Debian Med Project
Help us to see Debian used by medical practitioners and biomedical researchers! Join us on the Alioth page.
Summary
Bugs of package med-bio
Total bugs: 87
Open bugs: 61
Fixed bugs: 26
Links to other tasks
Tasks overview
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
adun.app (1) Homepage: http://diana.imim.es/Adun Vcs Debian Med Packaging Team
671226 adun.app: Please consider splitting up into GUI and non-GUI packages
altree (1) Homepage: http://claire.bardel.free.fr/software.html Vcs Debian Med Packaging Team
578550 altree: FTBFS with perl 5.12.0-1: long doubles
bowtie (1) Homepage: http://bowtie-bio.sourceforge.net/ Vcs Debian Med Packaging Team
705616 New upstream version bowtie 1.0.0 patch
emboss (5) Homepage: http://emboss.sourceforge.net Vcs Debian Med Packaging Team
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
fastqc (1) Homepage: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Vcs Debian Med Packaging Team
697604 Templates/Icons is not found
flexbar (1) Homepage: https://sourceforge.net/projects/flexbar/ Vcs Debian Med Packaging Team
705382 flexbar: FTBFS on unsupported architectures
garlic (1) Homepage: http://www.zucic.org/garlic/ Vcs Debichem Team
669296 garlic: debcheckout fails pending
gbrowse (2) Homepage: http://www.gbrowse.org/ Vcs Debian Med Packaging Team
645861 pod errors in source code upstream
669830 gbrowse: transition towards Apache 2.4
gdpc (1) Homepage: http://www.frantz.fi/software/gdpc.php Vcs Debian Med Packaging Team
640008 there is no icon for gdpc 2.2.5-1 from sid in GNOME->applications->science
ghemical (3) Homepage: http://bioinformatics.org/ghemical/ghemical/ Vcs Debichem Team
567600 ghemical should depend on xfonts-75dpi
639321 ghemical: Patch fixes 3 typos patch
687028 ghemical: Help -> Contents fails to open pending
gromacs (1) Homepage: http://www.gromacs.org/ Vcs Debichem Team
644397 gromacs: pdb2gmx, version 4.5.5, fails with 'Illegal instruction' on i686, 3.0.0.1-686-pae (testing) moreinfo, unreproducible
jalview (1) Homepage: http://www.jalview.org/ Vcs Vincent Fourmond
676623 Typos in package description patch
jellyfish (1) Homepage: http://www.cbcb.umd.edu/software/jellyfish/ Vcs Debian Med Packaging Team
701423 jellyfish: ftbfs with eglibc-2.17 sid
jmol (1) Homepage: http://jmol.sourceforge.net/ Vcs Debichem Team
698394 Jmol binary does not depend on a Java runtime (patch included) patch
logol (1) Homepage: http://logol.genouest.org Vcs Debian Med Packaging Team
679989 logol: FTBFS on ia64 and sparc with test suite errors
mafft (1) Homepage: http://mafft.cbrc.jp/alignment/software/ Vcs Debian Med Packaging Team
692683 mafft: missing (XS-)Testsuite: autopkgtest header in source stanza pending
massxpert (1) Homepage: http://www.massxpert.org Vcs The Debichem Group
701319 massxpert: ftbfs with GCC-4.8 sid
mira (1) Homepage: http://chevreux.org/projects_mira.html Vcs Debian Med Packaging Team
701322 mira: ftbfs with GCC-4.8 sid
ncbi-tools6 (1) Homepage: http://www.ncbi.nih.gov/BLAST/ Vcs Debian Med Packaging Team
225651 ncbi-tools-x11: want Cn3D++
neobio (1) Homepage: http://neobio.sourceforge.net/ Vcs Debian Med Packaging Team
684162 neobio: Transition package to default java implementation patch
njplot (1) Homepage: http://pbil.univ-lyon1.fr/software/njplot Vcs Debian Med Packaging Team
701756 njplot: does not link directly used libm patch
primer3 (1) Homepage: http://primer3.sourceforge.net Vcs Debian Med Packaging Team
702693 primer3: Distribute default parameter files in /etc.
