• using R version 2.14.0 (2011-10-31)
• using platform: i386-apple-darwin9.8.0 (32-bit)
• using session charset: ASCII
• checking for file 'penalized/DESCRIPTION' ... OK
• this is package 'penalized' version '0.9-37'
• checking package namespace information ... OK
• checking package dependencies ... NOTE
  Package suggested but not available for checking: 'globaltest'
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking whether package 'penalized' can be installed ... OK
• checking installed package size ... OK
• checking package directory ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... 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 namespace can be loaded with stated dependencies ... OK
• checking whether the namespace 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 ... NOTE
  File 'penalized/R/onattach.R':
  .onAttach calls:
  cat("Welcome to penalized. For extended examples, see vignette(\"penalized\").\n")
  
  Package startup functions should use 'packageStartupMessage' to
  generate messages.
  See section 'Good practice' in ?.onAttach.
  
• 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 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 sizes of PDF files under 'inst/doc' ... OK
• checking examples ... OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in 'inst/doc' ... OK
• checking running R code from vignettes ... WARNING
  Errors in running code in vignettes:
  when running code in 'penalized.Rnw'
  ...
  TSPYL5 Contig63649_RC NUSAP1 AA555029_RC ALDH4A1
  -0.08434359 1.25110142 2.47959605 0.10725996 1.03025029
  QSCN6L1 FGF18
  2.22365221 1.25928431
  
  > library(globaltest)
  
  When sourcing 'penalized.R':
  Error: there is no package called 'globaltest'
  Execution halted
  
• checking re-building of vignette PDFs ... NOTE
  Error in re-building vignettes:
  ...
  Loading required package: survival
  Loading required package: splines
  
  Error: processing vignette 'penalized.Rnw' failed with diagnostics:
  chunk 24 (label = globaltest)
  Error in library(globaltest) : there is no package called 'globaltest'
  Execution halted
  
• checking PDF version of manual ... OK
  WARNING: There was 1 warning, see
  '/Volumes/Tiger/Builds/Rdev-web/QA/Simon/packages/leopard-universal/results/2.14/penalized.Rcheck/00check.log'
  for details
• elapsed time (check, wall clock): 1:22