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addendum log file (check_x86_64_linux)
Tue Nov 10 09:48:36 2015: Checking package addendum (SVN revision 214) ...
* using log directory ‘/mnt/building/build_2015-11-10-09-29/RF_PKG_CHECK/PKGS/addendum.Rcheck’
* using R version 3.2.2 Patched (2015-11-06 r69607)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘addendum’ can be installed ... [6s/6s] 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
‘/mnt/building/build_2015-11-10-09-29/RF_PKG_CHECK/PKGS/addendum.Rcheck/00check.log’
for details.
Run time: 93.12 seconds.