You should _always_ use R-devel when using Bioc-devel. Kasper
On Fri, Feb 19, 2010 at 9:20 AM, Droit Arnaud <[email protected]> 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: [email protected]<mailto:[email protected]> > Meyerhofstrasse 1 - Postfach 10.2209 > 69102 Heidelberg, Germany > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected]<mailto:[email protected]> > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
