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'
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' > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html >-- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
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' > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html >