R CMD check failure on minimal code
Did you remember to declare a dependency on package 'methods'? I suspect not. Please see `Writing R Extensions'. setClass is not part of base R, and those checks are being run with base R only. I expect your package will not load when R is run with no default packages. (Quite a few people run R without package 'methods' for speed, especially on startup -- it takes about half the startup time.)
On Mon, 15 Aug 2005, Sean Davis 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.):
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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