Debian Med Project
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Bugs of task bio-dev
Total bugs: 89
Open bugs: 79
Fixed bugs: 10
Links to other tasks
Biology 167 (1428)
Phylogeny 3 (21)
Cloud 37 (315)
Covid-19 134 (1151)
Medical data 1 (3)
Dental 0 (0)
Epidemiology 3 (18)
Imaging 231 (1075)
Laboratory 1 (9)
Oncology 3 (48)
Pharmacology 1 (9)
Physics 25 (180)
Practice 3 (27)
Psychology 7 (65)
Research 0 (0)
Statistics 0 (0)
Tools 33 (218)
Typesetting 67 (538)
critical 0 0
grave 0 0
serious 1 0
important 7 2
normal 45 3
minor 4 0
wishlist 16 1

Summary bugs page of task Biology development

Immediately looking into bugs of the dependencies of this task is advised (571)*

Open bugs in dependent packages

1 serious, 7 important, 45 normal, 4 minor, 16 wishlist
865130 reapr FTBFS on big endian: Error sampling from files '00.Sample/fragCov.gz', '00.assembly.fa.gc.gz' ftbfs, upstream
983981 bamtools: ftbfs with GCC-11 bookworm, sid
749736 biococoa: GCC warnings that may lead to runtime issues with new GNUstep libraries bullseye, buster, jessie, sid, stretch
659824 biojava-live: New version available
950914 python3-biomaj3: Depends on python-influxdb wich ftbs, patch to remove dependency
505226 Please package jchempaint
929564 gatb-core-testdata: broken symlink: /usr/share/doc/gatb-core/test/gatb-core-cppunit -> ../../../../lib/gatb-core/gatb-core-cppunit
983926 gatb-core: ftbfs with -march=x86-64-v2
984145 gatb-core: ftbfs with GCC-11 bookworm, sid
638753 libhdf5-serial-1.8.7: threadsafe memory leaks moreinfo
715959 [Mayhem] Bug report on hdf5-tools: gif2h5 crashes with exit status 139
716008 [Mayhem] Bug report on hdf5-tools: h5copy crashes with exit status 139
716010 [Mayhem] Bug report on hdf5-tools: h5diff crashes with exit status 139
716011 [Mayhem] Bug report on hdf5-tools: h5dump crashes with exit status 139
716012 [Mayhem] Bug report on hdf5-tools: h5import crashes with exit status 139
740613 libhdf5-7: Please include support for compression with libaec
748587 Duplicate and conflicting definitions of variable FILENAME upstream
839784 libhdf5-dev: pkg-config file references ONLY the C library
915807 hdf5: CVE-2017-17507 security, upstream
958174 hdf5: please add the hdf5plugins
968559 libhdf5-openmpi-dev: hdf5-mpi.pc alternative sometimes goes missing moreinfo
972537 please add --enable-ros3-vfd to the build options to allow RO access to HDF5 on S3
973261 libhdf5-openmpi-dev: installing requires /proc being mounted
877590 FTBFS: error: package org.testng does not exist bullseye, buster, sid
920588 htsjdk: Autopkgtest for htsjdk
978835 htslib: ftbfs with autoconf 2.70 bookworm, sid
948463 libai-fann-perl: Integer overflow leading to heap buffer overflow
963866 libbio-cluster-perl: circular dependency hell
599961 libbio-scf-perl: FTBFS: Neither BIG nor LITTLE endian defined
984086 libbpp-core: ftbfs with GCC-11 bookworm, pending, sid
984089 libbpp-phyl: ftbfs with GCC-11 bookworm, sid
984091 libbpp-popgen: ftbfs with GCC-11 bookworm, sid
984088 libbpp-qt: ftbfs with GCC-11 bookworm, sid
984090 libbpp-raa: ftbfs with GCC-11 bookworm, sid
984094 libbpp-seq: ftbfs with GCC-11 bookworm, sid
984092 libbpp-seq-omics: ftbfs with GCC-11 bookworm, sid
982333 libcifpp: [INTL:pt] Portuguese translation - debconf messages l10n, patch
984093 libcifpp: ftbfs with GCC-11 bookworm, sid
984103 libedlib: ftbfs with GCC-11 bookworm, sid
984104 libfastahack: ftbfs with GCC-11 bookworm, sid
984106 libgenome: ftbfs with GCC-11 bookworm, sid
984188 libncl: ftbfs with GCC-11 bookworm, sid
984200 libpdb-redo: ftbfs with GCC-11 bookworm, sid
982054 librdp-taxonomy-tree-java: FTBFS with OpenJDK 17 due to javadoc errors bookworm, ftbfs, sid
832138 librostlab-blast: The package should compile without forcing the older -std=c++03
851472 librostlab-blast: autopkg test suite failure help
984210 libseqlib: ftbfs with GCC-11 bookworm, sid
984207 libsmithwaterman: ftbfs with GCC-11 bookworm, sid
976570 libstatgen: FTBFS on arm64: E: Build killed with signal TERM after 150 minutes of inactivity bullseye, ftbfs, sid
986555 mark one more symbol as optional patch
984139 freebayes: ftbfs with GCC-11 bookworm, fixed-upstream, sid, upstream
984212 libvcflib: ftbfs with GCC-11 bookworm, fixed-upstream, sid, upstream
225651 ncbi-tools-x11: want Cn3D++
985682 nim-kexpr-dev: broken long package description
966040 pyfai: Uses old name of sip module
986410 autopkg tests don't run with the same dependencies as during the build
965361 python-cooler: please make the build reproducible patch, pending
979625 autopkgtest: ModuleNotFoundError (ipytree) and AssertionError
984302 python-freecontact: ftbfs with GCC-11 bookworm, sid
970309 src:python-loompy: Please provide autopkgtest newcomer
976497 python-parasail: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.9 returned exit code 13 bullseye, ftbfs, help, sid
860158 python-pbcore: prints warnings with recent h5py on ppc64el
919052 python-pbcore: some docs for pbcore are not found
841073 python-ruffus: Needs 18 GB of RAM to build help, upstream
983517 pytorch: Build documentation
984304 pytorch: ftbfs with GCC-11 bookworm, sid
927955 python-rdkit: missing module pyAvalonTools
964773 rdkit: Please build rdkit with inchi support wontfix
983040 rdkit: doesn't ship with inchi support enabled wontfix
983077 rdkit doesn't ship with inchi support enabled wontfix
892222 seqan2: FTBFS on hppa: app_test_seqan_tcoffee fails on 2trx.mlcs.fasta upstream
917851 seqan2 2.4.0+dfsg-9: FTBFS, alignment problem ftbfs
984348 spoa: ftbfs with GCC-11 bookworm, sid

