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BioC 3.4: CHECK report for phenoTest on tokay1

This page was generated on 2017-04-15 16:16:30 -0400 (Sat, 15 Apr 2017).

Package 916/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phenoTest 1.23.1
Evarist Planet
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/phenoTest
Last Changed Rev: 125684 / Revision: 128728
Last Changed Date: 2017-01-05 01:58:15 -0500 (Thu, 05 Jan 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: phenoTest
Version: 1.23.1
Command: rm -rf phenoTest.buildbin-libdir phenoTest.Rcheck && mkdir phenoTest.buildbin-libdir phenoTest.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phenoTest.buildbin-libdir phenoTest_1.23.1.tar.gz >phenoTest.Rcheck\00install.out 2>&1 && cp phenoTest.Rcheck\00install.out phenoTest-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=phenoTest.buildbin-libdir --install="check:phenoTest-install.out" --force-multiarch --no-vignettes --timings phenoTest_1.23.1.tar.gz
StartedAt: 2017-04-15 00:04:15 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:10:17 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 362.0 seconds
RetCode: 0
Status:  OK  
CheckDir: phenoTest.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf phenoTest.buildbin-libdir phenoTest.Rcheck && mkdir phenoTest.buildbin-libdir phenoTest.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phenoTest.buildbin-libdir phenoTest_1.23.1.tar.gz >phenoTest.Rcheck\00install.out 2>&1 && cp phenoTest.Rcheck\00install.out phenoTest-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=phenoTest.buildbin-libdir --install="check:phenoTest-install.out" --force-multiarch --no-vignettes --timings phenoTest_1.23.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/phenoTest.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'phenoTest/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'phenoTest' version '1.23.1'
* 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 'phenoTest' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'annotate' 'GSEABase'
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
* 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 ... NOTE
Warning: no function found corresponding to methods exports from 'phenoTest' for: 'show'

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** 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 ... NOTE
Warning: no function found corresponding to methods exports from 'phenoTest' for: 'show'

