• using R Under development (unstable) (2012-02-07 r58290)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘pcalg/DESCRIPTION’ ... OK
• this is package ‘pcalg’ version ‘1.1-4’
• 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 ‘pcalg’ 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
  dsep: warning in wgtMatrix(gS, transp = FALSE): partial argument match
  of 'transp' to 'transpose'
  shd: warning in wgtMatrix(g1, transp = FALSE): partial argument match
  of 'transp' to 'transpose'
  shd: warning in wgtMatrix(g2, transp = FALSE): partial argument match
  of 'transp' to 'transpose'
• 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’ ... NOTE
  ‘qpdf’ made some significant size reductions:
  compacted ‘pcalgDoc.pdf’ from 440Kb to 338Kb
  consider running tools::compactPDF() on these files
• checking installed files from ‘inst/doc’ ... NOTE
  The following files are already in R: ‘jss.bst’, ‘jss.cls’
  Please remove them from your package.
  The following files should probably not be installed:
  ‘Makefile’
  The following directories should probably not be installed:
  ‘auto’, ‘jssStyle’
  
  Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
  or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
• checking examples ... ERROR
  Running examples in ‘pcalg-Ex.R’ failed
  The error most likely occurred in:
  
  > ### Name: gmG
  > ### Title: Graphical Model 8-Dimensional Gaussian Example Data
  > ### Aliases: gmG
  > ### Keywords: datasets
  >
  > ### ** Examples
  >
  > data(gmG)
  > str(gmG, max=3)
  List of 2
  $ x: num [1:5000, 1:8] 0.181 0.354 0.504 0.701 -0.705 ...
  $ g:Formal class 'graphNEL' [package "graph"] with 6 slots
  .. ..@ nodes : chr [1:8] "1" "2" "3" "4" ...
  .. ..@ edgeL :List of 8
  .. ..@ edgeData :Formal class 'attrData' [package "graph"] with 2 slots
  .. ..@ nodeData :Formal class 'attrData' [package "graph"] with 2 slots
  .. ..@ renderInfo:Formal class 'renderInfo' [package "graph"] with 4 slots
  .. ..@ graphData :List of 1
  > pairs(gmG$x, gap = 0,
  + panel=function(...) smoothScatter(..., add=TRUE))
  Error in loadNamespace(name) : there is no package called ‘KernSmooth’
  Calls: pairs ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  Execution halted