On Fri, Feb 19, 2010 at 8:51 AM, Nicolas Delhomme <[email protected]> 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 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
