[Bioc-devel] Update on SQLite-based annotation data package (prototype available)

[Wolfgang Huber]

Hi Seth,

I installed the package, but I get:

> ? hgu95av2db
No documentation for 'hgu95av2db' in specified packages and libraries:
you could try 'help.search("hgu95av2db")'

> ?getDb
No documentation for 'getDb' in specified packages and libraries:
you could try 'help.search("getDb")'

> ?hgu95av2CHRLOC
No documentation for 'hgu95av2CHRLOC' in specified packages and libraries:
you could try 'help.search("hgu95av2CHRLOC")'

and there is also no vignette

> sessionInfo()
R version 2.5.0 Under development (unstable) (2007-01-22 r40543)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=it_IT.UTF-8;LC_NUMERIC=C;LC_TIME=it_IT.UTF-8;LC_COLLATE=it_IT.UTF-8;LC_MONETARY=it_IT.UTF-8;LC_MESSAGES=it_IT.UTF-8;LC_PAPER=it_IT.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=it_IT.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"
[7] "methods"   "base"

other attached packages:
   hgu95av2db AnnotationDbi       RSQLite           DBI       Biobase
    "1.13.91"      "0.0.41"      "0.4-19"      "0.1-12"     "1.13.34"
     fortunes
      "1.3-2"
Cheers
 Wolfgang


> 
> We are making progress on converting the annotation data packages to
> use SQLite as the backend storage mechanism.
> 
> The devel annotation package repository has a prototype of a
> SQLite-based annotation data package (hgu95av2db).  If you are running
> R-devel, then you should be able to install it via biocLite (sorry,
> only source package at this point).
> 
> The SQLite-based annotation packages depend on the AnnotationDbi
> package which provides an environment-like interface that should be
> backwards compatible.  Advanced users can get a connection to the DB
> and issue raw SQL queries.  We are also planning to provide more
> convenience/accessor functions along the lines of the annotate
> package.
> 
> Our plan for the upcoming 2.0 release of Bioconductor is to include
> both environment-based and SQLite-based annotation packages.
> 
> If you maintain a package that makes use of annotation data packages,
> it would be good to see if the hgu95av2db prototype will work with
> your code (if not, please let us know).
> 
> + seth
> 
> _______________________________________________
> Bioc-devel at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel


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Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber