Debian Med Project
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Summary
Bugs of task bio
Total bugs: 145
Open bugs: 119
Fixed bugs: 26
Links to other tasks
Biology 119 (849)
Phylogeny 8 (66)
Cloud 40 (324)
Medical data 1 (9)
Dental 0 (0)
Epidemiology 0 (0)
Imaging 178 (940)
Laboratory 0 (0)
Oncology 1 (15)
Pharmacology 1 (9)
Physics 31 (273)
Practice 2 (9)
Psychology 6 (63)
Research 0 (0)
Statistics 2 (6)
Tools 34 (204)
Typesetting 95 (523)
Legend
SeverityDependentSuggested
critical 0 0
grave 0 1
serious 5 0
important 12 1
normal 52 7
minor 4 3
wishlist 30 4

Summary bugs page of task Biology

Immediately looking into bugs of the dependencies of this task is advised (849)*

Open bugs in dependent packages

5 serious, 12 important, 52 normal, 4 minor, 30 wishlist
859111 ariba FTBFS with bowtie2 2.3.1-1 fixed-upstream, pending, sid, upstream
852839 baitfisher: FTBFS (32-bit): mixes ::size_t and faststring::size_t
784451 [ball] Qt4's WebKit removal upstream
819617 FTBFS: any-i386 - floating point idiosyncracies
860682 bcftools: FTBFS on i386: Test failures sid, stretch
780428 beast-mcmc: restrict arch from all to amd64
747337 broken autopkgtest: missing dependency, not testing installed package, test failures upstream
860655 blasr: FTBFS on i386: unsatisfiable build-dependencies: libpbseq-dev (>= 0~20160912), libpbbam-dev sid, stretch
853859 bwa: Segmentation fault with specific data set
860639 circlator: FTBFS on i386: unsatisfiable build-dependencies: python3-pysam (>= 0.8.1), spades, bwa (>= 0.7.12) sid, stretch
856942 circos: broken symlinks: /usr/share/doc/circos/* -> /tools/*/*
859300 crac: please make the build reproducible patch
860690 crac: FTBFS on i386: build-dependency not installable: libjellyfish-2.0-dev sid, stretch
853375 disulfinder: ftbfs with GCC-7 buster, sid
846858 src:ea-utils: New version available
862118 ea-utils: New upstream version available
682042 emboss-data: ships bulky taxonomy and gene ontology data
853396 fastx-toolkit: ftbfs with GCC-7 buster, sid
851658 ffindex: autopkgtests need 6GB of memory to run
848335 Filo should be removed from Debian after Stretch release since it is unmaintained and can be replaced newcomer
860653 fitgcp: FTBFS on i386: build-dependency not installable: python-pysam sid, stretch
759006 flexbar: FTBFS on hppa: Flexbar.h:258: undefined reference to `tbb::pipeline::run(unsigned int)'
853403 flexbar: ftbfs with GCC-7 buster, sid
814617 freecontact: adequate reports symbol-size-mismatch /usr/bin/freecontact => _ZN11xercesc_3_16XMLUni18fgXercesLoadSchemaE
853405 freecontact: ftbfs with GCC-7 buster, sid
860661 fsm-lite: FTBFS on i386: build-dependency not installable: libsdsl-dev sid, stretch
750139 gamgi: Conflicting return types of function gamgi_engine_iarray_push
669296 garlic: debcheckout fails pending
715937 [Mayhem] Bug report on garlic: garlic crashes with exit status 139
749656 garlic: Conflicting declarations of function BlurMainWindow_ to cause undefined behaviour
857213 gbrowse: broken symlink: /usr/share/gbrowse/htdocs/i -> debian/gbrowse/var/cache/gbrowse/images
732691 Pressing "alignment or Ctrl+G" only results in a dialog with a cancel button
644397 Provide runtime detection for CPU SIMD capabilities upstream
853440 harvest-tools: ftbfs with GCC-7 buster, sid
749367 htslib FTBFS on testing for mips/mipsel moreinfo, patch, sid, stretch
774109 htslib: FTBFS on hppa
800469 htslib FTBFS on armhf, bus error. patch, sid, stretch
849667 htslib: FTBFS on armhf: [test] Bus error patch, sid, stretch
860640 iva: FTBFS on i386: build-dependency not installable: python3-pysam sid, stretch
849025 jalview: FTBFS: error: cannot find symbol EnumCallback
863015 jellyfish: please make the output reproducible patch
712791 jmol - exporting the image as PDF saves only partial image patch
851830 arm64 has flaky tests
862380 khmer: FTBFS with Python 3.6 patch
