• using R version 2.15.0 Patched (2012-05-19 r59366)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘abcdeFBA/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘abcdeFBA’ version ‘0.2’
• 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 whether package ‘abcdeFBA’ 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 ... 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 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 examples ... ERROR
  Running examples in ‘abcdeFBA-Ex.R’ failed
  The error most likely occurred in:
  
  > ### Name: PHPP
  > ### Title: PHPP, phenotypic phase plane analysis
  > ### Aliases: PHPP 'phenotypic phase plane analysis'
  >
  > ### ** Examples
  >
  > #Performing a phenotypic phase plane analysis of
  > #glucose and oxygen in Core E.coli Metabolism
  > data(Ecoli_core)
  > PHPP(reaction_number=c(28,36),fba_object=Ecoli_core,
  + PCS="glucose",flux_range=c(1,15))
  
  Probable Carbon Sources:
  [1] "D-Glucose exchange" "glucose 6-phosphate dehydrogenase"
  [3] "D-glucose transport via PEP:Pyr PTS" "glucose-6-phosphate isomerase"
  
  Select the Carbon source from the list above by serial number
  Alternate carbon source PhPP
  [1] 1
  [1] 2
  [1] 3
  [1] 4
  [1] 5
  [1] 6
  [1] 7
  [1] 8
  [1] 9
  [1] 10
  [1] 11
  [1] 12
  [1] 13
  [1] 14
  [1] 15
  Error in rgl.cur() : rgl_dev_getcurrent
  Calls: PHPP ... persp3d -> persp3d.default -> clear3d -> .check3d -> rgl.cur
  Execution halted