• using R version 3.0.1 Patched (2013-05-18 r62762)
• using platform: sparc-sun-solaris2.10 (32-bit)
• using session charset: UTF-8
• checking for file ‘BiomarkeR/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘BiomarkeR’ version ‘1.3’
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘BiomarkeR’ can be installed ... OK
• checking installed package size ... OK
• checking package directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over 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 namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... 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 ... NOTE
  prepare_Rd: BIdata.RData.Rd:27-28: Dropping empty section \details
  prepare_Rd: BIdata.RData.Rd:29-30: Dropping empty section \source
  prepare_Rd: BIdata.RData.Rd:31-32: Dropping empty section \references
  prepare_Rd: pBI.Rd:52-53: Dropping empty section \note
  prepare_Rd: pBIGraph.Rd:57-58: Dropping empty section \note
  prepare_Rd: pBIGraph.Rd:52-53: Dropping empty section \references
  prepare_Rd: uBI.Rd:53-54: Dropping empty section \note
  prepare_Rd: uBIGraph.Rd:54-55: Dropping empty section \note
  prepare_Rd: uBIGraph.Rd:49-50: Dropping empty section \references
• 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 for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking examples ... [69s/153s] OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... [73s/155s] ERROR
  Errors in running code in vignettes:
  when running code in ‘BiomarkeR.Rnw’
  ...
  9: withVisible(eval(ei, envir))
  10: source(output, echo = TRUE)
  11: doTryCatch(return(expr), name, parentenv, handler)
  12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  13: tryCatchList(expr, classes, parentenv, handlers)
  14: tryCatch({ source(output, echo = TRUE)}, error = function(e) { cat("\n When sourcing ", sQuote(output), ":\n", sep = "") stop(conditionMessage(e), call. = FALSE, domain = NA)})
  15: tools:::.run_one_vignette("BiomarkeR.Rnw", "/home/ripley/R/packages/tests32/BiomarkeR/inst/doc", pkgdir = "/home/ripley/R/packages/tests32/BiomarkeR")
  aborting ...
  
  ... incomplete output. Crash?