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

[Kasper Daniel Hansen]

You should _always_ use R-devel when using Bioc-devel.

Kasper

On Fri, Feb 19, 2010 at 9:20 AM, Droit Arnaud <Arnaud.Droit at ircm.qc.ca> wrote:
> Hi Nicolas,
>
> I had the same problem with the BSgenome packages from SVN.
> I tried different installation and desinstallation with different version of BSgenome, Biostrings, IRanges....
>
> Finally, I resolved my problem by installing the latest build of R-dev (version.string R version 2.11.0 Under development (unstable) (2010-02-18 r51149).
>
> Good luck,
>
> Arnaud.
>
>> sessionInfo()
>
> R version 2.11.0 Under development (unstable) (2010-02-18 r51149)
>
> x86_64-apple-darwin10.2.0
>
> locale:
>
> [1] fr_CA.UTF-8/fr_CA.UTF-8/C/C/fr_CA.UTF-8/fr_CA.UTF-8
>
> attached base packages:
>
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>
> [1] BSgenome_1.15.7    Biostrings_2.15.21 IRanges_1.5.47
>
> loaded via a namespace (and not attached):
>
> [1] Biobase_2.7.4
>
>
>
>
> Le 2010-02-19 à 08:51, Nicolas Delhomme a écrit :
>
> 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?
>
> Thanks for any help,
>
> Cheers,
>
> ---------------------------------------------------------------
> Nicolas Delhomme
>
> High Throughput Functional Genomics Center
>
> European Molecular Biology Laboratory
>
> Tel: +49 6221 387 8426
> Email: nicolas.delhomme at embl.de<mailto:nicolas.delhomme at embl.de>
> Meyerhofstrasse 1 - Postfach 10.2209
> 69102 Heidelberg, Germany
>
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