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: [email protected]
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
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