Back to Multiple platform build/check report for BioC 3.8
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CHECK report for a4Base on tokay1

This page was generated on 2019-04-13 11:21:37 -0400 (Sat, 13 Apr 2019).

Package 2/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
a4Base 1.30.0
Tobias Verbeke
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/a4Base
Branch: RELEASE_3_8
Last Commit: fc370b2
Last Changed Date: 2018-10-30 11:41:47 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: a4Base
Version: 1.30.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:a4Base.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings a4Base_1.30.0.tar.gz
StartedAt: 2019-04-13 00:23:52 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 00:29:57 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 365.2 seconds
RetCode: 1
Status:  ERROR  
CheckDir: a4Base.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:a4Base.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings a4Base_1.30.0.tar.gz
###
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##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/a4Base.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'a4Base/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'a4Base' version '1.30.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 NOTE
Package which this enhances but not available for checking: 'JavaGD'

Depends: includes the non-default packages:
  'grid' 'Biobase' 'AnnotationDbi' 'annaffy' 'mpm' 'genefilter' 'limma'
  'multtest' 'glmnet' 'a4Preproc' 'a4Core' 'gplots'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'a4Base' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpqEu0CU/R.INSTALL1bc4481b6ca/a4Base/man/ExpressionSetWithComputation.Rd:23: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpqEu0CU/R.INSTALL1bc4481b6ca/a4Base/man/ExpressionSetWithComputation.Rd:24: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpqEu0CU/R.INSTALL1bc4481b6ca/a4Base/man/ExpressionSetWithComputation.Rd:25: file link 'VersionedBiobase' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpqEu0CU/R.INSTALL1bc4481b6ca/a4Base/man/ExpressionSetWithComputation.Rd:26: file link 'Versioned' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpqEu0CU/R.INSTALL1bc4481b6ca/a4Base/man/ExpressionSetWithComputation.Rd:33: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpqEu0CU/R.INSTALL1bc4481b6ca/a4Base/man/a4palette.Rd:27: file link 'rainbow' in package 'grDevices' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpqEu0CU/R.INSTALL1bc4481b6ca/a4Base/man/combineTwoExpressionSet.Rd:22: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpqEu0CU/R.INSTALL1bc4481b6ca/a4Base/man/createExpressionSet.Rd:30: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpqEu0CU/R.INSTALL1bc4481b6ca/a4Base/man/tTest.Rd:40: file link 'rowttests' in package 'genefilter' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/a4Base.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
** 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 ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  'Biobase' 'grid'
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'Cairo' 'gridSVG'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'AnnotationDbi' 'a4Preproc' 'annaffy' 'genefilter' 'glmnet' 'gplots'
  'grid' 'mpm' 'multtest'
  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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
a4palette: no visible global function definition for 'rgb'
a4palette: no visible global function definition for 'rainbow'
addQuantilesColors: no visible global function definition for
  'quantile'
boxPlot: no visible global function definition for 'boxplot'
boxPlot: no visible global function definition for 'points'
boxPlot: no visible global function definition for 'legend'
fTest: no visible global function definition for 'rowFtests'
fTest: no visible global function definition for 'mt.rawp2adjp'
filterVarInt: no visible global function definition for 'pOverA'
filterVarInt : f2: no visible global function definition for 'IQR'
filterVarInt: no visible global function definition for 'filterfun'
filterVarInt: no visible global function definition for 'genefilter'
grid.imageGrob: no visible global function definition for 'grid.draw'
heatmap.expressionSet: no visible global function definition for 'unit'
heatmap.expressionSet: no visible global function definition for 'gpar'
heatmap.expressionSet: no visible global function definition for 'rgb'
heatmap.expressionSet: no visible binding for global variable 'dist'
heatmap.expressionSet : <anonymous>: no visible global function
  definition for 'hclust'
heatmap.expressionSet: no visible global function definition for
  'as.dendrogram'
heatmap.expressionSet: no visible global function definition for
  'cutree'
heatmap.expressionSet: no visible global function definition for
  'reorder'
heatmap.expressionSet: no visible global function definition for
  'order.dendrogram'
heatmap.expressionSet: no visible global function definition for
  'aggregate'
heatmap.expressionSet: no visible global function definition for
  'col2rgb'
heatmap.expressionSet : <anonymous>: no visible global function
  definition for 'colorpanel'
heatmap.expressionSet: no visible global function definition for
  'textGrob'
heatmap.expressionSet: no visible global function definition for
  'grid.layout'
heatmap.expressionSet: no visible global function definition for
  'grid.newpage'
heatmap.expressionSet: no visible global function definition for
  'convertUnit'
heatmap.expressionSet: no visible global function definition for
  'viewport'
heatmap.expressionSet: no visible global function definition for
  'pushViewport'
heatmap.expressionSet: no visible global function definition for