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'ggplot2' which was already attached by Depends.
  Please remove these calls from your code.
Namespace in Imports field not imported from: 'annotate'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'BMA' 'Heatplus' 'annotate' 'ggplot2' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'sortDragHtmlTable'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ClusterPhenoTest: no visible global function definition for 'pData'
ClusterPhenoTest : <anonymous>: no visible global function definition
  for 'pData'
ClusterPhenoTest : <anonymous>: no visible global function definition
  for 'kruskal.test'
ClusterPhenoTest : <anonymous>: no visible global function definition
  for 'chisq.test'
ClusterPhenoTest: no visible global function definition for 'p.adjust'
ExpressionPhenoTest : mycoxph: no visible global function definition
  for 'coefficients'
ExpressionPhenoTest : mycoxph: no visible global function definition
  for 'coef'
ExpressionPhenoTest : mycoxph: no visible global function definition
  for 'anova'
ExpressionPhenoTest : mycoxph: no visible global function definition
  for 'pData'
ExpressionPhenoTest : mycoxph: no visible global function definition
  for 'bic.surv'
ExpressionPhenoTest : postprobBic: no visible global function
  definition for 'BIC'
ExpressionPhenoTest : postprobBic: no visible global function
  definition for 'lm'
ExpressionPhenoTest: no visible global function definition for 'exprs'
ExpressionPhenoTest: no visible global function definition for 'pData'
ExpressionPhenoTest: no visible global function definition for
  'model.matrix'
ExpressionPhenoTest : <anonymous>: no visible global function
  definition for 'pData'
ExpressionPhenoTest: no visible global function definition for 'coef'
ExpressionPhenoTest: no visible binding for global variable 'y'
ExpressionPhenoTest: no visible global function definition for
  'featureNames'
ExpressionPhenoTest : <anonymous>: no visible global function
  definition for 'p.adjust'
ExpressionPhenoTest: no visible global function definition for 'new'
ExpressionPhenoTest: no visible global function definition for
  'annotation'
barplotCI: no visible global function definition for 'lm'
barplotCI: no visible global function definition for 'coef'
barplotCI: no visible global function definition for 'confint'
checkGsetSimmetry: no visible global function definition for 'pnorm'
checkGsetSimmetry: no visible global function definition for 'sd'
epheno2html: no visible global function definition for 'annotation'
epheno2html: no visible global function definition for 'featureNames'
epheno2html : export2html: no visible global function definition for
  'featureNames'
epheno2html : export2html: no visible global function definition for
  'annotation'
epheno2html : export2html: no visible global function definition for
  'write.csv'
epheno2html : export2html: no visible global function definition for
  'pData'
epheno2html : export2html: no visible global function definition for
  'exprs'
epheno2html : export2html : myFun: no visible global function
  definition for 'png'
epheno2html : export2html : myFun: no visible global function
  definition for 'featureNames'
epheno2html : export2html : myFun: no visible global function
  definition for 'legend'
epheno2html : export2html : myFun: no visible global function
  definition for 'dev.off'
epheno2html : export2html : myFun: no visible global function
  definition for 'pData'
epheno2html : export2html : myFun: no visible global function
  definition for 'exprs'
epheno2html : export2html : myFun: no visible global function
  definition for 'boxplot'
epheno2html : export2html : myFun: no visible global function
  definition for 'dotchart'
eset2genelevel: no visible global function definition for 'annotation'
eset2genelevel: no visible global function definition for
  'featureNames<-'
eset2genelevel: no visible global function definition for
  'annotation<-'
getChrWithMedVar: no visible global function definition for 'quantile'
getEsPositions: no visible global function definition for 'annotation'
getEsPositions: no visible global function definition for
  'featureNames'
getIndivPvals: no visible global function definition for 'pnorm'
getIndivPvals: no visible global function definition for 'sd'
getIndivPvals: no visible global function definition for 'density'
getIndivPvals: no visible global function definition for 'approxfun'
getIndivPvals: no visible global function definition for 'integrate'
getIndivPvals : getPval: no visible global function definition for
  'density'
getIndivPvals : getPval: no visible global function definition for
  'approxfun'
getIndivPvals : getPval: no visible global function definition for
  'integrate'
getIndivPvals : getPval: no visible global function definition for
  'pnorm'
getIndivPvals : getPval: no visible global function definition for 'sd'
getIndivPvals: no visible global function definition for 'p.adjust'
getPred: no visible global function definition for 'predict'
getSummary : getNesPval: no visible global function definition for
  'density'
getSummary : getNesPval: no visible global function definition for
  'approxfun'
getSummary : getNesPval: no visible global function definition for
  'integrate'
getSummary : gseaSignificance : getEsPval: no visible global function
  definition for 'density'
getSummary : gseaSignificance : getEsPval: no visible global function
  definition for 'approxfun'
getSummary : gseaSignificance : getEsPval: no visible global function
  definition for 'integrate'
getSummary : <anonymous>: no visible global function definition for
  'wilcox.test'
getSummary: no visible global function definition for 'p.adjust'
gsea: no visible global function definition for 'new'
gsea.go: no visible global function definition for 'featureNames'
gsea.kegg: no visible global function definition for 'featureNames'
gsea.selGsets: no visible global function definition for 'new'
