• using R Under development (unstable) (2013-05-17 r62757)
• using platform: x86_64-w64-mingw32 (64-bit)
• using session charset: ISO8859-1
• checking for file 'PKgraph/DESCRIPTION' ... OK
• this is package 'PKgraph' version '1.7'
• 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 hidden files and directories ... OK
• checking for portable file names ... OK
• checking whether package 'PKgraph' can be installed ... OK
• checking installed package size ... OK
• checking package directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over 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 loading without being on the library search path ... 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
  PKgraph: warning in ggroup(horizontal = FALSE, spacing = 0, cont = PKW,
  expand = TRUE): partial argument match of 'cont' to 'container'
  configFigureHandler: warning in ggroup(cont = gfigconfig.win,
  horizontal = FALSE): partial argument match of 'cont' to 'container'
  configFigureHandler: warning in glayout(cont = gf1): partial argument
  match of 'cont' to 'container'
  configFormatHandler: warning in ggroup(cont = gconfigsave.win,
  horizontal = FALSE): partial argument match of 'cont' to 'container'
  configFormatHandler: warning in glayout(cont = gf1): partial argument
  match of 'cont' to 'container'
  ggobi.diagose: warning in glabel("Step 1: Map data", cont = g1):
  partial argument match of 'cont' to 'container'
  ggobi.diagose: warning in gframe(horizontal = FALSE, expand = FALSE,
  cont = g1): partial argument match of 'cont' to 'container'
  ggobi.diagose: warning in glayout(cont = gf): partial argument match of
  'cont' to 'container'
  ggobi.diagose: warning in ggroup(cont = g1): partial argument match of
  'cont' to 'container'
  ggobi.diagose: warning in gbutton("Map Data", cont = bg1, handler =
  NULL): partial argument match of 'cont' to 'container'
  ggobi.diagose: warning in gbutton("Remove selection", cont = bg1,
  handler = NULL): partial argument match of 'cont' to 'container'
  ggobi.diagose: warning in glabel("Step 2: Configure plots", cont = g2):
  partial argument match of 'cont' to 'container'
  ggobi.diagose: warning in ggroup(horizontal = FALSE, expand = FALSE,
  cont = g2): partial argument match of 'cont' to 'container'
  ggobi.diagose: warning in gtable(items = c(letters[1:24]), cont = g22,
  expand = TRUE): partial argument match of 'cont' to 'container'
  ggobi.diagose: warning in ggroup(cont = g2): partial argument match of
  'cont' to 'container'
  ggobi.diagose: warning in gbutton("Plot selection", cont = bg2, handler
  = NULL): partial argument match of 'cont' to 'container'
  ggobi.diagose: warning in gbutton("Plot all", cont = bg2, handler =
  NULL): partial argument match of 'cont' to 'container'
  ggobi.diagose: warning in gbutton("Close plots", cont = bg2, handler =
  NULL): partial argument match of 'cont' to 'container'
  ggobi.map: warning in ggroup(cont = ggobi.map, horizontal = FALSE):
  partial argument match of 'cont' to 'container'
  ggobi.map: warning in glayout(cont = gf1): partial argument match of
  'cont' to 'container'
  ggobiPlotType: warning in ggroup(cont = ggobi.map, horizontal = FALSE):
  partial argument match of 'cont' to 'container'
  ggobiPlotType: warning in glayout(cont = gf1): partial argument match
  of 'cont' to 'container'
  openDataHandler: warning in ggroup(cont = gtmp.win, horizontal =
  FALSE): partial argument match of 'cont' to 'container'
  openDataHandler: warning in glayout(cont = gf1): partial argument match
  of 'cont' to 'container'
  selectDataDialog: warning in ggroup(cont = ggobi.gwin, horizontal =
  FALSE): partial argument match of 'cont' to 'container'
  selectDataDialog: warning in glabel(text = labelMessage1, cont =
  ggobi.group): partial argument match of 'cont' to 'container'
  selectDataDialog: warning in gframe(cont = ggobi.group): partial
  argument match of 'cont' to 'container'
  selectDataDialog: warning in gtable(alldata.name, cont = g1, expand =
  TRUE): partial argument match of 'cont' to 'container'
  selectDataDialog: warning in gbutton(">", cont = g1): partial argument
  match of 'cont' to 'container'
  selectDataDialog: warning in gtable(colnames(Theoph), cont = g1, expand
  = TRUE): partial argument match of 'cont' to 'container'
  selectDataDialog: warning in glabel(text = labelMessage2, cont =
  ggobi.group): partial argument match of 'cont' to 'container'
  selectDataDialog: warning in gbutton("Go to next step", cont =
  ggobi.group): partial argument match of 'cont' to 'container'