probalign (1) Homepage: http://cs.njit.edu/usman/probalign/ Vcs Debian Med Packaging Team
703253 probalign: package description is likely missing one important word pending
pymol (6) Homepage: http://www.pymol.org Vcs Debichem Team
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
rasmol (1) Homepage: http://rasmol.org Vcs Debian Science Maintainers
665605 rasmol: Including individual glib headers no longer supported patch
rnahybrid (1) Homepage: http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/submission.html Vcs Debian Med Packaging Team
701348 rnahybrid: ftbfs with GCC-4.8 sid
samtools (3) Homepage: http://samtools.sourceforge.net Vcs Debian Med Packaging Team
544976 samtools: Static library built with -fPIC.
549427 samtools 0.1.6~dfsg-1 FTBFS on sparc: bus error
602667 samtools: FTBFS on armel
sra-sdk (1) Homepage: http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software Vcs Debian Med Packaging Team
680436 sra-sdk: FTBFS: gcc/i386/atomic32.h:125:5: error: impossible constraint in 'asm' help, upstream
staden-io-lib (1) Homepage: http://staden.sourceforge.net/ Vcs Debian Med Packaging Team
541676 staden-io-lib: FTBFS on alpha: 5 of 5 tests failed
t-coffee (2) Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html Vcs Debian Med Packaging Team
631249 t-coffee: Never exits on armel, consuming 100 % CPU.
688630 t-coffee-doc: empty package
tabix (1) Homepage: http://samtools.sourceforge.net/tabix.shtml Vcs Debian Med Packaging Team
680473 dep8 test failed with message on stderr pending

Open bugs in suggested packages

2 serious, 3 important, 4 normal, 1 minor, 5 wishlist
abyss (1) Homepage: http://www.bcgsc.ca/platform/bioinfo/software/abyss Vcs Debian Med Packaging Team
702440 New upstream release available
autodocktools (2) Homepage: http://autodock.scripps.edu/ Vcs Debian Med Packaging Team
580670 autodocktools: Please split out non-gui/biochemistry-oriented python bits
585244 autodocktools: Python string exceptions no more allowed in Python 2.6 upstream
cufflinks (2) Homepage: http://cufflinks.cbcb.umd.edu/ Vcs Debian Med Packaging Team
675985 cufflinks: Do no force -m64 usage, especially on powerpc. patch
687968 New upstream version patch
emboss-explorer (2) Homepage: http://embossgui.sourceforge.net/ Vcs Debian-Med Packaging Team
485735 Can not serve images of help pages to other computers.
669738 emboss-explorer: transition towards Apache 2.4
igv (1) Homepage: http://www.broadinstitute.org/igv/ Vcs Debian Med Packaging Team
703721 igv: Please replace embedded jide-oss jar with libjide-oss-java
mobyle (1) Homepage: https://projets.pasteur.fr/projects/show/mobyle Vcs Debian Med Packaging Team
669884 mobyle: transition towards Apache 2.4
pdb2pqr (1) Homepage: http://pdb2pqr.poissonboltzmann.org/pdb2pqr/ Vcs Debian Med
674976 pdb2pqr: FTBFS on Debian GNU/Hurd [Patch attached] confirmed, patch, pending
rdkit (1) Homepage: http://www.rdkit.org Vcs Debichem Team
641788 python-rdkit: SyntaxWarning: assertion is always true, perhaps remove parentheses?
