Debian Med Project
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Summary
Bugs of task cloud
Total bugs: 70
Open bugs: 62
Fixed bugs: 8
Links to other tasks
Tasks overview
Biology 262 (2672)
Phylogeny 11 (153)
Cloud 62 (783)
Covid-19 175 (1703)
Medical data 0 (0)
Dental 2 (12)
Epidemiology 9 (57)
Imaging 205 (869)
Laboratory 1 (9)
Oncology 1 (3)
Pharmacology 1 (9)
Physics 28 (207)
Practice 6 (45)
Psychology 12 (133)
Research 0 (0)
Statistics 4 (16)
Tools 37 (257)
Typesetting 75 (570)
Legend
SeverityDependentSuggested
critical 0 0
grave 0 0
serious 7 0
important 29 0
normal 13 0
minor 7 0
wishlist 6 0

Summary bugs page of task Cloud

Immediately looking into bugs of the dependencies of this task is advised (783)*

Open bugs in dependent packages

7 serious, 29 important, 13 normal, 7 minor, 6 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 (2) Homepage: https://gitlab.inria.fr/NGS/ALTree Vcs Debian Med Packaging Team
1067631 src:altree: autopkgtest timeouts on armel, armhf and ppc64el
1096300 altree: ftbfs with GCC-15 forky, sid
ampliconnoise (1) Homepage: https://github.com/lanzen/ampliconnoise Vcs Debian Med Packaging Team
1096305 ampliconnoise: ftbfs with GCC-15 forky, sid
anfo (3) 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
1099985 Should anfo be removed from unstable?
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
coils (1) Homepage: http://www.russelllab.org/coils/ Vcs Debian Med Packaging Team
1096450 coils: ftbfs with GCC-15 forky, sid
datamash (4) 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
1096504 datamash: ftbfs with GCC-15 forky, 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, sid, trixie
1069142 emboss: build time testsuite is failing silently
1096578 emboss: ftbfs with GCC-15 forky, sid
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, sid
freecontact (1) Homepage: https://rostlab.org/ Vcs Debian Med Packaging Team
1096651 freecontact: ftbfs with GCC-15 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 (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
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
mafft (1) Homepage: https://mafft.cbrc.jp/alignment/software/ Vcs Debian Med Packaging Team
1097352 mafft: ftbfs with GCC-15 forky, 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 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] pending, trixie, ftbfs, sid
ncbi-blast+ (7) 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
1097434 ncbi-blast+: ftbfs with GCC-15 forky, sid
1100037 ncbi-blast+: missing commands (blastn_vdb, etc.)
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
prime-phylo (2) 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, sid
primer3 (1) Homepage: http://primer3.sourceforge.net Vcs Debian Med Packaging Team
1097649 primer3: ftbfs with GCC-15 forky, 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 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 sid, trixie, pending
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 (1) Homepage: http://www.bmsc.washington.edu/raster3d/raster3d.html Vcs Debian Med Packaging Team
1097773 raster3d: ftbfs with GCC-15 forky, sid
readseq (1) Homepage: http://iubio.bio.indiana.edu/soft/molbio/readseq/ Vcs Debian Med Packaging Team
1097779 readseq: ftbfs with GCC-15 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 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, sid
soapdenovo (1) Homepage: http://soap.genomics.org.cn/soapdenovo.html Vcs Debian Med Packaging Team
1097907 soapdenovo: ftbfs with GCC-15 forky, sid
soapdenovo2 (1) Homepage: http://soap.genomics.org.cn/soapdenovo.html Vcs Debian Med Packaging Team
1097909 soapdenovo2: ftbfs with GCC-15 forky, sid
sra-sdk (4) 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 patch, pending
1097930 sra-sdk: ftbfs with GCC-15 forky, sid
1099933 autopkgtest requires internet and ca-certificates patch
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
veryfasttree (1) Homepage: https://github.com/citiususc/veryfasttree Vcs Debian Med Packaging Team
1098063 veryfasttree: ftbfs with GCC-15 forky, sid
wise (1) Homepage: https://www.ebi.ac.uk/~birney/wise2/ Vcs Debian Med Packaging Team
1098098 wise: ftbfs with GCC-15 forky, sid

Open bugs in suggested packages

Done bugs

fastdnaml (1) Homepage: https://www.life.illinois.edu/gary/programs/fastDNAml.html Vcs Debian Med Packaging Team
1096609 fastdnaml: ftbfs with GCC-15 sid, forky
gmap (1) Homepage: http://research-pub.gene.com/gmap Vcs Debian Med Packaging Team
1096727 gmap: ftbfs with GCC-15 forky, patch, sid
last-align (1) Homepage: https://gitlab.com/mcfrith/last Vcs Debian Med Packaging Team
1098290 src:last-align: fails to migrate to testing for too long 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, trixie, sid, bullseye
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 sid, ftbfs, trixie
poa (1) Homepage: http://poamsa.sourceforge.net/ Vcs Debian Med Packaging Team
1097626 poa: ftbfs with GCC-15 forky, sid
r-cran-vegan (1) Homepage: https://cran.r-project.org/package=vegan Vcs Debian R Packages Maintainers
1099926 src:r-cran-vegan: fails to migrate to testing for too long sid, trixie
sra-sdk (1) Homepage: https://github.com/ncbi/sra-tools/ Vcs Debian Med Packaging Team
1099911 sra-sdk: FTBFS: Missing Build-Depends on python3-setuptools ftbfs, patch
*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: Thu, 13 Mar 2025 04:52:21 -0000