• using R version 2.14.1 (2011-12-22)
• using platform: i386-apple-darwin9.8.0 (32-bit)
• using session charset: ASCII
• checking for file 'caret/DESCRIPTION' ... OK
• this is package 'caret' version '5.12-04'
• checking package namespace information ... OK
• checking package dependencies ... NOTE
  Packages suggested but not available for checking:
  'vbmp' 'LogicReg' 'LogicForest' 'logicFS'
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking whether package 'caret' 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
• 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 'x86_64'
  ** 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
  bwplot.diff.resamples: no visible binding for global variable 'Metric'
  bwplot.resamples: no visible binding for global variable 'Model'
  bwplot.resamples: no visible binding for global variable 'Metric'
  checkConditionalX: no visible binding for global variable '.outcome'
  classLevels.splsda: no visible global function definition for 'ilevels'
  createGrid : somDims: no visible binding for global variable '.xdim'
  createGrid : somDims: no visible binding for global variable '.ydim'
  createGrid : lvqGrid: no visible binding for global variable '.k'
  createGrid : lvqGrid: no visible binding for global variable '.size'
  createModel: possible error in rda(trainX, trainY, gamma =
  tuneValue$.gamma, lambda = tuneValue$.lambda, ...): unused
  argument(s) (gamma = tuneValue$.gamma, lambda = tuneValue$.lambda)
  createModel: no visible global function definition for
  'randomForestNWS'
  createModel: no visible global function definition for 'rfLSF'
  createModel: no visible global function definition for 'vbmp'
  createModel: no visible global function definition for 'logreg'
  createModel: no visible global function definition for
  'logreg.tree.control'
  createModel: no visible global function definition for 'logforest'
  createModel: no visible global function definition for 'logic.bagging'
  densityplot.diff.resamples: no visible binding for global variable
  'Metric'
  densityplot.diff.resamples: no visible binding for global variable
  'ind'
  densityplot.resamples: no visible binding for global variable 'Model'
  densityplot.resamples: no visible binding for global variable 'Metric'
  dotplot.resamples: no visible binding for global variable 'Model'
  dotplot.resamples: no visible binding for global variable 'Metric'
  icr.formula: no visible binding for global variable 'thresh'
  levelplot.diff.resamples: no visible binding for global variable
  'Metric'
  lift: no visible binding for global variable 'liftModelVar'
  looRfeWorkflow: no visible binding for global variable 'Variables'
  looTrainWorkflow: no visible binding for global variable 'parm'
  nominalRfeWorkflow: no visible binding for global variable 'Variables'
  nominalRfeWorkflow: no visible binding for global variable 'method'
  nominalRfeWorkflow: no visible binding for global variable 'Resample'
  nominalSbfWorkflow: no visible binding for global variable 'dat'
  nominalTrainWorkflow: no visible binding for global variable 'parm'
  nominalTrainWorkflow: no visible binding for global variable 'Resample'
  oobTrainWorkflow: no visible binding for global variable 'parm'
  overSampleImpute: no visible global function definition for 'complete'
  overSampleImpute: no visible global function definition for 'mice'
  plot.rfe: no visible binding for global variable 'Selected'
  plot.train: no visible binding for global variable 'parameter'
  plotClassProbs: no visible binding for global variable 'Observed'
  predictionFunction: no visible global function definition for
  'predictCPP'
  predictionFunction: no visible binding for global variable '.alpha'
  predictors.gbm: no visible binding for global variable 'rel.inf'
  predictors.sda: no visible binding for global variable 'varIndex'
  predictors.smda: no visible binding for global variable 'varIndex'
  probFunction: no visible global function definition for 'predictCPP'
  QuinlanAttributes.data.frame: no visible binding for global variable
  'QuinlanDescription'
  QuinlanAttributes.matrix: no visible binding for global variable
  'QuinlanDescription'
  resamples.default: no visible binding for global variable 'Variables'
  rfe.default: no visible binding for global variable 'Variables'
  splom.resamples: no visible binding for global variable 'Model'
  splom.resamples: no visible binding for global variable 'Metric'
  tuneScheme: no visible binding for global variable '.alpha'
  tuneScheme: no visible binding for global variable '.phi'
  tuneScheme: no visible binding for global variable '.lambda'
  varImp.rfe: no visible binding for global variable 'Variables'
• 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 line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking compiled code ... OK
• checking sizes of PDF files under 'inst/doc' ... OK
• checking examples ...
  ** running examples for arch 'i386' ... OK
  ** running examples for arch 'x86_64' ... OK
• 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:
  ...
  
  loadings
  
  randomForest 4.6-6
  Type rfNews() to see new features/changes/bug fixes.
  Loading required package: leaps
  Loading required package: plotmo
  Loading required package: plotrix
  
  Attaching package: 'proxy'
  
  The following object(s) are masked from 'package:stats':
  
  as.dist, dist
  
  Loading required package: ellipse
  Warning in draw.key(simpleKey(...), draw = FALSE) :
  not enough rows for columns
  Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
  Running 'texi2dvi' on 'caretMisc.tex' failed.
  Messages:
  /usr/bin/texi2dvi: pdflatex exited with bad status, quitting.
  /usr/bin/texi2dvi: see caretMisc.log for errors.
  Calls: buildVignettes -> texi2pdf -> texi2dvi
  Execution halted
  
• checking PDF version of manual ... OK
• elapsed time (check, wall clock): 11:09