  'grid.text'
heatmap.expressionSet: no visible global function definition for
  'grid.rect'
heatmap.expressionSet: no visible global function definition for
  'popViewport'
heatmap.expressionSet: no visible global function definition for
  'unit.c'
heatmap.expressionSet: no visible global function definition for
  'grid.lines'
heatmap.expressionSet: no visible global function definition for
  'grid.xaxis'
histpvalueplotter: no visible global function definition for 'hist'
histpvalueplotter: no visible global function definition for 'abline'
histpvalueplotter: no visible global function definition for 'legend'
imageGrob: no visible global function definition for 'gTree'
imageGrob: no visible global function definition for 'gList'
lassoReg: no visible global function definition for 'glmnet'
limmaTwoLevels: no visible global function definition for
  'model.matrix'
logReg: no visible global function definition for 'glm'
logReg: no visible global function definition for 'fitted'
logReg: no visible global function definition for 'par'
logReg: no visible global function definition for 'plot'
logReg: no visible global function definition for 'lines'
logReg: no visible global function definition for 'axis'
logReg: no visible global function definition for 'box'
makeImageRect: no visible global function definition for 'rectGrob'
makeImageRect: no visible global function definition for 'gpar'
oaColors: no visible global function definition for 'hcl'
oaColors: no visible global function definition for 'rainbow'
panel.cor: no visible global function definition for 'par'
panel.cor: no visible global function definition for 'cor'
panel.cor: no visible global function definition for 'strwidth'
panel.cor: no visible global function definition for 'cor.test'
panel.cor: no visible global function definition for 'symnum'
panel.cor: no visible global function definition for 'text'
panel.plotSmoothScat: no visible global function definition for
  'points'
panel.plotSmoothScat: no visible global function definition for
  'densCols'
panel.plotSmoothScat: no visible global function definition for
  'abline'
plot1gene: no visible global function definition for 'points'
plot1gene: no visible global function definition for 'axis'
plot1gene: no visible global function definition for 'mtext'
plot1gene: no visible global function definition for 'lines'
plot1gene: no visible global function definition for 'legend'
plotComb2Samples: no visible global function definition for 'plot'
plotComb2Samples: no visible global function definition for 'axis'
plotComb2Samples: no visible global function definition for 'box'
plotComb2Samples: no visible global function definition for 'densCols'
plotComb2Samples: no visible global function definition for 'points'
plotComb2Samples: no visible global function definition for 'text'
plotCombMultSamples: no visible global function definition for 'pairs'
plotCombination2genes: no visible global function definition for 'plot'
plotCombination2genes: no visible global function definition for
  'points'
plotCombination2genes: no visible global function definition for
  'legend'
plotLogRatio: no visible global function definition for 'addGeneInfo'
plotLogRatio: no visible global function definition for 'hclust'
plotLogRatio: no visible global function definition for 'dist'
plotLogRatio : <anonymous>: no visible global function definition for
  'quantile'
plotLogRatio: no visible global function definition for 'rainbow'
plotLogRatio: no visible global function definition for 'x11'
plotLogRatio: no visible global function definition for 'JavaGD'
plotLogRatio: no visible global function definition for 'pdf'
plotLogRatio: no visible global function definition for 'png'
plotLogRatio: no visible global function definition for 'CairoPNG'
plotLogRatio: no visible global function definition for 'viewport'
plotLogRatio: no visible global function definition for 'grid.layout'
plotLogRatio: no visible global function definition for 'pushViewport'
plotLogRatio: no visible global function definition for 'grid.rect'
plotLogRatio: no visible global function definition for 'gpar'
plotLogRatio: no visible global function definition for 'grid.text'
plotLogRatio: no visible global function definition for 'grid.garnish'
plotLogRatio: no visible global function definition for 'popViewport'
plotLogRatio: no visible global function definition for 'colors'
plotLogRatio: no visible global function definition for 'grid.lines'
plotLogRatio : <anonymous>: no visible global function definition for
  'grid.lines'
plotLogRatio : <anonymous>: no visible global function definition for
  'gpar'
plotLogRatio: no visible global function definition for 'grid.segments'
plotLogRatio: no visible global function definition for
  'grid.hyperlink'
plotLogRatio: no visible global function definition for 'gPath'
plotLogRatio: no visible global function definition for 'grid.script'
plotLogRatio: no visible global function definition for 'gridToSVG'
plotLogRatio: no visible global function definition for 'browseURL'
plotLogRatio: no visible global function definition for 'dev.off'
probabilitiesPlot: no visible global function definition for 'par'
probabilitiesPlot: no visible global function definition for 'axis'
probabilitiesPlot: no visible global function definition for 'abline'
probabilitiesPlot: no visible global function definition for 'points'
probabilitiesPlot: no visible global function definition for 'title'
probabilitiesPlot: no visible global function definition for 'rgb'
probabilitiesPlot: no visible global function definition for 'rect'
probabilitiesPlot: no visible global function definition for 'barplot'
probe2gene: no visible global function definition for 'aafSymbol'
