Summary

Bugs of task cloud

Total bugs: 63

Open bugs: 46

Fixed bugs: 17

Links to other tasks

Tasks overview

Biology 287 (2532)

Biology development 136 (1184)

Next generation sequencing 8 (87)

Phylogeny 7 (54)

Cloud 46 (504)

Content management 0 (0)

Covid-19 180 (1800)

Medical data 2 (10)

Dental 2 (12)

Epidemiology 11 (102)

Hospital information systems 1 (9)

Imaging 198 (826)

Imaging development 79 (576)

Laboratory 1 (9)

Oncology 1 (3)

Pharmacology 1 (9)

Physics 27 (192)

Practice 8 (51)

Psychology 12 (121)

Rehabilitation 0 (0)

Research 0 (0)

Statistics 4 (16)

Tools 39 (240)

Typesetting 68 (543)

Legend

Severity	Dependent	Suggested
critical	0	0
grave	0	0
serious	6	0
important	11	0
normal	14	0
minor	11	0
wishlist	4	0

Summary bugs page of task Cloud

Immediately looking into bugs of the dependencies of this task is advised (504)^*

Open bugs in dependent packages

6 serious, 11 important, 14 normal, 11 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
anfo (2) Homepage: https://bioinf.eva.mpg.de/anfo/ Vcs Debian Med Packaging Team
1012893	anfo: ftbfs with GCC-12	bookworm, ftbfs, help, sid, trixie
1061888	anfo: NMU diff for 64-bit time_t transition	patch
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
bioperl-run (1) Homepage: https://metacpan.org/release/BioPerl-Run Vcs Debian Med Packaging Team
1077454	bioperl-run: FTBFS: dh_auto_test: error: /usr/bin/perl Build test --verbose 1 returned exit code 255	confirmed, ftbfs, sid, trixie, upstream
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
discosnp (1) Homepage: http://colibread.inria.fr/discosnp/ Vcs Debian Med Packaging Team
1085542	discosnp: Python SyntaxWarning
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
glam2 (1) Homepage: http://acb.qfab.org/acb/glam2/ Vcs Debian Med Packaging Team
1081315	glam2: homepage defunct
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
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
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]	ftbfs, pending, sid, trixie
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-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, ftbfs, sid, trixie
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
1078584	prime-phylo fails to build with mpi-defaults 1.17 on armhf	wontfix
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 (2) Homepage: https://qiime2.org Vcs Debian Med Packaging Team
1076314	qiime hard-codes python 3.11 without depending on it	sid, trixie
1084668	qiime: removal of Python standard libraries in Python 3.13
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
samtools (1) Homepage: https://www.htslib.org/ Vcs Debian Med Packaging Team
1087456	samtools: autopkgtest regression with htslib 1.21
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
sra-sdk (2) Homepage: https://github.com/ncbi/sra-tools/ Vcs Debian Med Packaging Team
1084404	sra-sdk: move from fuse to fuse3
1087096	sra-sdk: Python SyntaxWarning
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

Open bugs in suggested packages

Done bugs

arden (3) 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)
1085326	arden: Python SyntaxWarning
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
gromacs (1) Homepage: https://www.gromacs.org/ Vcs Debichem Team
1086272	gromacs: FTBFS with OpenMPI 5 on systems with less than 4 CPUs	ftbfs
htslib (3) Homepage: https://github.com/samtools/htslib Vcs Debian Med Packaging Team
1086364	metabat: FTBFS: Package 'bzip2', required by 'htslib', not found	ftbfs, sid, trixie
1086367	libhts-dev: Missing dependency on libbz2-dev	ftbfs
1086368	libhts-dev: Missing dependency on libbz2-dev	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, bullseye, sid, trixie
phyml (1) Homepage: http://www.atgc-montpellier.fr/phyml Vcs Debian Med Packaging Team
1086912	phyml: depends on openmpi on 32-bit architectures	sid, trixie
prime-phylo (1) Homepage: http://prime.sbc.su.se Vcs Debian Med Packaging Team
1086370	prime-phylo: FTBFS: fatal error: mpicxx.h: No such file or directory	ftbfs
python-biopython (1) Homepage: https://biopython.org Vcs Debian Med Packaging Team
1086156	ftbfs: test failure: DSSP failed to produce an output	ftbfs
sra-sdk (1) 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
tree-puzzle (4) Homepage: http://www.tree-puzzle.de Vcs Debian Med Packaging Team
1049170	tree-puzzle: Fails to build source after successful build	ftbfs, sid, trixie
1082806	tree-puzzle: please make the build reproducible	patch
1086203	src:tree-puzzle: fails to migrate to testing for too long	sid, trixie
1086907	tree-puzzle: depends on openmpi on 32-bit architectures

^*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