[R] R.oo installation warnings?

[Henrik Bengtsson]

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.ut at 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
>
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