probe2gene: no visible global function definition for 'getText'
profilesPlot: no visible global function definition for 'matplot'
profilesPlot: no visible global function definition for 'axis'
profilesPlot: no visible global function definition for 'legend'
tTest: no visible global function definition for 'rowttests'
tTest: no visible global function definition for 'mt.rawp2adjp'
tTest2 : ttestfun: no visible global function definition for 't.test'
tTest2: no visible global function definition for 'rowttests'
tTest2: no visible global function definition for 'mt.rawp2adjp'
volcanoplotter: no visible global function definition for
  'grid.newpage'
volcanoplotter: no visible global function definition for
  'plotViewport'
volcanoplotter: no visible global function definition for
  'pushViewport'
volcanoplotter: no visible global function definition for 'textGrob'
volcanoplotter: no visible global function definition for 'unit'
volcanoplotter: no visible global function definition for 'gpar'
volcanoplotter: no visible global function definition for 'grobWidth'
volcanoplotter: no visible global function definition for
  'convertHeight'
volcanoplotter: no visible global function definition for
  'dataViewport'
volcanoplotter: no visible global function definition for 'grid.pretty'
volcanoplotter: no visible global function definition for
  'current.viewport'
volcanoplotter: no visible global function definition for 'xaxisGrob'
volcanoplotter: no visible global function definition for 'grid.yaxis'
volcanoplotter: no visible global function definition for 'editGrob'
volcanoplotter: no visible global function definition for 'gEditList'
volcanoplotter: no visible global function definition for 'gEdit'
volcanoplotter: no visible global function definition for 'grid.draw'
volcanoplotter: no visible global function definition for 'densCols'
volcanoplotter: no visible global function definition for 'grid.points'
volcanoplotter: no visible global function definition for 'grid.text'
spectralMap,ExpressionSet-character: no visible global function
  definition for 'na.omit'
spectralMap,ExpressionSet-character: no visible global function
  definition for 'par'
spectralMap,ExpressionSet-character: no visible global function
  definition for 'legend'
topTable,MArrayLM: no visible global function definition for
  'topTableF'
topTable,MArrayLM: no visible binding for global variable 'number'
topTable,MArrayLM: no visible global function definition for 'toptable'
topTable,fTest: no visible global function definition for 'head'
topTable,limma: no visible global function definition for 'topTableF'
topTable,limma: no visible binding for global variable 'number'
topTable,limma: no visible global function definition for 'toptable'
topTable,tTest: no visible global function definition for 'head'
Undefined global functions or variables:
  CairoPNG IQR JavaGD aafSymbol abline addGeneInfo aggregate
  as.dendrogram axis barplot box boxplot browseURL col2rgb colorpanel
  colors convertHeight convertUnit cor cor.test current.viewport cutree
  dataViewport densCols dev.off dist editGrob filterfun fitted gEdit
  gEditList gList gPath gTree genefilter getText glm glmnet gpar
  grid.draw grid.garnish grid.hyperlink grid.layout grid.lines
  grid.newpage grid.points grid.pretty grid.rect grid.script
  grid.segments grid.text grid.xaxis grid.yaxis gridToSVG grobWidth hcl
  hclust head hist legend lines matplot model.matrix mt.rawp2adjp mtext
  na.omit number order.dendrogram pOverA pairs par pdf plot
  plotViewport png points popViewport pushViewport quantile rainbow
  rect rectGrob reorder rgb rowFtests rowttests strwidth symnum t.test
  text textGrob title topTableF toptable unit unit.c viewport x11
  xaxisGrob
Consider adding
  importFrom("grDevices", "col2rgb", "colors", "densCols", "dev.off",
             "hcl", "pdf", "png", "rainbow", "rgb", "x11")
  importFrom("graphics", "abline", "axis", "barplot", "box", "boxplot",
             "hist", "legend", "lines", "matplot", "mtext", "pairs",
             "par", "plot", "points", "rect", "strwidth", "text",
             "title")
  importFrom("stats", "IQR", "aggregate", "as.dendrogram", "cor",
             "cor.test", "cutree", "dist", "fitted", "glm", "hclust",
             "model.matrix", "na.omit", "order.dendrogram", "quantile",
             "reorder", "symnum", "t.test")
  importFrom("utils", "browseURL", "head")
to your NAMESPACE file.
* 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 ... 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 examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'a4Base-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: spectralMap
> ### Title: Draw a Spectral Map
> ### Aliases: spectralMap
> ### Keywords: hplot
> 
> ### ** Examples
> 
> if (require(ALL)){
+   data(ALL, package = "ALL")
+   ALL <- addGeneInfo(ALL)
+ 
+   spectralMap(object = ALL, groups = "BT", legendPos = 'bottomright')
+ 
+   spectralMap(object = ALL, groups = "BT",
+       plot.mpm.args = list(label.tol = 10, rot = c(-1, 1), sub = "", lab.size = 0.65,
+ 	    dim = c(1,2), sampleNames = FALSE, zoom = c(1,5), col.size = 2, 
+ 	    do.smoothScatter = TRUE))
+ 	  
+   spectralMap(object = ALL, groups = "BT",
+ 	  plot.mpm.args = list(label.tol = 10, rot = c(-1, 1), sub = "", lab.size = 0.65,
+ 	      dim = c(1,2), sampleNames = as.character(pData(ALL)$BT),
+           zoom = c(1,5), col.size = 2, do.smoothScatter = TRUE))
+ }
Loading required package: ALL
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
spectralMap     9.76   1.03   10.79
computeLogRatio 9.39   0.14    9.53
plotLogRatio    8.85   0.08    8.92
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/a4Base.Rcheck/00check.log'
for details.

