R Development Page

addendum log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2015-11-10-09-29/RF_PKG_CHECK/PKGS/addendum.Rcheck'
* using R version 3.2.2 Patched (2015-11-05 r69602)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'addendum/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'addendum' version '1.7.7'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Nick Sabbe '
New submission

The Title field should be in title case, current version then in title case:
'Things that R needs for day to day use'
'Things that R Needs for Day to Day Use'

The Date field is over a month old.
* checking package namespace information ... OK
* checking package dependencies ... NOTE
  No repository set, so cyclic dependency check skipped
* 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 'addendum' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'glmnet'
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 use of S3 registration ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  'Matrix' 'glmnet' 'rgl' 'snowfall'
  Please remove these calls from your code.
'library' or 'require' call to 'brglm' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'mgcv'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  allLevels.data.frame allLevels.data.frame.rep
  allOrderedFacts.data.frame allOrderedFacts.data.frame.rep
  applyTransform.mapCleanItem as.data.frame.data.frame.rep
  as.double.data.frame.rep as.list.data.frame.rep
  as.matrix.data.frame.rep coef.Matrix colsAsNumericMatrix.data.frame
  colsAsNumericMatrix.default combineSimilarDfrList.data.frame
  combineSimilarDfrList.default dim.data.frame.rep
  dimnames.data.frame.rep dimnames<-.data.frame.rep
  display.data.frame.rep display.default
  factorsToDummyVariables.data.frame.rep
  factorsToDummyVariables.default findCatColNums.data.frame
  findCatColNums.data.frame.rep findOrderedColNums.data.frame
  getBeta.cv.glmnet getBeta.glmnet is.na.data.frame.rep
  length.data.frame.rep makeDatasetFormulaSafe.data.frame
  matches.mapCleanItem names.data.frame.rep names<-.data.frame.rep
  originalDataset.data.frame.rep originalDataset.default plot.cv.glmnet
  print.checkSig print.data.frame.rep print.missingInfo
  reduce.data.frame reduce.default restrictForLambda.cv.glmnet
  restrictForLambda.glmnet restrictForVars.cv.glmnet
  restrictForVars.glmnet showInterestingCoef.Matrix
  showInterestingCoef.cv.glmnet showInterestingCoef.default
  showInterestingCoef.glmnet showInterestingCoef.list
  showInterestingCoef.matrix showMemoryUsageList.default
  showMemoryUsageList.environment showNonZeroCoef.Matrix
  showNonZeroCoef.cv.glmnet showNonZeroCoef.default
  showNonZeroCoef.glmnet simpleplot.cv.glmnet simpleplot.default
  simpleplot.glmnet str.data.frame.rep unreduce.data.frame.rep
  unreduce.default
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
sfInitEx: no visible global function definition for 'getMPIcluster'

Found the following assignments to the global environment:
File 'addendum/R/Helpers.r':
  assign(toname, to, envir = globalenv())
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'addCVPlot.Rd':
  \usage lines wider than 90 characters:
     addCVPlot(cvobj, xvar=c("norm", "lambda", "dev"), numTicks, smoothed=FALSE, errorbarcolor="darkgrey", centercolor="red", fillsidecolor= ... [TRUNCATED]
     addLamIndexAxis(cvobj, xvar=c("norm", "lambda", "dev"), numTicks=5,..., addIdxAx=TRUE, addTitle=TRUE, coldata, verbosity=0)

Rd file 'addLegend.Rd':
  \usage lines wider than 90 characters:
     addLegend(cvobj, matplotCols=1:6, repsNeededForFirstOccurrence=3, topHowMany=20, beta.type=NULL,

Rd file 'basisExpansionFormula.Rd':
  \usage lines wider than 90 characters:
     basisExpansionFormula(dfr, outCol, patternNumericCols = "X", subPatternCol = "X", fixed = TRUE, onlyCols=NULL, allowDot=(!is.null(onlyC ... [TRUNCATED]

Rd file 'categoricalUniqueIdentifiers.Rd':
  \examples lines wider than 100 characters:
     aDfr<-do.call(data.frame,replicate(10, factor(sample(c("a", "b", "c"), 20, replace=TRUE)), simplify=FALSE))

Rd file 'catif.Rd':
  \usage lines wider than 90 characters:
     curfnfinder(skipframes=0, cils=typicalCleanItemList(), defaultCI=mapCleanItem("(.*)", 1), retIfNone="Not in function", retStack=FALSE,  ... [TRUNCATED]

