Debian Med Project
Help us to see Debian used by medical practitioners and biomedical researchers! Join us on the Salsa page.
Summary
Bugs of task cloud
Total bugs: 56
Open bugs: 27
Fixed bugs: 29
Links to other tasks
Tasks overview
Biology 179 (1609)
Phylogeny 7 (30)
Cloud 27 (215)
Covid-19 172 (1662)
Medical data 0 (0)
Dental 2 (18)
Epidemiology 16 (193)
Imaging 200 (889)
Laboratory 0 (0)
Oncology 0 (0)
Pharmacology 1 (30)
Physics 26 (180)
Practice 7 (60)
Psychology 14 (89)
Research 0 (0)
Statistics 8 (12)
Tools 35 (242)
Typesetting 71 (612)
Legend
SeverityDependentSuggested
critical 0 0
grave 0 0
serious 2 0
important 5 1
normal 6 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 (215)*

Open bugs in dependent packages

2 serious, 5 important, 6 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
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
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
1069142 emboss: build time testsuite is failing silently
1131851 emboss: consider namespecing binaries
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.
htslib (1) Homepage: https://github.com/samtools/htslib Vcs Debian Med Packaging Team
1131493 htslib: CVE-2026-31962 CVE-2026-31963 CVE-2026-31964 CVE-2026-31965 CVE-2026-31966 CVE-2026-31967 CVE-2026-31968 CVE-2026-31969 CVE-2026-31970 CVE-2026-31971 security, upstream
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
mapsembler2 (1) Homepage: http://colibread.inria.fr/mapsembler2/ Vcs Debian Med Packaging Team
1145433 Add loong64 support for mapsembler2 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
1147220 python-biopython-doc prevents python3-biopython from upgrading
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 important
cufflinks (1) Homepage: https://cufflinks.cbcb.umd.edu Vcs Debian Med Packaging Team
1110578 cufflinks ftbfs with boost1.88 forky, sid

Done bugs

acedb (3) Homepage: https://www.sanger.ac.uk/tool/acedb/ 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
1134595 control Homepage seems not existent
1147991 Should acedb be removed from unstable? moreinfo
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
cufflinks (2) Homepage: https://cufflinks.cbcb.umd.edu Vcs Debian Med Packaging Team
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, sid
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
embassy-domainatrix (1) Homepage: https://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMAINATRIX Vcs Debian Med Packaging Team
1137443 embassy-domainatrix: Please drop dependencies on virtual packages from mysql-defaults
embassy-domalign (1) Homepage: https://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMALIGN Vcs Debian Med Packaging Team
1137457 embassy-domalign: Please drop dependencies on virtual packages from mysql-defaults
embassy-domsearch (1) Homepage: https://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMSEARCH Vcs Debian Med Packaging Team
1137455 embassy-domsearch: Please drop dependencies on virtual packages from mysql-defaults
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
freecontact (3) Homepage: https://rostlab.org/ Vcs Debian Med Packaging Team
1143654 freecontact: FTBFS: BioXSD-1.1_xsd.hxx:9342:5: error: expected unqualified-id before 'concept' forky, ftbfs, sid
1144302 freecontact: non-standard gcc/g++ used for build (gcc-15) forky, sid
1146616 freecontact: FTBFS: devlibs error: There is no package matching [libgfortran-15-dev] and noone provides it ftbfs
htslib (1) Homepage: https://github.com/samtools/htslib Vcs Debian Med Packaging Team
1148751 htslib 1.24-2: dpkg-gensymbols failure on 12 arches – missing (arch=...) qualifier sid
jellyfish (2) Homepage: https://www.genome.umd.edu/jellyfish.html Vcs Debian Med Packaging Team
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
1148450 jellyfish: FTBFS against python 3.15rc2 forky, ftbfs, patch, 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
1047612 macs: 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 forky, ftbfs, sid, trixie
mira (1) 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
mrbayes (1) Homepage: http://mrbayes.csit.fsu.edu/ Vcs Debian Med Packaging Team
1143178 mrbayes-mpi: Spawns instances of regular mb instead of running one parallel instance
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
probabel (1) Homepage: http://www.genabel.org Vcs Debian Med Packaging Team
1143692 probabel: FTBFS: phedata.cpp:83:28: error: no match for 'operator>>' (operand types are 'std::stringstream' {aka 'std::__cxx11::basic_stringstream<char>'} and 'char*') forky, ftbfs, 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 (1) Homepage: https://github.com/ncbi/sra-tools/ Vcs Debian Med Packaging Team
1144917 sra-sdk: autopkgtest regression: Segmentation fault
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: Wed, 30 Sep 2026 16:04:07 -0000