* using log directory 'd:/Rcompile/CRANpkg/local/3.0/PKgraph.Rcheck' * using R version 3.0.3 (2014-03-06) * using platform: i386-w64-mingw32 (32-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 ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: 'RGtk2' 'gWidgetsRGtk2' A package should be listed in only one of these fields. * 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 dependencies in R code ... NOTE Package in Depends field not imported from: 'cairoDevice' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. See the information on DESCRIPTION files in the chapter 'Creating R packages' of the 'Writing R Extensions' manual. * 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 : : : no visible binding for '<<-' assignment to 'test' openDataHandler : : : 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 files in 'vignettes' ... 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 outputs ... OK * checking PDF version of manual ... OK NOTE: There were 4 notes.