gsea.selVars: no visible global function definition for 'new'
gsea2html: no visible global function definition for 'annotation'
gsea2html: no visible global function definition for 'exprs'
gsea2html: no visible global function definition for 'pData'
gsea2html: no visible global function definition for 'featureNames'
gsea2html: no visible global function definition for 'Term'
gsea2html: no visible global function definition for 'png'
gsea2html: no visible global function definition for 'dev.off'
pca: no visible global function definition for 'prcomp'
pca: no visible global function definition for 'exprs'
pca.2d: no visible global function definition for 'pData'
pca.2d: no visible global function definition for 'dist'
pca.2d: no visible global function definition for 'cov'
pca.2d: no visible global function definition for 'qplot'
pca.2d: no visible binding for global variable 'pc1'
pca.2d: no visible binding for global variable 'pc2'
pca.2d: no visible global function definition for 'geom_point'
pca.2d: no visible global function definition for 'coord_cartesian'
pca.2d: no visible global function definition for 'theme'
pca.2d: no visible global function definition for 'ggtitle'
plotCopyNumber: no visible global function definition for 'par'
plotCopyNumber: no visible global function definition for 'layout'
plotCopyNumber: no visible global function definition for 'densCols'
plotCopyNumber: no visible global function definition for 'lines'
plotCopyNumber: no visible global function definition for 'abline'
plotCopyNumber : <anonymous>: no visible global function definition for
  'rect'
plotCopyNumber : <anonymous>: no visible global function definition for
  'rgb'
plotGSEA : plot1.perm: no visible global function definition for
  'approx'
plotGSEA : plot1.perm: no visible global function definition for
  'abline'
plotGSEA : plot1.perm: no visible global function definition for 'axis'
plotGSEA : plot1.wilcox: no visible global function definition for
  'density'
plotGSEA : plot1.wilcox: no visible global function definition for
  'abline'
plotGSEA : plot2: no visible global function definition for 'par'
plotGSEA : plot2: no visible global function definition for 'approx'
plotGSEA : plot2: no visible global function definition for 'abline'
plotGSEA : plot2: no visible global function definition for 'axis'
plotGSEA : plot2: no visible global function definition for 'polygon'
plotGSEA : plot3: no visible global function definition for 'par'
plotGSEA : plot3: no visible global function definition for 'quantile'
plotGSEA : plot3: no visible global function definition for 'image'
plotGSEA : plot3: no visible global function definition for 'rgb'
plotGSEA : plot4: no visible global function definition for 'par'
plotGSEA : plot4: no visible global function definition for 'axTicks'
plotGSEA : plot4: no visible global function definition for 'axis'
plotGSEA : plot4: no visible global function definition for 'densCols'
plotGSEA : plot4: no visible global function definition for 'abline'
plotGSEA: no visible global function definition for 'par'
plotGSEA: no visible global function definition for 'layout'
preProcessX: no visible global function definition for 'complete.cases'
preProcessX: no visible global function definition for 'median'
qcPlot: no visible global function definition for 'pdf'
qcPlot: no visible global function definition for 'densCols'
qcPlot: no visible global function definition for 'lm'
qcPlot: no visible global function definition for 'abline'
qcPlot: no visible global function definition for 'boxplot'
qcPlot: no visible global function definition for 'density'
qcPlot: no visible global function definition for 'lines'
qcPlot: no visible global function definition for 'dev.off'
smoothCoxph: no visible global function definition for 'predict'
smoothCoxph: no visible global function definition for 'median'
smoothCoxph: no visible global function definition for 'lines'
smoothCoxph: no visible global function definition for 'abline'
[,epheno-ANY-ANY-ANY: no visible global function definition for
  'featureNames'
[,epheno-ANY-ANY-ANY: no visible global function definition for
  'exprs<-'
[,epheno-ANY-ANY-ANY: no visible global function definition for 'exprs'
[,epheno-ANY-ANY-ANY: no visible global function definition for 'pData'
[,epheno-ANY-ANY-ANY: no visible global function definition for 'new'
[,epheno-ANY-ANY-ANY: no visible global function definition for
  'annotation'
barplotSignatures,epheno-list : <anonymous>: no visible global function
  definition for 'featureNames'
barplotSignatures,epheno-list : <anonymous> : <anonymous>: no visible
  global function definition for 'featureNames'
barplotSignatures,epheno-list: no visible global function definition
  for 'abline'
barplotSignatures,epheno-list : <anonymous>: no visible global function
  definition for 'wilcox.test'
barplotSignatures,epheno-list: no visible global function definition
  for 'p.adjust'
barplotSignatures,epheno-list: no visible global function definition
  for 'text'
barplotSignatures,epheno-list: no visible global function definition
  for 'par'
barplotSignifSignatures,epheno-list : <anonymous>: no visible global
  function definition for 'featureNames'
barplotSignifSignatures,epheno-list : myFun1 : <anonymous>: no visible
  global function definition for 'featureNames'
barplotSignifSignatures,epheno-list : myFun2: no visible global
  function definition for 'binom.test'
barplotSignifSignatures,epheno-list : myFun3 : <anonymous>: no visible
  global function definition for 'chisq.test'
barplotSignifSignatures,epheno-list : myFun4 : <anonymous>: no visible
  global function definition for 'chisq.test'
barplotSignifSignatures,epheno-list: no visible global function
  definition for 'p.adjust'
barplotSignifSignatures,epheno-list : <anonymous>: no visible global
  function definition for 'p.adjust'
barplotSignifSignatures,epheno-list: no visible global function