  subset.okButtonHandler: warning in glayout(cont = gframe.subset):
  partial argument match of 'cont' to 'container'
  subset.okButtonHandler: warning in gbutton(text = "Subset", border =
  TRUE, cont = gframe.subset, handler = function(h, ...) {: partial
  argument match of 'cont' to 'container'
  subset.okButtonHandler: warning in sapply(1:length(subset.var),
  function(i) {: partial argument match of 'cont' to 'container'
  subset.okButtonHandler: warning in currentData <<-
  subset.f1(svalue(tbl.value[[i * 3 - 2]]), svalue(tbl.value[[i * 3 -
  1]]), svalue(tbl.value[[i * 3]]), currentData): partial argument
  match of 'cont' to 'container'
  subset.okButtonHandler: warning in }): partial argument match of 'cont'
  to 'container'
  subset.okButtonHandler: warning in thisDatano <- getTotalDataLen() + 1:
  partial argument match of 'cont' to 'container'
  subset.okButtonHandler: warning in datatype <- "Subset": partial
  argument match of 'cont' to 'container'
  subset.okButtonHandler: warning in thisDataName <-
  paste(getTotalDataLen() + 1, "_", datatype, sep = ""): partial
  argument match of 'cont' to 'container'
  subset.okButtonHandler: warning in setDatasets(currentData,
  thisDatano): partial argument match of 'cont' to 'container'
  subset.okButtonHandler: warning in setCurrentDataType(datatype,
  thisDataName): partial argument match of 'cont' to 'container'
  subset.okButtonHandler: warning in ptable = gtable(currentData,
  multiple = TRUE, expand = TRUE): partial argument match of 'cont' to
  'container'
  subset.okButtonHandler: warning in pkmain.add(ptable,
  as.character(thisDataName), override.closebutton = TRUE): partial
  argument match of 'cont' to 'container'
  subset.okButtonHandler: warning in dispose(gwin.subset): partial
  argument match of 'cont' to 'container'
  subset.okButtonHandler: warning in svalue(PKENV$pmg.statusBar) <-
  "Subset sucessfully!": partial argument match of 'cont' to
  'container'
  subset.okButtonHandler: warning in }): partial argument match of 'cont'
  to 'container'
  cleanFigureButtonHandler: no visible binding for global variable
  'pk.dialog.notebook'
  com.hist.okButtonHandler: no visible binding for global variable
  'pk.dialog.notebook'
  com.hist.okButtonHandler.0125: no visible binding for global variable
  'pk.dialog.notebook'
  com.scatter.okButtonHandler: no visible binding for global variable
  'pk.dialog.notebook'
  com.scatter.okButtonHandler.0125: no visible binding for global
  variable 'pk.dialog.notebook'
  com.time.okButtonHandler: no visible binding for global variable
  'pk.dialog.notebook'
  com.time.okButtonHandler.back: no visible binding for global variable
  'pk.dialog.notebook'
  compare.pred.ggobiImageHandler: no visible binding for global variable
  'pk.dialog.notebook'
  model.cov.okButtonHandler: no visible binding for global variable
  'pk.dialog.notebook'
  model.ggobiImageHandler: no visible binding for global variable
  'pk.dialog.notebook'
  model.gof.okButtonHandler: no visible binding for global variable
  'pk.dialog.notebook'
  model.ind.okButtonHandler: no visible binding for global variable
  'pk.dialog.notebook'
  model.para.okButtonHandler: no visible binding for global variable
  'pk.dialog.notebook'
  model.random.okButtonHandler: no visible binding for global variable
  'pk.dialog.notebook'
  model.resid.okButtonHandler: no visible binding for global variable
  'pk.dialog.notebook'
  model.struct.okButtonHandler: no visible binding for global variable
  'pk.dialog.notebook'
  openDataHandler : <anonymous> : <anonymous>: no visible binding for
  '<<-' assignment to 'test'
  openDataHandler : <anonymous> : <anonymous>: no visible binding for
  global variable 'test'
  psn.bootstrap: no visible binding for global variable
  'minimization.successful'
  psn.bootstrap: no visible binding for global variable
  'covariance.step.successful'
  psn.bootstrap: no visible binding for global variable
  'covariance.step.warnings'
  psn.bootstrap: no visible binding for global variable
  'estimate.near.boundary'
  psn.bootstrap: no visible binding for global variable
  'pk.dialog.notebook'
  psn.bootstrap.sum.okButtonHandler: no visible binding for global
  variable 'pk.dialog.notebook'
  psn.bootstrap.sum.okButtonHandler: no visible binding for global
  variable 'minimization.successful'
  psn.bootstrap.sum.okButtonHandler: no visible binding for global
  variable 'covariance.step.successful'
  psn.bootstrap.sum.okButtonHandler: no visible binding for global
  variable 'covariance.step.warnings'
  psn.bootstrap.sum.okButtonHandler: no visible binding for global
