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
