Debian Med Project
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Bugs of task bio-dev
Total bugs: 74
Open bugs: 54
Fixed bugs: 20
Links to other tasks
Biology 119 (1036)
Phylogeny 5 (33)
Cloud 40 (399)
Medical data 1 (0)
Dental 0 (0)
Epidemiology 0 (0)
Imaging 218 (1143)
Laboratory 0 (0)
Oncology 0 (0)
Pharmacology 3 (27)
Physics 30 (225)
Practice 2 (0)
Psychology 9 (100)
Research 0 (0)
Statistics 2 (4)
Tools 35 (209)
Typesetting 94 (653)
critical 0 0
grave 0 0
serious 12 1
important 7 0
normal 14 1
minor 3 0
wishlist 16 0

Summary bugs page of task Biology development

Immediately looking into bugs of the dependencies of this task is advised (613)*

Open bugs in dependent packages

12 serious, 7 important, 14 normal, 3 minor, 16 wishlist
865130 reapr FTBFS on big endian: Error sampling from files '00.Sample/fragCov.gz', '00.assembly.fa.gc.gz' upstream
749736 biococoa: GCC warnings that may lead to runtime issues with new GNUstep libraries buster, jessie, sid, stretch
843712 biojava4-live: FTBFS (failing tests)
659824 biojava-live: New version available
866073 bioperl: autopkgtest regression
880347 bioperl-run: FTBFS: Test failures buster, sid
814617 freecontact: adequate reports symbol-size-mismatch /usr/bin/freecontact => _ZN11xercesc_3_16XMLUni18fgXercesLoadSchemaE
881114 freecontact: Transition to xerces-c 3.2 buster, sid
860674 htseq: FTBFS on i386: build-dependency not installable: python-pysam buster, sid, stretch
877590 FTBFS: error: package org.testng does not exist buster, sid
866137 htslib autopkgtest is broken in 1.4.1-2
879885 htslib FTCBFS: configures for the build architecture patch
881149 htslib FTBFS: test failures on i386 buster, sid
881170 htslib: please do not package cram/*.h headers
881359 htslib: please revert pkg-config change in fix_pkg-config.patch
881360 htslib: please do not package htslib*.mk makefile fragments
860636 kineticstools: FTBFS on i386: build-dependency not installable: python-pbcore (>= 1.2.8) buster, sid, stretch
875009 [libbpp-qt] Future Qt4 removal from Buster upstream
858524 libhmsbeagle-dev: broken symlink: /usr/include/libhmsbeagle -> libhmsbeagle-2
832138 librostlab-blast: The package should compile without forcing the older -std=c++03
851472 librostlab-blast: autopkg test suite failure
847013 src:libsbml: build python3 bindings
860665 libvcflib: FTBFS on i386: build-dependency not installable: libssw-dev buster, sid, stretch
225651 ncbi-tools-x11: want Cn3D++
879619 ncbi-tools6: Please provide autopkgtest
813559 ngs-sdk: FTBFS: most platforms explicitly unsupported
784502 [openms] Qt4's WebKit removal buster, sid
816562 libopenms2.0: fails to upgrade from 'jessie' - trying to overwrite /usr/share/man/man3/libopenms.3.gz
822412 openms: non-free WSDL-Schema (ND); incomplete copyright (missing DSL, BSL-1.0 licenses)
853595 openms: ftbfs with GCC-7 buster, sid
865240 Please update dependencies from latex-xcolor to tl-latex-recommended buster, sid
871297 libopenms2.0: requires rebuild against GCC 7 and symbols/shlibs bump buster, sid
875073 [openms] Future Qt4 removal from Buster
881026 openms: Transition to xerces-c3.2
829741 pbbam: FTBFS (32-bit): pbmerge assertion failure
860616 pbh5tools: FTBFS on i386: build-dependency not installable: python-pbcore buster, sid, stretch
860671 pbseqlib: FTBFS on i386: build-dependency not installable: libpbbam-dev buster, sid, stretch
710121 pyfai: Please package the latest pyFAI
866460 pyfai: depends on obsolete python-imaging (replace with python3-pil or python-pil) buster, sid
876739 pyfai FTBFS: help2man: can't get `--help' info from /tmp/check_calib_0hk8odnh
820060 python-biom-format: broken on big-endian architectures
672407 python-biopython: duplicate mathml2.dtd
881555 python-csb: Please migrate away from Epydoc if possible
860615 python-pbcommand: FTBFS on i386: build-dependency not installable: python-pbcore buster, sid, stretch
860158 python-pbcore: prints warnings with recent h5py on ppc64el
860644 python-pbcore: FTBFS on i386: build-dependency not installable: python-pysam (>= 0.9.0) buster, sid, stretch
841073 python-ruffus: Needs 18 GB of RAM to build
751414 rdkit: postgresql cartridge not built
872246 rdkit: FTBFS with Sphinx 1.6: Needs build-dep on latexmk buster, patch, sid
881562 rdkit: Please migrate away from Epydoc if possible
873865 relion: Please add arm64
876840 staden-io-lib FTBFS on non-i386 32bit: FAIL: java help, upstream

Open bugs in suggested packages

1 serious, 1 normal
852654 src:pbcopper: no point to releasing it without `unanimity`
855625 r-bioc-iranges: ships dangling symlink /usr/share/doc/r-bioc-iranges/RleTricks.pdf

Done bugs

876283 autopkg test command1 fails buster, sid
742921 python-htseq: python.numpy dtype size error
749367 htslib FTBFS on testing for mips/mipsel buster, moreinfo, patch, sid, stretch
800469 htslib FTBFS on armhf, bus error. buster, patch, sid, stretch
849667 htslib: FTBFS on armhf: [test] Bus error buster, patch, sid, stretch
871314 htslib: new version break python-pysam sid
877670 bcftools FTBFS on armel, armhf and ppc64el patch
879886 libhts2: libhts2 needs to handle ABI changes
881023 librcsb-core-wrapper: FTBFS with xerces-c3.2 buster, patch, sid
880805 pbseqlib: please support HDF5 1.10.1 patch
872222 python-biopython: broken symlinks: /usr/share/doc/python-biopython/{NEWS, DEPRECATED, CONTRIB} -> *.rst
880236 python-biopython: FTBFS: Test failures buster, sid
730515 cd-hit-est is cdhit-est in Debian [Why?]
880309 python-gffutils: FTBFS: build-dependency not installable: python3-pybedtools buster, sid
868927 python-pybedtools FTBFS with more than one supported Python3 version buster, patch, sid
871083 python-pysam: FTBFS: Test failures sid
879867 python3-pysam: import pysam throws ImportError undefined symbol: hts_log buster
878820 python-skbio FTBFS with Python 3.6 as default
877723 r-base: Rebuilding r-bioc-biocgenerics with new R changes behaviour fixed-upstream
871315 samtools: new version breaks python-pysam sid
*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: Sun, 19 Nov 2017 18:32:42 -0000