[Bioc-sig-seq] BSgenome installation error from SVN

[Sean Davis]

On Fri, Feb 19, 2010 at 8:51 AM, Nicolas Delhomme <delhomme at embl.de> wrote:
> Hi all,
>
> Since a few days, I get the following error message when trying to install
> BSgenome from my svn checkout directory (R CMD INSTALL --preclean --clean
> BSgenome):
>
>  installing *source* package ‘BSgenome’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Error in conformMethod(signature, mnames, fnames, f, fdef, definition) :
>  in method for ‘start<-’ with signature ‘x="GRanges"’: formal arguments
> (check = "NA") omitted in the method definition cannot be in the signature
> Error : unable to load R code in package 'BSgenome'
> ERROR: lazy loading failed for package ‘BSgenome’
>
> The details about the checkout are (svn info BSgenome/):
>
> Path: BSgenome
> URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BSgenome
> Repository Root: https://hedgehog.fhcrc.org/bioconductor
> Repository UUID: bc3139a8-67e5-0310-9ffc-ced21a209358
> Revision: 44766
>
> My current sessionInfo:
>
> R version 2.10.1 Patched (2010-02-14 r51142)
> x86_64-unknown-linux-gnu
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] BSgenome_1.15.4    Biostrings_2.15.21 IRanges_1.5.47
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.7.4 tools_2.10.1
>
> Any idea what is happening there? Instead of patching my R with the
> R-release.diff.gz, should I install R-devel?

Hi, Nicolas.

The best way to install devel packages is to use biocLite(), as it
will choose the correct version for your version of R.  More
importantly, you will also get the devel versions of other packages
which often depend on one another.

So, if you want to use devel packages, install R-devel and then use
biocLite() to install the packages of interest.

Hope that helps.
Sean