[R] R CMD check failure on minimal code

[Douglas Bates]

On 8/15/05, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> I have a peculiar problem that I'm sure is a simple one, but I can't figure
> out what my mistake is.  Can someone enlighten me?  I have a simple file,
> class.R:
> 
> ##
> setClass("abc",representation(a = "character", b = "ANY"))
> 
> I have a package directory ExpressCGH1 made with package.skeleton.  The
> package happily builds and installs, but R CMD check fails with (ignoring
> the documenation warnings, etc.):

Can you declare a slot to have class "ANY"?  You can use class "ANY"
in a method signature but I don't think you can use it for a slot.

Try to see if you can attach the package in R.  That may give more
informative errors.

> 
> > version
>          _
> platform powerpc-apple-darwin7.9.0
> arch     powerpc
> os       darwin7.9.0
> system   powerpc, darwin7.9.0
> status   Patched
> major    2
> minor    1.1
> year     2005
> month    08
> day      12
> language R
> 
> 
> 
> %%% R CMD check -l '/User
> s/sdavis/Library/R/library' ExpressCGH1
> * checking for working latex ... OK
> * using log directory
> '/Users/sdavis/Work/R-Programs/packages/devel/ExpressCGH/E
> xpressCGH1.Rcheck'
> * using R version 2.1.1, 2005-08-12
> * checking for file 'ExpressCGH1/DESCRIPTION' ... OK
> * checking extension type ... Package
> * this is package 'ExpressCGH1' version '1.0'
> * checking if this is a source package ... OK
> 
> * Installing *source* package 'ExpressCGH1' ...
> ** libs
> WARNING: no source files found
> chmod: /Users/sdavis/Library/R/library/ExpressCGH1/libs/*: No such file or
> direc
> tory
> ** R
> ** help
>  >>> Building/Updating help pages for package 'ExpressCGH1'
>      Formats: text html latex example
>   convertDNAcopyOutput              text    html    latex   example
>      missing link(s):  ~~fun~~
> ** building package indices ...
> * DONE (ExpressCGH1)
> 
> * checking package directory ... OK
> * checking for portable file names ... OK
> * checking for sufficient/correct file permissions ... OK
> * checking DESCRIPTION meta-information ... OK
> * checking package dependencies ... OK
> * checking index information ... OK
> * checking package subdirectories ... WARNING
> Subdirectory 'src' contains no source files.
> * checking R files for syntax errors ... OK
> * checking R files for library.dynam ... OK
> * checking S3 generic/method consistency ... WARNING
> Error: unable to load R code in package 'ExpressCGH1'
> Call sequence:
> 2: stop(gettextf("unable to load R code in package '%s'",
> libraryPkgName(package
> )),
>        call. = FALSE, domain = NA)
> 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
> FALSE)
> Execution halted
> See section 'Generic functions and methods' of the 'Writing R Extensions'
> manual.
> * checking replacement functions ... WARNING
> Error: unable to load R code in package 'ExpressCGH1'
> Call sequence:
> 2: stop(gettextf("unable to load R code in package '%s'",
> libraryPkgName(package
> )),
>        call. = FALSE, domain = NA)
> 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
> FALSE)
> Execution halted
> In R, the argument of a replacement function which corresponds to the right
> hand side must be named 'value'.
> * checking foreign function calls ... WARNING
> Error: unable to load R code in package 'ExpressCGH1'
> Call sequence:
> 2: stop(gettextf("unable to load R code in package '%s'",
> libraryPkgName(package
> )),
>        call. = FALSE, domain = NA)
> 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
> FALSE)
> Execution halted
> See section 'System and foreign language interfaces' of the 'Writing R
> Extensions' manual.
> * checking Rd files ... WARNING
> Rd files with likely Rd problems:
> Unaccounted top-level text in file
> '/Users/sdavis/Work/R-Programs/packages/devel
> /ExpressCGH/ExpressCGH1/man/convertDNAcopyOutput.Rd':
> Following section 'note':
> "\n\n ~Make other sections like Warning with \\section{Warning }{....}
> ~\n\n"
> 
> Rd files with non-standard keywords:
> 
> /Users/sdavis/Work/R-Programs/packages/devel/ExpressCGH/ExpressCGH1/man/conv
> er
> tDNAcopyOutput.Rd:
>     ~kwd1 ~kwd2
> Each '\keyword' entry should specify one of the standard keywords (as
> listed in file 'KEYWORDS.db' in the 'doc' subdirectory of the R home
> directory).
> 
> See chapter 'Writing R documentation files' in manual 'Writing R
> Extensions'.
> * checking for missing documentation entries ... ERROR
> Error: unable to load R code in package 'ExpressCGH1'
> 
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