• using R Under development (unstable) (2012-02-27 r58511)
• using platform: x86_64-pc-mingw32 (64-bit)
• using session charset: ISO8859-1
• 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 whether package 'pcalg' can be installed ... OK
• checking installed package size ... 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
• loading checks for arch 'i386'
  ** 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
• loading checks for arch 'x64'
  ** 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 ...
  ** running examples for arch 'i386' ... OK
  ** running examples for arch 'x64' ... OK
• checking for unstated dependencies in tests ... OK
• checking tests ...
  ** running tests for arch 'i386' OK
  Running 'test_amat2dag.R'
  Running 'test_compareGraphs.R'
  Running 'test_dag2cpdag.R'
  Running 'test_dsep.R'
  Running 'test_fci.R'
  Running 'test_gSquareBin.R'
  Running 'test_gSquareDis.R'
  Running 'test_getNextSet.R'
  Running 'test_ida.R'
  Running 'test_idaFast.R'
  Running 'test_pc.R'
  Running 'test_pcAlgo.R'
  Running 'test_pcSelect.R'
  Running 'test_pcorOrder.R'
  Running 'test_pdag2dag.R'
  Running 'test_randomDAG.R'
  Running 'test_rfci.R'
  Running 'test_rmvDAG.R'
  Running 'test_shd.R'
  Running 'test_skeleton.R'
  Running 'test_udag2pag.R'
  Running 'test_udag2pdag.R'
  Running 'test_wgtMatrix.R'
  ** running tests for arch 'x64' OK
  Running 'test_amat2dag.R'
  Running 'test_compareGraphs.R'
  Running 'test_dag2cpdag.R'
  Running 'test_dsep.R'
  Running 'test_fci.R'
  Running 'test_gSquareBin.R'
  Running 'test_gSquareDis.R'
  Running 'test_getNextSet.R'
  Running 'test_ida.R'
  Running 'test_idaFast.R'
  Running 'test_pc.R'
  Running 'test_pcAlgo.R'
  Running 'test_pcSelect.R'
  Running 'test_pcorOrder.R'
  Running 'test_pdag2dag.R'
  Running 'test_randomDAG.R'
  Running 'test_rfci.R'
  Running 'test_rmvDAG.R'
  Running 'test_shd.R'
  Running 'test_skeleton.R'
  Running 'test_udag2pag.R'
  Running 'test_udag2pdag.R'
  Running 'test_wgtMatrix.R'
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in 'inst/doc' ... OK
• checking running R code from vignettes ... OK
• checking re-building of vignette PDFs ... NOTE
  Error in re-building vignettes:
  ...
  A specification for S3 class "file" in package 'BiocGenerics' seems equivalent to one from package 'graph' and is not turning on duplicate class definitions for this class
  Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "gzfile" in package 'BiocGenerics' seems equivalent to one from package 'graph' and is not turning on duplicate class definitions for this class
  Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "url" in package 'BiocGenerics' seems equivalent to one from package 'graph' and is not turning on duplicate class definitions for this class
  Warning in fun(libname, pkgname) :
  Rgraphviz built with Graphviz version 2.20.3.
  Found installed Graphviz version 2.25.20090912.445. This _may_ cause problems.
  
  Attaching package: 'Rgraphviz'
  
  The following object(s) are masked from 'package:grid':
  
  bezierPoints
  
  
  (Rterm.exe:8012): Pango-WARNING **: couldn't load font "Times New Not-Rotated 14", falling back to "Sans Not-Rotated 14", expect ugly output.
  make[1]: Entering directory `/cygdrive/d/RCompile/CRANpkg/local/2.15/pcalg.Rcheck/vign_test/pcalg/inst/doc'
  TEXINPUTS=.;.;;D:/RCompile/recent/R/share/texmf/tex/latex;;d:/RCompile/recent/R/share/texmf/tex/latex;:/usr/local/app/R/current/share/texmf// texi2pdf pcalgDoc.tex
  Syntax error: ";;" unexpected
  make[1]: *** [pcalgDoc.pdf] Error 2
  make[1]: Leaving directory `/cygdrive/d/RCompile/CRANpkg/local/2.15/pcalg.Rcheck/vign_test/pcalg/inst/doc'
  Error in buildVignettes(dir = "d:/Rcompile/CRANpkg/local/2.15/pcalg.Rcheck/vign_test/pcalg") :
  running 'make' failed
  Execution halted
  
• checking PDF version of manual ... OK
  NOTE: There were 4 notes.
  See
  'd:/Rcompile/CRANpkg/local/2.15/pcalg.Rcheck/00check.log'
  for details.