  definition for 'barplot'
barplotSignifSignatures,epheno-list: no visible global function
  definition for 'text'
boxplotSignatures,epheno-list : <anonymous>: no visible global function
  definition for 'featureNames'
boxplotSignatures,epheno-list: no visible global function definition
  for 'boxplot'
boxplotSignatures,epheno-list: no visible global function definition
  for 'abline'
boxplotSignatures,epheno-list : <anonymous>: no visible global function
  definition for 'wilcox.test'
boxplotSignatures,epheno-list: no visible global function definition
  for 'text'
boxplotSignatures,epheno-list: no visible global function definition
  for 'par'
dim,epheno: no visible global function definition for 'exprs'
dim,epheno: no visible global function definition for 'pData'
export2CSV,epheno: no visible global function definition for 'fData'
export2CSV,epheno: no visible global function definition for
  'featureNames'
export2CSV,epheno: no visible global function definition for
  'write.csv'
getFc,epheno: no visible global function definition for 'pData'
getFc,epheno: no visible global function definition for 'exprs'
getHr,epheno: no visible global function definition for 'pData'
getHr,epheno: no visible global function definition for 'exprs'
getMeans,epheno: no visible global function definition for 'pData'
getMeans,epheno: no visible global function definition for 'exprs'
getPostProbs,epheno: no visible global function definition for 'pData'
getPostProbs,epheno: no visible global function definition for 'exprs'
getPvals,epheno: no visible global function definition for 'pData'
getPvals,epheno: no visible global function definition for 'exprs'
getSignif,epheno: no visible global function definition for 'pData'
getSignif,epheno: no visible global function definition for 'exprs'
getSummaryDif,epheno: no visible global function definition for 'pData'
getSummaryDif,epheno: no visible global function definition for 'exprs'
getVars2test,epheno: no visible global function definition for 'pData'
gseaSignatures,epheno-list: no visible global function definition for
  'new'
gseaSignatures,matrix-list: no visible global function definition for
  'new'
gseaSignatures,numeric-list: no visible global function definition for
  'new'
gseaSignificance,gseaSignaturesSign: no visible global function
  definition for 'new'
gseaSignificance,gseaSignaturesVar: no visible global function
  definition for 'new'
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for 'pData'
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for 'featureNames'
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for 'annotation'
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for 'exprs<-'
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for 'exprs'
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for 'hclust'
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for 'as.dist'
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for 'cor'
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for 'dist'
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for 'cutree'
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for 'model.matrix'
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for 'coef'
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for 'gray'
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for 'as.dendrogram'
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for 'par'
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for 'heatmap_plus'
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for 'pchisq'
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for 'text'
heatmapPhenoTest,ExpressionSet-missing: no visible global function
  definition for 'featureNames'
pAdjust,epheno: no visible global function definition for 'pData'
pAdjust,epheno: no visible global function definition for 'new'
pAdjust,epheno: no visible global function definition for 'exprs'
pAdjust,epheno : <anonymous>: no visible global function definition for
  'p.adjust'
pAdjust,epheno: no visible global function definition for 'annotation'
phenoClass,epheno: no visible global function definition for 'pData'
phenoNames,epheno: no visible global function definition for 'pData'
show,epheno: no visible global function definition for 'featureNames'
show,epheno: no visible global function definition for 'annotation'
Undefined global functions or variables:
  BIC Term abline annotation annotation<- anova approx approxfun
  as.dendrogram as.dist axTicks axis barplot bic.surv binom.test
  boxplot chisq.test coef coefficients complete.cases confint
  coord_cartesian cor cov cutree densCols density dev.off dist dotchart
  exprs exprs<- fData featureNames featureNames<- geom_point ggtitle
  gray hclust heatmap_plus image integrate kruskal.test layout legend
  lines lm median model.matrix new p.adjust pData par pc1 pc2 pchisq
  pdf png pnorm polygon prcomp predict qplot quantile rect rgb sd text
  theme wilcox.test write.csv y
Consider adding
  importFrom("grDevices", "densCols", "dev.off", "gray", "pdf", "png",
             "rgb")
  importFrom("graphics", "abline", "axTicks", "axis", "barplot",
             "boxplot", "dotchart", "image", "layout", "legend", "lines",
             "par", "polygon", "rect", "text")
  importFrom("methods", "new")
  importFrom("stats", "BIC", "anova", "approx", "approxfun",
             "as.dendrogram", "as.dist", "binom.test", "chisq.test",
             "coef", "coefficients", "complete.cases", "confint", "cor",
             "cov", "cutree", "density", "dist", "hclust", "integrate",
             "kruskal.test", "lm", "median", "model.matrix", "p.adjust",
             "pchisq", "pnorm", "prcomp", "predict", "quantile", "sd",
             "wilcox.test")
  importFrom("utils", "write.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... NOTE
S3 methods shown with full name in documentation object 'plot.gseaData':
  'plot.gseaData'

