[Bioc-devel] Update on SQLite-based annotation data package (prototype available)
Wolfgang Huber
huber at ebi.ac.uk
Thu Feb 1 17:10:34 CET 2007
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
>
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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