860636 kineticstools: FTBFS on i386: build-dependency not installable: python-pbcore (>= 1.2.8) sid, stretch
860665 libvcflib: FTBFS on i386: build-dependency not installable: libssw-dev sid, stretch
804579 logol-bin: bogus hardcoded dependency on libncursesw5
765285 mapsembler2: FTBFS on mips mipsel ppc sparc when 8 byte __sync* builtins are used
860672 mhap: FTBFS on i386: build-dependency not installable: libssw-java sid, stretch
853568 nanopolish: ftbfs with GCC-7 buster, sid
225651 ncbi-tools-x11: want Cn3D++
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
860676 pbalign: FTBFS on i386: build-dependency not installable: python-pbcore (>= 0.8.5) sid, stretch
860631 pbbarcode: FTBFS on i386: unsatisfiable build-dependencies: python-pbcore, pbh5tools sid, stretch
860711 pbdagcon: FTBFS on i386: unsatisfiable build-dependencies: libpbseq-dev, libpbbam-dev sid, stretch
860669 pbgenomicconsensus: FTBFS on i386: build-dependency not installable: python-pbcore (>= 1.2.9) sid, stretch
860616 pbh5tools: FTBFS on i386: build-dependency not installable: python-pbcore sid, stretch
853604 pbsim: ftbfs with GCC-7 buster, sid
853609 perm: ftbfs with GCC-7 buster, sid
861367 pirs: Please do not depend on transitional dummy pkg ttf-liberation
848332 src:poa: Please add autopkgtest newcomer
716580 [Mayhem] Bug report on populations: populations crashes with exit status 139
813250 prime-phylo: FTBFS on hppa: undefined boost references
853621 primer3: ftbfs with GCC-7 buster, sid
848333 src:proda: Please add autopkgtest newcomer
602610 Package freemol.mengine for full modeling capabilities
651609 pymol: Setting-Error: type read mismatch (int) 667
703782 pymol: Unable to launch the Menu
709306 pymol: Crashes when running within xrdp/vnc (no 3D support)
765794 Race condition when running scripts in "stdin" mode
783653 pymol: Segmentation fault immediately after loading pdb
820308 qiime: many unsatisfiable dependencies
857454 qtltools: please make the build reproducible patch, pending
845753 r-cran-treescape FTBFS on armhf, i386: Error: segfault from C stack overflow
860688 rapmap: FTBFS on i386: build-dependency not installable: libjellyfish-2.0-dev sid, stretch
767296 rasmol: ftbfs on ppc64el -- conflict with vector keyword patch
790196 rasmol: depends on vte which is deprecated sid, stretch
821023 rasmol: Short descriptions should begin with lowercase l10n, patch
861281 rnahybrid: FTBFS on armel help
847569 rsem: New version available
860681 salmon: FTBFS on i386: unsatisfiable build-dependencies: libjellyfish-2.0-dev (> 2.2.3-2), libbwa-dev sid, stretch
862484 seqan2: please make the build reproducible patch
853656 sga: ftbfs with GCC-7 buster, sid
860643 sga: FTBFS on i386: build-dependency not installable: python-pysam sid, stretch
848589 snap-aligner: Build requires 188 GB of memory (fortunately not used, just allocated)
860652 snap-aligner: FTBFS on i386: SNAPLib/SortedDataWriter.cpp:338:70: error: no matching function for call to 'max(long unsigned int, _int64)' sid, stretch
818505 sortmerna FTBFS on !x86 sid
853113 spades: Fails to build with unhelpful error message in a "low" memory machine
853666 spades: ftbfs with GCC-7 buster, sid
860677 spades: FTBFS on i386: unsatisfiable build-dependencies: libssw-dev, bwa sid, stretch
710225 staden-io-lib: library name should follow ABI version (not project version)
716373 [Mayhem] Bug report on t-coffee: t_coffee crashes with exit status 139 help
853677 t-coffee: ftbfs with GCC-7 buster, sid
853681 theseus: ftbfs with GCC-7 buster, sid
780816 tophat: contains and uses convience copy of samtools 0.1.18
806214 tree-puzzle: Package fails test suite
846481 src:treeviewx: Please remove statically linked code copy of libncl
853687 trinityrnaseq: ftbfs with GCC-7 buster, sid
860645 trinityrnaseq: FTBFS on i386: unsatisfiable build-dependencies: jellyfish (>= 2.1.4), parafly sid, stretch
855340 Spurious build dep on libssl-dev pending

