2) Homepage: https://www.gromacs.org/ Vcs Debichem Team
644397	Provide runtime detection for CPU SIMD capabilities	upstream
983942	gromacs: ftbfs with -march=x86-64-v3
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
infernal (1) Homepage: http://eddylab.org/infernal/ Vcs Debian Med Packaging Team
1045517	infernal: Fails to build source after successful build	ftbfs, sid, trixie
jellyfish (1) 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
kissplice (2) Homepage: https://kissplice.prabi.fr/ Vcs Debian Med Packaging Team
1073482	kissplice: FTBFS: make[3]: *** [doc/CMakeFiles/doc.dir/build.make:78: doc/user_guide.pdf] Error 1	ftbfs, sid, trixie
1074658	kissplice: FTBFS: dh_auto_test: error: cd obj-x86_64-linux-gnu && make -j8 test ARGS\+=--verbose ARGS\+=-j8 returned exit code 2	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	ftbfs, sid, trixie
maq (1) Homepage: http://maq.sourceforge.net/ Vcs Debian Med Packaging Team
1075253	maq: ftbfs with GCC-14	sid, ftbfs, trixie
melting (1) Homepage: https://www.ebi.ac.uk/compneur-srv/melting/ Vcs Debian Med Packaging Team
1048833	melting: Fails to build source after successful build	ftbfs, sid, trixie
mlv-smile (1) Homepage: http://www-igm.univ-mlv.fr/~marsan/smile_english.html Vcs Debian Med Packaging Team
1066525	mlv-smile: FTBFS: src/allocateurs.c:45:39: error: implicit declaration of function âgetpagesizeâ [-Werror=implicit-function-declaration]	pending, trixie, ftbfs, sid
ncbi-blast+ (3) 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
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	ftbfs, confirmed, trixie, sid
plink2 (1) Homepage: https://www.cog-genomics.org/plink/2.0/ Vcs Debian Med Packaging Team
1048822	plink2: Fails to build source after successful build	ftbfs, sid, trixie
prime-phylo (1) Homepage: http://prime.sbc.su.se Vcs Debian Med Packaging Team
1075397	prime-phylo: ftbfs with GCC-14	sid, ftbfs, trixie
primer3 (1) Homepage: http://primer3.sourceforge.net Vcs Debian Med Packaging Team
1045454	primer3: Fails to build source after successful build	ftbfs, sid, trixie
python-cogent (1) Homepage: https://github.com/cogent3/cogent3 Vcs Debian Med Packaging Team
1058479	python-cogent: please (temporarily) drop python3-numba dependencies	wontfix
qiime (1) Homepage: https://qiime2.org Vcs Debian Med Packaging Team
1076314	qiime hard-codes python 3.11 without depending on it	sid, trixie
seqan2 (2) Homepage: https://www.seqan.de/ Vcs Debian Med Packaging Team
917851	seqan2 2.4.0+dfsg-9: FTBFS, alignment problem	ftbfs
1047218	seqan2: Fails to build source after successful build	ftbfs, sid, trixie
soapdenovo2 (1) Homepage: http://soap.genomics.org.cn/soapdenovo.html Vcs Debian Med Packaging Team
1075524	soapdenovo2: ftbfs with GCC-14	trixie, sid, ftbfs
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
tree-puzzle (2) Homepage: http://www.tree-puzzle.de Vcs Debian Med Packaging Team
1049170	tree-puzzle: Fails to build source after successful build	ftbfs, sid, trixie
1075584	tree-puzzle: ftbfs with GCC-14	ftbfs, sid, trixie
velvet (1) Homepage: https://github.com/dzerbino/velvet Vcs Debian Med Packaging Team
1075617	velvet: ftbfs with GCC-14	sid, ftbfs, trixie
wise (1) Homepage: https://www.ebi.ac.uk/~birney/wise2/ Vcs Debian Med Packaging Team
1075638	wise: ftbfs with GCC-14	trixie, sid, ftbfs

Open bugs in suggested packages

Done bugs

bamtools (1) Homepage: https://github.com/pezmaster31/bamtools/wiki Vcs Debian Med Packaging Team
1075990	bamtools corrupts output data on bigendian architectures	patch, upstream
dialign (1) Homepage: https://dialign.gobics.de/ Vcs Debian Med Packaging Team
1074909	dialign: ftbfs with GCC-14	trixie, sid
epcr (1) Homepage: https://www.ncbi.nlm.nih.gov/tools/epcr/ Vcs Debian Med Packaging Team
1076879	epcr: FTBFS: re-PCR_main.cpp:30:10: fatal error: epcr/defaults.h: No such file or directory	ftbfs
fastdnaml (1) Homepage: ftp://ftp.bio.indiana.edu/molbio/evolve/fastdnaml/fastDNAml.html Vcs Debian Med Packaging Team
1074947	fastdnaml: ftbfs with GCC-14	trixie, sid
hisat2 (1) Homepage: https://daehwankimlab.github.io/hisat2/ Vcs Debian Med Packaging Team
1074739	hisat2: FTBFS: make[1]: *** [debian/rules:39: override_dh_auto_build] Error 1	trixie, ftbfs, sid, experimental
ncbi-blast+ (3) Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/ Vcs Debian Med Packaging Team
891197	Please switch to pcre2	sid, trixie
1074316	ncbi-blast+: Please package version 2.13+ as needed by q2-feature-classifier
1075867	ncbi-blast+: FTBFS with MbedTLS 3.6	ftbfs
ncbi-tools6 (1) Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/ Vcs Debian Med Packaging Team
1075307	ncbi-tools6: ftbfs with GCC-14	trixie, sid, ftbfs
parsinsert (1) Homepage: http://sourceforge.net/projects/parsinsert/ Vcs Debian Med Packaging Team
964082	parsinsert fails it's tests when built with -O2	bookworm, trixie, sid, bullseye
python-cogent (2) Homepage: https://github.com/cogent3/cogent3 Vcs Debian Med Packaging Team
1030885	python-cogent: FTBFS (some tests require more than one CPU)	ftbfs, patch
1074562	python-cogent: binary-any FTBFS	ftbfs
qiime (1) Homepage: https://qiime2.org Vcs Debian Med Packaging Team
1068006	qiime: Please replace python3-appdirs dependency with platformdirs	sid, trixie
r-bioc-hilbertvis (1) Homepage: https://bioconductor.org/packages/HilbertVis Vcs Debian R Packages Maintainers
1071343	r-bioc-hilbertvis: FTBFS: make_wiggle_vector.c:16:17: error: format not a string literal and no format arguments	ftbfs
sra-sdk (2) Homepage: https://github.com/ncbi/sra-tools/ Vcs Debian Med Packaging Team
1040391	sra-toolkit: broken symlink: /usr/lib/debian-med/bin/kget -> ../../../bin/vdb-get
1065961	sra-sdk: Please drop dependencies on python3-distutils	ftbfs
ssake (1) Homepage: https://www.bcgsc.ca/platform/bioinfo/software/ssake Vcs Debian Med Packaging Team
1073105	ssake: replace to-be-removed markdown build-dependency	trixie, 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