seaview (1) Homepage: http://pbil.univ-lyon1.fr/software/seaview.html Vcs Debian Med Packaging Team
688632 seaview: CFLAGS hardening flags missing for csrc/* patch
ugene (3) Homepage: http://ugene.unipro.ru Vcs Debian Med Packaging Team
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

autodocktools (1) Homepage: http://autodock.scripps.edu/ Vcs Debian Med Packaging Team
633362 autodocktools has circular Depends on mgltools-pmv
ball (1) Homepage: http://www.ballview.org Vcs Debian Med Packaging Team
653626 error: passing 'const BALL::PeriodicBoundary' as 'this' argument of 'BALL::Size BALL::PeriodicBoundary::addSolvent(const BALL::String&)' discards qualifiers [-fpermissive]
beast-mcmc (2) Homepage: http://beast.bio.ed.ac.uk/ Vcs Debian Med Packaging Team
683509 beast-mcmc: Transition package to use default java implementation patch
698497 Missing license information
bowtie2 (1) Homepage: http://bowtie-bio.sourceforge.net/bowtie2 Vcs Debian Med Packaging Team
668123 bowtie2: FTBFS: cc1plus: error: unrecognized command line option '-m32'
emboss (2) Homepage: http://emboss.sourceforge.net Vcs Debian Med Packaging Team
650237 emboss: Fails to link mysqlclient with linker set for --as-needed patch
683190 emboss is built without PostgreSQL support patch
figtree (1) Homepage: http://tree.bio.ed.ac.uk/software/figtree/ Vcs Debian Med Packaging Team
683532 figtree: Transition package to default java implementation + support java 7 patch
gbrowse (2) Homepage: http://www.gbrowse.org/ Vcs Debian Med Packaging Team
662922 gbrowse: Upstream bug issue with make test target upstream
677381 Please package and upload new version (2.49)
gentle (1) Homepage: http://gentle.magnusmanske.de Vcs Debian Med Packaging Team
685149 missing source for included Windows libraries
igv (1) Homepage: http://www.broadinstitute.org/igv/ Vcs Debian Med Packaging Team
683538 igv: Transition package to use default java implementation patch
mrbayes (2) Homepage: http://mrbayes.csit.fsu.edu/ Vcs Debian Med Packaging Team
671666 mrbayes-doc: typo in package description
678175 mrbayes: FTBFS with ld --as-needed patch, upstream
ncbi-blast+ (1) Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/ Vcs Debian Med Packaging Team
644962 ncbi-blast+: [blastp] Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer. moreinfo, upstream
ncbi-tools6 (1) Homepage: http://www.ncbi.nih.gov/BLAST/ Vcs Debian Med Packaging Team
644237 blast2: update_blastdb.pl should not default to stderr for output
phy-spread (1) Homepage: http://www.kuleuven.be/aidslab/phylogeography/SPREAD.html Vcs Debian Med Packaging Team
684168 phy-spread: Transition package to default java implementation patch
picard-tools (1) Homepage: http://picard.sourceforge.net/ Vcs Debian Med Packaging Team
684172 picard-tools: Transition package to default java implementation patch
primer3 (1) Homepage: http://primer3.sourceforge.net Vcs Debian Med Packaging Team
650477 primer3: 'man ntdpal oligotm' typos: "achored", "penaltiy" x 2, and "postion"; "deoxynycleotide" and "desoxyribooligonucleotide" patch
qiime (1) Homepage: http://www.qiime.org/ Vcs Debian Med Packaging Team
651983 qiime: Recommends: not available 'cd-hit' package
samtools (2) Homepage: http://samtools.sourceforge.net Vcs Debian Med Packaging Team
653042 segfault in mpileup when alignment is outside of the ref patch
671524 samtools depth caps coverage at 8000
theseus (1) Homepage: http://www.theseus3d.org Vcs Debian Med Packaging Team
682994 theseus: suggests clustlaw instead of clustalw
tophat (1) Homepage: http://tophat.cbcb.umd.edu/ Vcs Debian Med Packaging Team
671813 Bashism in tophat2 that prevents to run on systems where dash is default.
vcftools (2) Homepage: http://vcftools.sourceforge.net Vcs Debian Med Packaging Team
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