Debian Med Project
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Summary
Bugs of package med-bio
Total bugs: 87
Open bugs: 61
Fixed bugs: 26
Links to other tasks
Biology 61 (477)
Phylogeny 6 (48)
Cloud 10 (87)
Medical data 2 (30)
Dental 0 (0)
Epidemiology 0 (0)
Imaging 145 (966)
Laboratory 0 (0)
Oncology 0 (0)
Pharmacology 0 (0)
Physics 17 (132)
Practice 3 (18)
Psychology 8 (47)
Research 0 (0)
Statistics 4 (5)
Tools 20 (117)
Typesetting 125 (719)
Legend
SeverityDependentSuggested
critical 0 0
grave 1 0
serious 2 2
important 14 3
normal 12 4
minor 7 1
wishlist 10 5

Summary bugs page of Biology meta package

Immediately looking into bugs of the dependencies of this metapackage is advised (477)*

Open bugs in dependent packages

1 grave, 2 serious, 14 important, 12 normal, 7 minor, 10 wishlist
671226 adun.app: Please consider splitting up into GUI and non-GUI packages
578550 altree: FTBFS with perl 5.12.0-1: long doubles
705616 New upstream version bowtie 1.0.0 patch
441063 emboss: Bash auto-completion for EMBOSS
558852 Resolve unresolved symbols in shared libraries help
682042 emboss-data: ships bulky taxonomy and gene ontology data
690651 jemboss: bashism in /bin/sh script
694908 Contains non-free data pending, wheezy-ignore
697604 Templates/Icons is not found
705382 flexbar: FTBFS on unsupported architectures
669296 garlic: debcheckout fails pending
645861 pod errors in source code upstream
669830 gbrowse: transition towards Apache 2.4
640008 there is no icon for gdpc 2.2.5-1 from sid in GNOME->applications->science
567600 ghemical should depend on xfonts-75dpi
639321 ghemical: Patch fixes 3 typos patch
687028 ghemical: Help -> Contents fails to open pending
644397 gromacs: pdb2gmx, version 4.5.5, fails with 'Illegal instruction' on i686, 3.0.0.1-686-pae (testing) moreinfo, unreproducible
676623 Typos in package description patch
701423 jellyfish: ftbfs with eglibc-2.17 sid
698394 Jmol binary does not depend on a Java runtime (patch included) patch
679989 logol: FTBFS on ia64 and sparc with test suite errors
692683 mafft: missing (XS-)Testsuite: autopkgtest header in source stanza pending
701319 massxpert: ftbfs with GCC-4.8 sid
701322 mira: ftbfs with GCC-4.8 sid
225651 ncbi-tools-x11: want Cn3D++
684162 neobio: Transition package to default java implementation patch
701756 njplot: does not link directly used libm patch
702693 primer3: Distribute default parameter files in /etc.
703253 probalign: package description is likely missing one important word pending
506202 Please split up package into pymol and pymol-data
602610 Package freemol.mengine for full modeling capabilities
651609 pymol: Setting-Error: type read mismatch (int) 667
668586 pymol: Segfaults when opening saved session or show upstream
689445 pymol fail to load its own session (pse files) upstream
703782 pymol: Unable to launch the Menu
665605 rasmol: Including individual glib headers no longer supported patch
701348 rnahybrid: ftbfs with GCC-4.8 sid
544976 samtools: Static library built with -fPIC.
549427 samtools 0.1.6~dfsg-1 FTBFS on sparc: bus error
602667 samtools: FTBFS on armel
680436 sra-sdk: FTBFS: gcc/i386/atomic32.h:125:5: error: impossible constraint in 'asm' help, upstream
541676 staden-io-lib: FTBFS on alpha: 5 of 5 tests failed
631249 t-coffee: Never exits on armel, consuming 100 % CPU.
688630 t-coffee-doc: empty package
680473 dep8 test failed with message on stderr pending

Open bugs in suggested packages

2 serious, 3 important, 4 normal, 1 minor, 5 wishlist
702440 New upstream release available
580670 autodocktools: Please split out non-gui/biochemistry-oriented python bits
585244 autodocktools: Python string exceptions no more allowed in Python 2.6 upstream
675985 cufflinks: Do no force -m64 usage, especially on powerpc. patch
687968 New upstream version patch
485735 Can not serve images of help pages to other computers.
669738 emboss-explorer: transition towards Apache 2.4
703721 igv: Please replace embedded jide-oss jar with libjide-oss-java
669884 mobyle: transition towards Apache 2.4
674976 pdb2pqr: FTBFS on Debian GNU/Hurd [Patch attached] confirmed, patch, pending
641788 python-rdkit: SyntaxWarning: assertion is always true, perhaps remove parentheses?
688632 seaview: CFLAGS hardening flags missing for csrc/* patch
675298 ugene: FTBFS in experimental: reverseInPlace' was not declared in this scope experimental
693655 ugene: Please update ugene to the latest version 1.11.3
694044 ugene: Source contains non-free components experimental, upstream

Done bugs

633362 autodocktools has circular Depends on mgltools-pmv
653626 error: passing 'const BALL::PeriodicBoundary' as 'this' argument of 'BALL::Size BALL::PeriodicBoundary::addSolvent(const BALL::String&)' discards qualifiers [-fpermissive]
683509 beast-mcmc: Transition package to use default java implementation patch
698497 Missing license information
668123 bowtie2: FTBFS: cc1plus: error: unrecognized command line option '-m32'
650237 emboss: Fails to link mysqlclient with linker set for --as-needed patch
683190 emboss is built without PostgreSQL support patch
683532 figtree: Transition package to default java implementation + support java 7 patch
662922 gbrowse: Upstream bug issue with make test target upstream
677381 Please package and upload new version (2.49)
685149 missing source for included Windows libraries
683538 igv: Transition package to use default java implementation patch
671666 mrbayes-doc: typo in package description
678175 mrbayes: FTBFS with ld --as-needed patch, upstream
644962 ncbi-blast+: [blastp] Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer. moreinfo, upstream
644237 blast2: update_blastdb.pl should not default to stderr for output
684168 phy-spread: Transition package to default java implementation patch
684172 picard-tools: Transition package to default java implementation patch
650477 primer3: 'man ntdpal oligotm' typos: "achored", "penaltiy" x 2, and "postion"; "deoxynycleotide" and "desoxyribooligonucleotide" patch
651983 qiime: Recommends: not available 'cd-hit' package
653042 segfault in mpileup when alignment is outside of the ref patch
671524 samtools depth caps coverage at 8000
682994 theseus: suggests clustlaw instead of clustalw
671813 Bashism in tophat2 that prevents to run on systems where dash is default.
689058 Bad description
689059 Bad use of perl: qw(...) as parentheses is deprecated
*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: Wed, 17 Apr 2013 17:09:18 -0000