Debian Med Project
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Summary
Bugs of task cloud
Total bugs: 62
Open bugs: 47
Fixed bugs: 15
Links to other tasks
Tasks overview
Biology 287 (2555)
Biology development 134 (1144)
Phylogeny 7 (54)
Cloud 47 (543)
Covid-19 178 (1743)
Medical data 2 (10)
Dental 2 (12)
Epidemiology 11 (102)
Imaging 197 (791)
Laboratory 1 (9)
Oncology 1 (3)
Pharmacology 1 (9)
Physics 27 (192)
Practice 8 (51)
Psychology 12 (136)
Research 0 (0)
Statistics 4 (16)
Tools 39 (240)
Typesetting 68 (534)
Legend
SeverityDependentSuggested
critical 0 0
grave 0 0
serious 8 0
important 9 0
normal 15 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 (543)*

Open bugs in dependent packages

8 serious, 9 important, 15 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 ‘add_history’ [-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
1087997 ampliconnoise: build-deps on libopenmpi-dev, which is no longer available on 32-bit arches
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 (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
1087589 FTBFS on ppc64el: [ FAILED ] CooperativePool/CooperativePoolTest.Ints/3, where GetParam() = 4 ftbfs
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 ‘getpagesize’ [-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
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

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
samtools (1) Homepage: https://www.htslib.org/ Vcs Debian Med Packaging Team
1087456 samtools: autopkgtest regression with htslib 1.21
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:
critical10
grave10
serious10
important5
normal3
minor1
wishlist0
Last update: Sat, 23 Nov 2024 18:19:10 -0000