  variable 'estimate.near.boundary'
  psn.bootstrap.vis.okButtonHandler: no visible binding for global
  variable 'pk.dialog.notebook'
  psn.bootstrap.vis.okButtonHandler: no visible binding for global
  variable 'ID'
  psn.bootstrap.vis.okButtonHandler: no visible binding for global
  variable 'resampleID'
  psn.bootstrap.vis.okButtonHandler: no visible binding for global
  variable 'para'
  psn.bootstrap.vis.okButtonHandler: no visible binding for global
  variable 'VAR'
  psn.cdd: no visible binding for global variable
  'minimization.successful'
  psn.cdd: no visible binding for global variable
  'covariance.step.successful'
  psn.cdd: no visible binding for global variable
  'covariance.step.warnings'
  psn.cdd: no visible binding for global variable
  'estimate.near.boundary'
  psn.cdd: no visible binding for global variable 'outside.n.sd'
  psn.outlier.okButtonHandler: no visible binding for global variable
  'pk.dialog.notebook'
  psn.outlier.okButtonHandler: no visible binding for global variable
  'ID'
  psn.outlier.okButtonHandler: no visible binding for global variable
  'cook.scores'
  psn.outlier.okButtonHandler: no visible binding for global variable
  'cov.ratios'
  saveImageHandler: no visible binding for global variable
  'pk.dialog.notebook'
  saveImageHandler.matrix: no visible binding for global variable
  'pk.dialog.notebook'
  saveImageHandler.pkmodel: no visible binding for global variable
  'pk.dialog.notebook'
  summary.bi.ggobiImageHandler: no visible binding for global variable
  'pk.dialog.notebook'
  summary.bi.okButtonHandler: no visible binding for global variable
  'pk.dialog.notebook'
  summary.heat.okButtonHandler: no visible binding for global variable
  'pk.dialog.notebook'
  summary.matrix.ggobiImageHandler: no visible binding for global
  variable 'pk.dialog.notebook'
  summary.matrix.okButtonHandler: no visible binding for global variable
  'pk.dialog.notebook'
  summary.para.ggobiImageHandler: no visible binding for global variable
  'pk.dialog.notebook'
  summary.para.okButtonHandler: no visible binding for global variable
  'pk.dialog.notebook'
  summary.tri.okButtonHandler: no visible binding for global variable
  'pk.dialog.notebook'
  summary.uni.ggobiImageHandler: no visible binding for global variable
  'pk.dialog.notebook'
  summary.uni.okButtonHandler: no visible binding for global variable
  'pk.dialog.notebook'
  val.okButtonHandler: no visible binding for global variable
  'pk.dialog.notebook'
  validation.ggobiImageHandler: no visible binding for global variable
  'pk.dialog.notebook'
  vis.outlier.okButtonHandler: no visible binding for global variable
  'pk.dialog.notebook'
  vis.outlier.okButtonHandler: no visible binding for global variable
  'runID'
  vis.outlier.okButtonHandler: no visible binding for global variable
  'deleteID'
  vis.outlier.okButtonHandler: no visible binding for global variable
  'ID'
  vis.outlier.okButtonHandler: no visible binding for global variable
  'para'
  vis.outlier.okButtonHandler: no visible binding for global variable
  'resampleID'
  vis.outlier.okButtonHandler: no visible global function definition for
  'namerows'
  vis.outlier.okButtonHandler: no visible global function definition for
  'melt'
  vis.outlier.okButtonHandler: no visible global function definition for
  'ddply'
  vis.outlier.okButtonHandler: no visible binding for global variable
  'variable'
  vis.outlier.okButtonHandler: no visible global function definition for
  'rescaler'
  vis.outlier.okButtonHandler: no visible binding for global variable
  'value'
  vis.outlier.okButtonHandler: no visible binding for global variable
  'rng'
  vis.outlier.okButtonHandler: no visible binding for global variable
  'cor1'
  vis.outlier.okButtonHandler: no visible binding for global variable
  'cor2'
• checking Rd files ... NOTE
  prepare_Rd: PKgraph.Rd:11-13: Dropping empty section \arguments
  prepare_Rd: PKgraph.Rd:17-19: Dropping empty section \examples
  prepare_Rd: pkdata.Rd:9-11: Dropping empty section \format
  prepare_Rd: pkdata.Rd:14-16: Dropping empty section \examples
  prepare_Rd: pkdata2.Rd:9-11: Dropping empty section \format
  prepare_Rd: pkdata2.Rd:14-16: Dropping empty section \examples
• 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 installed files from 'inst/doc' ... OK
• checking examples ... NONE
• 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 ... OK
• checking PDF version of manual ... OK
  NOTE: There were 2 notes.
  See
  'd:/Rcompile/CRANpkg/local/3.1/PKgraph.Rcheck/00check.log'
  for details.