Rd file 'clean_cs.Rd':
  \usage lines wider than 90 characters:
     applyCleanItemMatch(towhat, cils=typicalCleanItemList(), defaultCI=mapCleanItem("(.*)", 1))

Rd file 'colorsForPlotEx.Rd':
  \usage lines wider than 90 characters:
     colorsForPlotEx(cvobj, matplotCols, repsNeededForFirstOccurrence=3, topHowMany=20, beta.type=NULL, altColNameIn=NULL, altColExpressionO ... [TRUNCATED]

Rd file 'combineGlmnets.Rd':
  \usage lines wider than 90 characters:
     glmnetNoPredictors(y, xvarnames, family=c("gaussian","binomial","poisson","multinomial","cox","mgaussian"), weights, lambda)
  \examples lines wider than 100 characters:
     tstg<-glmnetNoPredictors(y=tsty, xvarnames=c("aVar", "anotherVar"), family="binomial", lambda=c(0.02,0.03,0.04,0.05))

Rd file 'cv.glmnet.stability.Rd':
  \usage lines wider than 90 characters:
     cv.glmnet.stability(orgx, orgy, nfolds=10, stability.type=c("MC", "MCR", "FP", "FPR", "FN", "FNR", "FDR", "DST", "DSTPV"), unbiasFullCo ... [TRUNCATED]
  \examples lines wider than 100 characters:
     tststab<-cv.glmnet.stability(orgx=x, orgy=y, stability.type=c("MC", "MCR", "FP", "FPR", "FN", "FNR", "FDR"),
             unbiasFullCorrectionType="dont", unbiasFoldCorrectionType="dont", family="binomial", verbosity=1)

Rd file 'data.frame.rep.Rd':
  \usage lines wider than 90 characters:
     rbind(..., original.data, ensure.unique.rownames=FALSE, separator=".", postfixcol=NULL, allowemptypostfix=TRUE, deparse.level = 1)

Rd file 'factorsToDummyVariables.Rd':
  \examples lines wider than 100 characters:
     irisdcp<-dfrConversionProps(dfr = iristmp, betweenColAndLevel = "", includeBaseLevel = FALSE, verbosity = 4)
     irismat<-factorsToDummyVariables(dfr=iristmp, dfrConvData=irisdcp, betweenColAndLevel="", verbosity=5)

Rd file 'findUnivariateSignificancePVal.Rd':
  \usage lines wider than 90 characters:
     findUnivariateSignificancePVal(dfr, outcomecol, betweenColAndLevel="", returnPValBelow=0.05, splitCats=TRUE)

Rd file 'getAsFunction.Rd':
  \examples lines wider than 100 characters:
     getAsFunction("thisFunctionProbablyDoesntExist", returnIfNotFound=function(x){return(x)}, verbosity=1)

Rd file 'getColorRange.Rd':
  \usage lines wider than 90 characters:
     getColorRange(x, mini = min(x), maxi = max(x), minFirstColor = 0.5, maxSecondColor = 0.5, constThirdColor = 0, returnAsString = FALSE,  ... [TRUNCATED]

Rd file 'linearPredict.Rd':
  \usage lines wider than 90 characters:
     linearPredict(dfr, coefs, itcname="(Intercept)", dfrconv, betweenColAndLevel="", verbosity=0)

Rd file 'lognetUnbias.Rd':
  \usage lines wider than 90 characters:
     lognetUnbias(lnet, orgx, orgy, outname="out", verbosity=0, methodForNonConvergence=c("ridge", "brglm", "none"))

Rd file 'makeNamesFormulaSafe.Rd':
  \examples lines wider than 100 characters:
             cat("Original column names:", colnames(iris.cpy), "\n\tLevels of Species:", levels(iris.cpy$Species), "\n")
             cat("Safe column names:", colnames(iris.cpy2), "\n\tLevels of Species:", levels(iris.cpy2$Species), "\n")

Rd file 'matplotsd.Rd':
  \usage lines wider than 90 characters:
     matplotsd(x, y, sdpostfix="sd", type = "p", lty = 1:5, lwd = 1, lend = par("lend"), pch = NULL, col = 1:6, cex = NULL, bg = NA, xlab =  ... [TRUNCATED]

