Hi, don't worry about those setGenericS3()/setMethodS3(0 warnings - they are just informative.
I am aware of that last warning: Warning: package 'R.oo' claims to be built under R version 2.10.0 but is missing some help files and needs to be re-installed but it does not go away when you reinstall. It is also reported in all of the CRAN checks, which obviously are built on the correct version, cf. http://cran.r-project.org/web/checks/check_results_R.oo.html I haven't had time to track down what triggers this warning. I wouldn't worry about this warning either - R.oo is used in many downstream packages with tons of CPU hours/testing, and I haven't got any reports that this would cause a problem. /Henrik On Wed, Jan 20, 2010 at 7:23 AM, Peng Yu <pengyu...@gmail.com> wrote: > I got the following warnings when I install R.oo. Are these warnings > normal? Should I reinstall the package as mentioned in the warnings? > How to reinstall? The sessionInfo() is at the end. > > > > >> install.packages("R.oo", dependencies=T) > Warning in install.packages("R.oo", dependencies = T) : > argument 'lib' is missing: using '/utility/R' > also installing the dependency ‘R.methodsS3’ > > trying URL > 'http://cran.sixsigmaonline.org/src/contrib/R.methodsS3_1.1.0.tar.gz' > Content type 'application/x-gzip' length 16263 bytes (15 Kb) > opened URL > ================================================== > downloaded 15 Kb > > trying URL 'http://cran.sixsigmaonline.org/src/contrib/R.oo_1.6.6.tar.gz' > Content type 'application/x-gzip' length 361830 bytes (353 Kb) > opened URL > ================================================== > downloaded 353 Kb > >> tools:::.install_packages() > * installing *source* package ‘R.methodsS3’ ... > ** R > ** inst > ** preparing package for lazy loading > ** help > *** installing help indices > ** building package indices ... > * DONE (R.methodsS3) >> >> tools:::.install_packages() > * installing *source* package ‘R.oo’ ... > ** R > ** inst > ** preparing package for lazy loading > R.methodsS3 v1.1.0 (2010-01-02) successfully loaded. See ?R.methodsS3 for > help. > Warning in setGenericS3.default(name, envir = envir, validators = validators) > : > Renamed the preexisting function attach to attach.default, which was > defined in environment base. > Warning in setGenericS3.default(name, envir = envir, validators = validators) > : > Renamed the preexisting function detach to detach.default, which was > defined in environment base. > Warning in setGenericS3.default(name, envir = envir, validators = validators) > : > Renamed the preexisting function save to save.default, which was > defined in environment base. > Warning in setGenericS3.default(name, envir = envir, validators = validators) > : > Renamed the preexisting function load to load.default, which was > defined in environment base. > Warning in setGenericS3.default(name, envir = envir, validators = validators) > : > Renamed the preexisting function extend to extend.default, which was > defined in environment R.oo. > Warning in setGenericS3.default(name, envir = envir, validators = validators) > : > Renamed the preexisting function gc to gc.default, which was defined > in environment base. > Warning in setGenericS3.default(name, envir = envir, validators = validators) > : > Renamed the preexisting function getMethods to getMethods.default, > which was defined in environment base. > Warning in setGenericS3.default(name, envir = envir, validators = validators) > : > Renamed the preexisting function getClasses to getClasses.default, > which was defined in environment base. > Warning in setMethodS3.default("throw", "default", function(...) { : > Method already existed and was overwritten: throw.default > ** help > Warning: package 'R.oo' claims to be built under R version 2.10.0 but > is missing some help files and needs to be re-installed > *** installing help indices > ** building package indices ... > * DONE (R.oo) >> > > The downloaded packages are in > ‘/tmp/Rtmp6iZyqg/downloaded_packages’ > >> sessionInfo() > R version 2.10.0 (2009-10-26) > 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 > > loaded via a namespace (and not attached): > [1] tools_2.10.0 > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.