• using R version 2.11.1 Patched (2010-07-29 r52657)
• using session charset: ISO8859-1
• checking for file 'IsoGene/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'IsoGene' version '1.0-17'
• checking package name space information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking whether package 'IsoGene' can be installed ... OK
• 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 package can be unloaded cleanly ... OK
• checking whether the name space can be loaded with stated dependencies ... OK
• checking whether the name space can be unloaded cleanly ... 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 metadata ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking data for non-ASCII characters ... OK
• checking examples ... ERROR
  Running examples in 'IsoGene-Ex.R' failed.
  The error most likely occurred in:
  
  > ### * IsoTestSAM
  >
  > flush(stderr()); flush(stdout())
  >
  > ### Name: IsoTestSAM
  > ### Title: Obtaining the list of significant genes using the SAM procedure
  > ### Aliases: IsoTestSAM
  > ### Keywords: htest
  >
  > ### ** Examples
  >
  > set.seed(1234)
  > x <- c(rep(1,3),rep(2,3),rep(3,3))
  > y1 <- matrix(rnorm(4500, 1,1),500,9) ## 500 genes with no trends
  > y2 <- matrix(c(rnorm(1500, 1,1),rnorm(1500,2,1),rnorm(1500,3,1)),500,9) ## 500 genes with increasing trends
  > y <- data.frame(rbind(y1, y2)) ##y needs to be a data frame
  > SAM.obj <- IsoTestSAM(x, y, fudge="pooled", niter=50, FDR=0.05, stat="E2")
  Error in `colnames<-`(`*tmp*`, value = c("Row.names", "t.stat", "q.val" :
  attempt to set colnames on object with less than two dimensions
  Calls: IsoTestSAM -> Isoqval -> colnames<-
  Execution halted