[R] R CMD check failure on minimal code

[Sean Davis]

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.):

> 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'