Debian Med Project
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Bugs of task bio-dev
Total bugs: 68
Open bugs: 50
Fixed bugs: 18
Links to other tasks
Biology 116 (1040)
Phylogeny 5 (30)
Cloud 34 (372)
Medical data 1 (0)
Dental 0 (0)
Epidemiology 1 (9)
Imaging 208 (1113)
Laboratory 0 (0)
Oncology 0 (0)
Pharmacology 3 (27)
Physics 27 (213)
Practice 2 (0)
Psychology 8 (93)
Research 0 (0)
Statistics 2 (6)
Tools 36 (219)
Typesetting 88 (602)
critical 0 0
grave 0 0
serious 11 2
important 7 0
normal 12 1
minor 2 0
wishlist 15 0

Summary bugs page of task Biology development

Immediately looking into bugs of the dependencies of this task is advised (572)*

Open bugs in dependent packages

11 serious, 7 important, 12 normal, 2 minor, 15 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
859958 biojava-live: please make the build reproducible
866073 bioperl: autopkgtest regression
876283 autopkg test command1 fails buster, sid
814617 freecontact: adequate reports symbol-size-mismatch /usr/bin/freecontact => _ZN11xercesc_3_16XMLUni18fgXercesLoadSchemaE
860674 htseq: FTBFS on i386: build-dependency not installable: python-pysam buster, sid, stretch
866137 htslib autopkgtest is broken in 1.4.1-2
871314 htslib: new version break python-pysam sid
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++
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
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
820060 python-biom-format: broken on big-endian architectures
672407 python-biopython: duplicate mathml2.dtd
872222 python-biopython: broken symlinks: /usr/share/doc/python-biopython/{NEWS, DEPRECATED, CONTRIB} -> *.rst
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
868927 python-pybedtools FTBFS with more than one supported Python3 version buster, patch, sid
834856 python-pysam: FTBFS on 32-bit architectures: segmentation fault in testsuite help
871083 python-pysam: FTBFS: Test failures sid
841073 python-ruffus: Needs 18 GB of RAM to build
868962 python-skbio: FTBFS: Test failures buster, sid
751414 rdkit: postgresql cartridge not built
872246 rdkit: FTBFS with Sphinx 1.6: Needs build-dep on latexmk buster, sid
873865 relion: Please add arm64
710225 staden-io-lib: library name should follow ABI version (not project version)

Open bugs in suggested packages

2 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
871315 samtools: new version breaks python-pysam sid

Done bugs

875334 FTBFS with Java 9: javax.xml.bind
873745 bioperl: please Build-Depend on rename buster, sid
868073 bioperl-run: FTBFS: t/Bowtie.t failure buster, sid, upstream
866074 bio-tradis: autopkgtest regression
875991 fast5: FTBFS: debian/python-fast5-bin/usr/bin/ is not a directory
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
871085 libbpp-phyl: FTBFS: collect2: error: ld returned 1 exit status buster, sid
854341 libchado-perl: FTBFS: The following enviroment variables not detected: CHADO_DB_USERNAME help, moreinfo, unreproducible
866514 src:ngs.sdk: Excessive build-depends complicate python3 transition patch
866547 python-biomaj3 encoding issue during build fixed-upstream, patch
866548 src:python-biomaj3: Excessive build-depends complicate python3 transition patch
871160 python-biomaj3: FTBFS: UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 1781: ordinal not in range(128) buster, sid
866528 src:python-biotools: Inappropriate use of arch:any vice arch:all patch
730515 cd-hit-est is cdhit-est in Debian [Why?]
845752 r-bioc-shortread FTBFS on armel: Error: segfault from C stack overflow
*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: Wed, 20 Sep 2017 19:25:48 -0000