Open bugs in suggested packages

1 grave, 1 important, 7 normal, 3 minor, 4 wishlist
857283 arb-common: broken symlinks: /usr/lib/arb/bin/mafft-*, /etc/arb/inputMasks/format.readme
862913 [INTL:id] initial Indonesian debconf translation l10n, patch
580670 autodocktools: Please split out non-gui/biochemistry-oriented python bits
585244 autodocktools: Python string exceptions no more allowed in Python 2.6 upstream
732858 Add MariaDB as alternative dependency
803116 biomaj: references to non-existent license "CeCILL-A"
848497 src:biomaj: New upstream version available
732862 Add MariaDB as an alternative dependency
715587 [Mayhem] Bug report on cain-solvers: HomogeneousHistogramsAverage crashes with exit status 139 help
715588 [Mayhem] Bug report on cain-solvers: HomogeneousHistogramsAverageAps crashes with exit status 139 help
772407 science-config: bashism in /bin/sh script
796771 science-geography: Depends on no longer built qgis-plugin-grass
861038 emboss-explorer: broken symlink: /usr/share/doc/emboss-explorer/html -> ../../EMBOSS/doc/html/emboss/apps
855485 runPmv script does not work
855494 mgltools-pmv: runPmv does not start
855701 runPmv script does not work

Done bugs

749733 adun.app: GCC warnings that may lead to runtime issues with new GNUstep libraries jessie, sid, stretch
859660 artemis running issue moreinfo
767144 autodocktools: fails to start the GUI
767145 autodocktools: fails to start the GUI
783547 TclError: cannot use geometry manager
852743 dialign FTCBFS: uses the build architecture compiler patch
861911 e-mem: FTBFS on non-x86: unrecognized command line option '-mpopcnt' upstream
862161 e-mem FTBFS on armel/armhf/ppc64el: recipe for target 'override_dh_auto_test' failed
826458 gbrowse: Unescaped left brace in regex is deprecated
833885 gbrowse: ships a deterministic/predictable OpenID consumer secret security
836230 FTBFS in a low memory machine with poor error message
853830 gentle: CXXFLAGS aren't passed properly and package might FTBFS on all archs that don't have PIE enabled
863208 mash sometimes FTBFS in parallel builds patch
793193 mgltools-pmv: FTBFS due to pyversions: error parsing Python-Version attribute
853211 phyml: Fails to use mpi
853737 phyml: Beagle library causes trouble on machines without proper graphics hardware
853738 phyml: MPI version uses different number of bootstrap steps breaking applications like seaview
848334 src:picard-tools: Please add autopkgtest newcomer
848329 src:prank: Please add autopkgtest newcomer
730515 cd-hit-est is cdhit-est in Debian [Why?]
862039 r-bioc-gviz: accesses the internet during build
853835 seaview: Wrong results in connection with multi-processing phyml
848464 stacks-web: Should Depends/Recommends the metapackage default-mysql-*
815174 staden: Missing links in /usr/bin
815176 staden: Gap4 contig editor does not show sequences
785035 ugene: FTBFS on amd64
*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: Mon, 29 May 2017 06:20:20 -0000