* using log directory 'd:/Rcompile/CRANpkg/local/2.9/GSA.Rcheck'
* using R version 2.9.2 Patched (2009-09-02 r49531)
* using session charset: ISO8859-1
* checking for file 'GSA/DESCRIPTION' ... OK
* this is package 'GSA' version '1.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GSA' can be installed ... WARNING
Found the following significant warnings:
  Warning: invalid whitespace before brace in file 'GSA.Rd' at ' \item{y} {Vector of response values:  1,2 for two class problem, or 1,2,3 ... for multiclass problem, or real numbers for quantitative or survival problems}'
  Warning: invalid whitespace before brace in file 'GSA.Rd' at ' \item{y} {Vector of response values:  1,2 for two class problem, or 1,2,3 ... for multiclass problem, or real numbers for quantitative or survival problems}'
  Warning: unmatched right brace in file 'GSA.correlate.Rd' on line 7
  Warning: unmatched right brace in file 'GSA.correlate.Rd' on line 7
  Warning: invalid whitespace before brace in file 'GSA.func.Rd' at ' \item{y} {Vector of response values:  1,2 for two class problem, or 1,2,3 ... for multiclass problem, or real numbers for quantitative or survival problems}'
  Warning: invalid whitespace before brace in file 'GSA.func.Rd' at ' \item{y} {Vector of response values:  1,2 for two class problem, or 1,2,3 ... for multiclass problem, or real numbers for quantitative or survival problems}'
  Warning: invalid whitespace before brace in file 'GSA.genescores.Rd' at ' \item{genesets} {The gene set collection}'
  Warning: invalid whitespace before brace in file 'GSA.genescores.Rd' at ' \item{genesets} {The gene set collection}'
  Warning: unmatched right brace in file 'GSA.listsets.Rd' on line 6
  Warning: unmatched right brace in file 'GSA.listsets.Rd' on line 6
  Warning: unmatched right brace in file 'GSA.plot.Rd' on line 6
  Warning: unmatched right brace in file 'GSA.plot.Rd' on line 6
See 'd:/Rcompile/CRANpkg/local/2.9/GSA.Rcheck/00install.out' for details.
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd files against version 2 parser ... WARNING
Warning in parse_Rd("./man/GSA.Rd", encoding = "unknown") :
  bad markup (extra space?) at GSA.Rd:22:9
Warning: ./man/GSA.Rd:22-24: Unnecessary braces at '{Vector of response values:  1,2 for two class
problem, or 1,2,3 ... for multiclass problem, or real numbers for quantitative
or survival problems}'
*** error on file ./man/GSA.correlate.Rd
Error in parse_Rd("./man/GSA.correlate.Rd", encoding = "unknown") : 
  ./man/GSA.correlate.Rd:7:1: unexpected '}'
6: on the overlap between the collection and the list of genes}
7: }
   ^

Warning in parse_Rd("./man/GSA.func.Rd", encoding = "unknown") :
  bad markup (extra space?) at GSA.func.Rd:24:9
Warning: ./man/GSA.func.Rd:24-26: Unnecessary braces at '{Vector of response values:  1,2 for two class
problem, or 1,2,3 ... for multiclass problem, or real numbers for quantitative
or survival problems}'
Warning in parse_Rd("./man/GSA.genescores.Rd", encoding = "unknown") :
  bad markup (extra space?) at GSA.genescores.Rd:12:16
Warning: ./man/GSA.genescores.Rd:12: Unnecessary braces at '{The gene set collection}'
*** error on file ./man/GSA.listsets.Rd
Error in parse_Rd("./man/GSA.listsets.Rd", encoding = "unknown") : 
  ./man/GSA.listsets.Rd:6:1: unexpected '}'
5: List the results from a call to  GSA  (Gene set analysis)}
6: }
   ^

*** error on file ./man/GSA.plot.Rd
Error in parse_Rd("./man/GSA.plot.Rd", encoding = "unknown") : 
  ./man/GSA.plot.Rd:6:1: unexpected '}'
5: Plots the results from a call to  GSA  (Gene set analysis)}
6: }
   ^

problems found in 'GSA.correlate.Rd', 'GSA.listsets.Rd', 'GSA.plot.Rd'
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking examples ... OK
* checking PDF version of manual ... OK