Rd file 'plot4d.Rd':
  \examples lines wider than 100 characters:
     ## Not run: plot4d(x,y,z,u, main="demo", xlab="normal", ylab="uniform", zlab="exponential", ulab="ordinal")

Rd file 'plotAllScatters.Rd':
  \usage lines wider than 90 characters:
     plotAllScatters(comparingColName, dfr, ylab, markCols = c(), onlyMarkCols = FALSE, indicateObs = c(), excludeOrg = FALSE, avoidUnivaria ... [TRUNCATED]

Rd file 'plotGeneralDistr.Rd':
  \usage lines wider than 90 characters:
     plotGeneralDistr(DPQfuncs=list(d=dnorm, p=pnorm, q=qnorm), params=list(mean=0, sd=1), minQuant=0.01, maxQuant=0.99, topmult=1.1, numpts ... [TRUNCATED]

Rd file 'plotROCFromRepPredProb.Rd':
  \usage lines wider than 90 characters:
     plotROCFromRepPredProb(obsrepprob, out, thres=seq(0,1, length.out=round(min(dim(obsrepprob))/2, 1)), doPlot=TRUE, showThres=10, verbosi ... [TRUNCATED]

Rd file 'plotWSD.Rd':
  \usage lines wider than 90 characters:
     plotWSD(x, y, ysd, ylim, erbarwidth=0.01, col="red", erbarcol=makeTransparent(col, alpha=50), ..., add=FALSE)

Rd file 'plotex.Rd':
  \usage lines wider than 90 characters:
     plotex(cvobj, xvar=c("norm", "lambda", "dev"), numTicks=5, lamIndexAxisCol="red", lamIndexAxisPos=NULL, legendPos="topright", legendCex ... [TRUNCATED]

Rd file 'predict2.Rd':
  \usage lines wider than 90 characters:
     predict2(object, orgx, orgy, outname="out", newx, methodForNonConvergence=c("ridge", "brglm", "none"), s = NULL, type=c("link","respons ... [TRUNCATED]

Rd file 'randomString.Rd':
  \examples lines wider than 100 characters:
     fixedRnaString<-randomString(maxLength=20, minLength=20, alphabet=c("A", "C", "G", "U"), separator=";")

Rd file 'run.parallel.Rd':
  \usage lines wider than 90 characters:
     run.parallel(..., paramcreationname, functionname, paramname, logdir,   savedir=logdir, logorsavename= paste(functionname, "parallel",  ... [TRUNCATED]
     do.parallel(i, functionname, paramname, logdir, savedir=logdir, logorsavename= paste(functionname, "parallel", sep="_"), postprocessnam ... [TRUNCATED]
                                             restore = NULL, slaveOutfile = NULL, nostart = FALSE, useRscript = FALSE)

Rd file 'smartpairs.Rd':
  \usage lines wider than 90 characters:
     smartpairs(truex, labels, panel = points, ..., lower.panel = panel, upper.panel = panel, diag.panel = NULL, text.panel = textPanel, lab ... [TRUNCATED]

These lines will be truncated in the PDF manual.
* 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 examples ... ERROR
Running examples in 'addendum-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotex
> ### Title: Plots both crossvalidation plot and coefficient plot from glmnet
> ###   in one plot
> ### Aliases: plotex simpleplot simpleplot.default simpleplot.glmnet
> ###   simpleplot.cv.glmnet firstRepeatedAppearance getOrderOfAppearance
> ### Keywords: glmnet plot crossvalidation
> 
> ### ** Examples
> 
> set.seed(1010)
> n=1000;p=100
> nzc=trunc(p/10)
> x=matrix(rnorm(n*p),n,p)
> beta=rnorm(nzc)
> fx= (x[,seq(nzc)] %*% beta)
> eps=rnorm(n)*5
> y=drop(fx+eps)
> px=exp(fx)
> px=px/(1+px)
> ly=rbinom(n=length(px),prob=px,size=1)
> cvob1=cv.glmnet(x,y)
> plotex(cvob1, xvar="lambda", numTicks=5)
Error in xy.coords(x, y) : 'x' and 'y' lengths differ
Calls: plotex ... addLamIndexAxis -> approx -> regularize.values -> xy.coords
Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 7 NOTEs
See
  'R:/run/building/build_2015-11-10-09-29/RF_PKG_CHECK/PKGS/addendum.Rcheck/00check.log'
for details.

Run time: 106.64 seconds.