Open bugs in suggested packages

2 important, 3 normal, 1 wishlist
928076 bcbio: Workflows not ready for non-developers to depend on.
970312 src:intake: Please provide autopkgtest newcomer
984107 libfreecontact-perl: ftbfs with GCC-11 bookworm, sid
934619 libmaus2 FTBFS (mostly 32bit): error: no matching function for call ftbfs, help, upstream
947882 python3-networkx: SyntaxWarning on package upgrade fixed-upstream
982139 q2-quality-control: test skipped on ppc64el

Done bugs

987023 bamtools: autopkgtest failure: times out on armhf and s390x
986524 freecontact: FTBFS: devlibs error: There is no package matching [libgfortran-8-dev] and noone provides it, please report bug to d-shlibs maintainer bullseye, ftbfs, sid
749367 htslib FTBFS on testing for mips/mipsel bullseye, buster, moreinfo, patch, sid, stretch
800469 htslib FTBFS on armhf, bus error. bullseye, buster, ftbfs, patch, sid, stretch
849667 htslib: FTBFS on armhf: [test] Bus error bullseye, buster, ftbfs, patch, sid, stretch
958471 src:kineticstools: Non-free data included in source
912586 python-cobra still fails it's autopkg tests bullseye, buster, help, sid
920545 python-intervaltree breaks python-intervaltree-bio autopkgtest help, patch, upstream
985281 r-cran-dt: unhandled symlink to directory conversion: /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables-extensions -> ../../../../../../share/javascript/jquery-datatables-extensions
986768 snakemake: autopkgtest regression: Missing input files for rule remote_ancient
*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:
Last update: Fri, 16 Apr 2021 16:07:23 -0000