Debian Med Project
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Summary
Bugs of task cloud
Total bugs: 59
Open bugs: 37
Fixed bugs: 22
Links to other tasks
Tasks overview
Biology 234 (2158)
Biology development 133 (1371)
Phylogeny 9 (90)
Cloud 37 (413)
Covid-19 194 (2091)
Medical data 1 (3)
Dental 3 (21)
Epidemiology 20 (277)
Imaging 201 (816)
Laboratory 1 (30)
Oncology 0 (0)
Pharmacology 1 (30)
Physics 32 (309)
Practice 8 (54)
Psychology 16 (159)
Research 0 (0)
Statistics 8 (12)
Tools 37 (236)
Typesetting 73 (629)
Legend
SeverityDependentSuggested
critical 0 0
grave 0 0
serious 6 1
important 8 2
normal 8 0
minor 7 0
wishlist 5 0

Summary bugs page of task Cloud

Immediately looking into bugs of the dependencies of this task is advised (413)*

Open bugs in dependent packages

6 serious, 8 important, 8 normal, 7 minor, 5 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
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
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 (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
flexbar (1) Homepage: https://github.com/seqan/flexbar Vcs Debian Med Packaging Team
1125731 flexbar: FTBFS: /<<PKGBUILDDIR>>/src/FlexbarTypes.h:96:17: error: 'seqan' does not name a type forky, ftbfs, sid
freecontact (1) Homepage: https://rostlab.org/ Vcs Debian Med Packaging Team
1129505 freecontact build-depends on legacy GCC 14 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 (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
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
1047612 macs: Fails to build source after successful build ftbfs, sid, trixie
mapsembler2 (1) Homepage: http://colibread.inria.fr/mapsembler2/ Vcs Debian Med Packaging Team
1125550 mapsembler2: FTBFS with CMake 4.2 forky, ftbfs, sid
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 (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, forky, 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
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 fixed-upstream, 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

Open bugs in suggested packages

1 serious, 2 important
cufflinks (3) 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
1127186 cufflinks: libboost-system-dev package is obsolete with boost 1.89 and newer forky, pending, sid

Done bugs

aevol (4) Homepage: https://www.aevol.fr/ Vcs Debian Med Packaging Team
1127160 aevol: libboost-system-dev package is obsolete with boost 1.89 and newer forky, sid
1128075 aevol: FTBFS with boost 1.90 forky, ftbfs, sid
1128076 aevol: FTBFS with boost 1.90 forky, ftbfs, sid
1128077 aevol: FTBFS with boost 1.90 forky, ftbfs, sid
autodock-vina (1) Homepage: https://vina.scripps.edu Vcs Debian Med Packaging Team
1128110 autodock-vina: FTBFS with boost 1.90 forky, ftbfs, sid
bedtools (1) Homepage: https://github.com/arq5x/bedtools2 Vcs Debian Med Packaging Team
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
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
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
kalign (1) Homepage: https://msa.sbc.su.se/ Vcs Debian Med Packaging Team
1127766 kalign: autopkgtest failure with glibc 2.43 due to out of bounds access upstream
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
mira (2) Homepage: https://sourceforge.net/p/mira-assembler/wiki/Home/ Vcs Debian Med Packaging Team
1045311 mira: Fails to build source after successful build ftbfs, sid, trixie
1127240 mira: libboost-system-dev package is obsolete with boost 1.89 and newer forky, sid
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 (2) Homepage: http://www.atgc-montpellier.fr/phyml Vcs Debian Med Packaging Team
1106652 phyml FTCBFS: cross compilation support reverted patch, upstream
1124953 src:phyml: fails to migrate to testing for too long forky, sid
raster3d (1) Homepage: http://www.bmsc.washington.edu/raster3d/raster3d.html Vcs Debian Med Packaging Team
1127473 raster3d: Fails to build source after successful build forky, ftbfs, patch, 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 forky, ftbfs, patch, sid, trixie
sra-sdk (2) Homepage: https://github.com/ncbi/sra-tools/ Vcs Debian Med Packaging Team
1126172 sra-sdk ftbfs with abseil 20260107 forky, ftbfs, sid
1128753 sra-sdk: FTBFS with glibc 2.43 due to ISO C23 const return types ftbfs, upstream
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
*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: Tue, 03 Mar 2026 03:58:07 -0000