S3 methods shown with full name in documentation object 'plot.gseaSignatures':
  'plot.gseaSignaturesSign'

S3 methods shown with full name in documentation object 'summary.gseaData':
  'summary.gseaData'

S3 methods shown with full name in documentation object 'summary.gseaSignificance':
  'summary.gseaSignificanceSign'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
ExpressionPhenoTest 5.14   0.03    5.17
findCopyNumber      5.06   0.09    5.15
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
ExpressionPhenoTest 6.44   0.03    6.47
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 6 NOTEs
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/phenoTest.Rcheck/00check.log'
for details.


phenoTest.Rcheck/00install.out:


install for i386

* installing *source* package 'phenoTest' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'

install for x64

* installing *source* package 'phenoTest' ...
** testing if installed package can be loaded
Warning: replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
* MD5 sums
packaged installation of 'phenoTest' as phenoTest_1.23.1.zip
* DONE (phenoTest)

phenoTest.Rcheck/examples_i386/phenoTest-Ex.timings:

nameusersystemelapsed
ClusterPhenoTest0.170.080.25
ExpressionPhenoTest5.140.035.17
epheno-class000
epheno0.050.000.05
epheno2html000
eset0.160.020.17
eset.genelevel0.090.000.10
eset2genelevel000
findCopyNumber5.060.095.15
genesInArea0.210.020.22
getEsPositions0.200.010.22
getGo000
getKegg000
getVars2test0.010.020.04
gsea0.220.010.23
gsea.kegg.go0.020.000.02
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phenoTest.Rcheck/examples_x64/phenoTest-Ex.timings:

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pca0.550.030.58
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