Debian Med Project
Help us to see Debian used by medical practitioners and biomedical researchers! Join us on the Alioth page.
Bugs of task bio-dev
Total bugs: 73
Open bugs: 55
Fixed bugs: 18
Links to other tasks
Biology 144 (1426)
Phylogeny 9 (75)
Cloud 43 (507)
Medical data 1 (9)
Dental 0 (0)
Epidemiology 1 (9)
Imaging 190 (1158)
Laboratory 0 (0)
Oncology 2 (30)
Pharmacology 3 (27)
Physics 30 (288)
Practice 2 (9)
Psychology 8 (93)
Research 0 (0)
Statistics 2 (6)
Tools 35 (209)
Typesetting 64 (322)
critical 0 0
grave 0 0
serious 13 1
important 13 1
normal 11 1
minor 2 0
wishlist 13 0

Summary bugs page of task Biology development

Immediately looking into bugs of the dependencies of this task is advised (708)*

Open bugs in dependent packages

13 serious, 13 important, 11 normal, 2 minor, 13 wishlist
866074 bio-tradis: autopkgtest regression
749736 biococoa: GCC warnings that may lead to runtime issues with new GNUstep libraries buster, jessie, sid, stretch
659824 biojava-live: New version available
859958 biojava-live: please make the build reproducible
843712 biojava4-live: FTBFS (failing tests)
866073 bioperl: autopkgtest regression
868073 bioperl-run: FTBFS: t/Bowtie.t failure buster, sid
814617 freecontact: adequate reports symbol-size-mismatch /usr/bin/freecontact => _ZN11xercesc_3_16XMLUni18fgXercesLoadSchemaE
853405 freecontact: ftbfs with GCC-7 buster, sid
860674 htseq: FTBFS on i386: build-dependency not installable: python-pysam buster, sid, stretch
866137 htslib autopkgtest is broken in 1.4.1-2
860636 kineticstools: FTBFS on i386: build-dependency not installable: python-pbcore (>= 1.2.8) buster, sid, stretch
868455 libbiod: FTBFS with new ldc?
868794 libbpp-qt-dev: postinst removal makes bppphyview FTBFS buster, sid
868924 bppphyview: FTBFS: TreeDocument.h:47:27: fatal error: Bpp/Phyl/Io.all: No such file or directory buster, sid
853482 libbpp-seq-omics: ftbfs with GCC-7 buster, sid
854341 libchado-perl: FTBFS: The following enviroment variables not detected: CHADO_DB_USERNAME help, moreinfo, unreproducible
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
866514 src:ngs.sdk: Excessive build-depends complicate python3 transition patch
784502 [openms] Qt4's WebKit removal
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
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
866547 python-biomaj3 encoding issue during build fixed-upstream, patch
866548 src:python-biomaj3: Excessive build-depends complicate python3 transition patch
672407 python-biopython: duplicate mathml2.dtd
869597 python-biopython FTBFS: We need the Python library setuptools to be installed.
866528 src:python-biotools: Inappropriate use of arch:any vice arch:all patch
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
867017 src:python-pysam: FTBFS during rebuild for python3.6 transition
867018 python-pysam FTBFS with libhts-dev 1.4.1-2 buster, 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
710225 staden-io-lib: library name should follow ABI version (not project version)

Open bugs in suggested packages

1 serious, 1 important, 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
845752 r-bioc-shortread FTBFS on armel: Error: segfault from C stack overflow

Done bugs

851658 ffindex: autopkgtests need 6GB of memory to run patch
742921 python-htseq: python.numpy dtype size error
749367 htslib FTBFS on testing for mips/mipsel buster, moreinfo, patch, sid, stretch
774109 htslib: FTBFS on hppa
800469 htslib FTBFS on armhf, bus error. buster, patch, sid, stretch
849667 htslib: FTBFS on armhf: [test] Bus error buster, patch, sid, stretch
865010 htslib: use -fPIC to fix FTBFS on s390x patch
865012 htslib FTBFS on i386: test_vcf_{api,sweep} failed patch, upstream
864188 libbpp-core2v5: symbols removed without soname bump
865552 libbpp-phyl FTBFS with test failures
866365 libbpp-phyl FTBFS on mips/mipsel: test failures
865900 bppsuite FTBFS on i386: CMake fails to find bpp-popgen
866069 libbpp-seq installs broken header VectorProbabilisticSiteContainer.h patch
865901 libbpp-phyl-omics FTBFS on i386: CMake fails to find bpp-seq-omics
865007 libtabixpp FTBFS with htslib 1.4.1-2: devlibs error: There is no package matching [libhts2-dev] and noone provides it buster, sid
730515 cd-hit-est is cdhit-est in Debian [Why?]
865008 samtools FTBFS with htslib 1.4.1-2: error: conflicting types for 'errmod_t' buster, sid
826505 swissknife: FTBFS with perl 5.26: Unescaped left brace in regex buster, patch, 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: Mon, 24 Jul 2017 18:42:41 -0000