Debian Med Project
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Summary
Bugs of task cloud
Total bugs: 55
Open bugs: 35
Fixed bugs: 20
Links to other tasks
Tasks overview
Biology 223 (1893)
Biology development 137 (1521)
Phylogeny 10 (99)
Cloud 35 (342)
Covid-19 205 (2308)
Medical data 0 (0)
Dental 3 (21)
Epidemiology 30 (408)
Imaging 210 (936)
Laboratory 1 (30)
Oncology 0 (0)
Pharmacology 1 (15)
Physics 28 (270)
Practice 7 (45)
Psychology 16 (144)
Research 0 (0)
Statistics 8 (12)
Tools 36 (240)
Typesetting 73 (629)
Legend
SeverityDependentSuggested
critical 0 0
grave 0 0
serious 4 1
important 8 1
normal 7 0
minor 8 0
wishlist 6 0

Summary bugs page of task Cloud

Immediately looking into bugs of the dependencies of this task is advised (342)*

Open bugs in dependent packages

4 serious, 8 important, 7 normal, 8 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] 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
autodock-vina (1) Homepage: https://vina.scripps.edu Vcs Debian Med Packaging Team
1110595 autodock-vina ftbfs with boost1.88 forky, sid
biosquid (1) Homepage: http://eddylab.org/software.html Vcs Debian-Med Packaging Team
1120351 biosquid: please make the build reproducible patch
datamash (1) Homepage: https://savannah.gnu.org/projects/datamash/ Vcs Debian Science Maintainers
1044977 datamash: Fails to build source after successful build forky, ftbfs, sid, trixie
emboss (3) 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
1069142 emboss: build time testsuite is failing silently
gmap (1) Homepage: http://research-pub.gene.com/gmap Vcs Debian Med Packaging Team
1107772 gmap inlining failed in call to ‘always_inline’ ‘_mm_alignr_epi8’: 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
hisat2 (1) Homepage: https://daehwankimlab.github.io/hisat2/ Vcs Debian Med Packaging Team
1076524 hisat2: autopkgtest uses absurd amount of memory on s390x
hmmer (1) Homepage: http://hmmer.org/ Vcs Debian Med Packaging Team
1120150 hmmer: Ship easel miniapps instead of easel source code.
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
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
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 (2) Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/ Vcs Debian Med Packaging Team
225651 ncbi-tools-x11: want Cn3D++
1117994 vecscreen: UniVec is not packaged, UniVec_Core should be default + default path issue
parsinsert (2) 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
1119520 parsinsert: please build using the default build flags wontfix
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
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-biopython (1) Homepage: https://biopython.org Vcs Debian Med Packaging Team
1123673 python-biopython: CVE-2025-68463 security, upstream
python-cogent (3) 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
1123705 Should python-cogent be removed from unstable? wontfix
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
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
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

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
datamash (1) Homepage: https://savannah.gnu.org/projects/datamash/ Vcs Debian Science Maintainers
1123967 datamash: Missing comma separator in Uploaders field
dnaclust (1) Homepage: https://dnaclust.sourceforge.net/ Vcs Debian Med Packaging Team
1110576 dnaclust ftbfs with boost1.88 forky, sid
emboss (1) Homepage: https://emboss.sourceforge.net Vcs Debian Med Packaging Team
1069098 emboss: all executables segfault on s390x bookworm, bullseye, forky, pending, sid, trixie
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
genometools (1) 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
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
macs (1) Homepage: https://github.com/taoliu/MACS/ Vcs Debian Med Packaging Team
1120217 macs: FTBFS: NameError: name 'long' is not defined 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
ncbi-tools6 (1) Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/ Vcs Debian Med Packaging Team
1123553 ncbi-tools6: autopktest failure on amd64 with libc6 2.42-6 due to unspecified return value patch
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
1106652 phyml FTCBFS: cross compilation support reverted patch, upstream
r-cran-pvclust (1) Homepage: https://cran.r-project.org/package=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
1119545 raster3d: please build using the default build flags
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, patch, sid, trixie
soapdenovo2 (1) Homepage: http://soap.genomics.org.cn/soapdenovo.html Vcs Debian Med Packaging Team
1105578 soapdenovo2: FTBFS with make --shuffle=reverse: ld: cannot find sparsePregraph/*.o: No such file or directory forky, ftbfs, sid
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
*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, 01 Jan 2026 03:56:44 -0000