Installation output

a4Base.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/a4Base_1.30.0.tar.gz && rm -rf a4Base.buildbin-libdir && mkdir a4Base.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=a4Base.buildbin-libdir a4Base_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL a4Base_1.30.0.zip && rm a4Base_1.30.0.tar.gz a4Base_1.30.0.zip
###
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100  344k  100  344k    0     0  7644k      0 --:--:-- --:--:-- --:--:-- 8402k

install for i386

* installing *source* package 'a4Base' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'a4Base'
    finding HTML links ... done
    ExpressionSetWithComputation            html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpqEu0CU/R.INSTALL1bc4481b6ca/a4Base/man/ExpressionSetWithComputation.Rd:23: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpqEu0CU/R.INSTALL1bc4481b6ca/a4Base/man/ExpressionSetWithComputation.Rd:24: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpqEu0CU/R.INSTALL1bc4481b6ca/a4Base/man/ExpressionSetWithComputation.Rd:25: file link 'VersionedBiobase' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpqEu0CU/R.INSTALL1bc4481b6ca/a4Base/man/ExpressionSetWithComputation.Rd:26: file link 'Versioned' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpqEu0CU/R.INSTALL1bc4481b6ca/a4Base/man/ExpressionSetWithComputation.Rd:33: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    a4palette                               html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpqEu0CU/R.INSTALL1bc4481b6ca/a4Base/man/a4palette.Rd:27: file link 'rainbow' in package 'grDevices' does not exist and so has been treated as a topic
    addQuantilesColors                      html  
    boxPlot                                 html  
    combineTwoExpressionSet                 html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpqEu0CU/R.INSTALL1bc4481b6ca/a4Base/man/combineTwoExpressionSet.Rd:22: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    computeLogRatio                         html  
    createExpressionSet                     html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpqEu0CU/R.INSTALL1bc4481b6ca/a4Base/man/createExpressionSet.Rd:30: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    filterVarInt                            html  
    heatmap.expressionSet                   html  
    histPvalue                              html  
    histpvalueplotter                       html  
    lassoReg                                html  
    limmaTwoLevels                          html  
    logReg                                  html  
    nlcvTT                                  html  
    plot1gene                               html  
    plotComb2Samples                        html  
    plotCombMultSamples                     html  
    plotCombination2genes                   html  
    plotLogRatio                            html  
    probabilitiesPlot                       html  
    probe2gene                              html  
    profilesPlot                            html  
    propDEgenes-methods                     html  
    propDEgenes                             html  
    propdegenescalculation                  html  
    replicates                              html  
    spectralMap-methods                     html  
    spectralMap                             html  
    tTest                                   html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpqEu0CU/R.INSTALL1bc4481b6ca/a4Base/man/tTest.Rd:40: file link 'rowttests' in package 'genefilter' does not exist and so has been treated as a topic
    topTable-methods                        html  
    volcanoPlot-methods                     html  
    volcanoPlot                             html  
    volcanoplotter                          html  
** building package indices
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'a4Base' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'a4Base' as a4Base_1.30.0.zip
* DONE (a4Base)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'a4Base' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

Example timings

a4Base.Rcheck/examples_i386/a4Base-Ex.timings

nameusersystemelapsed
a4palette0.040.010.04
addQuantilesColors2.010.062.08
boxPlot2.530.052.57
combineTwoExpressionSet000
computeLogRatio8.620.168.94
createExpressionSet0.050.000.05
filterVarInt2.310.042.36
heatmap.expressionSet000
histPvalue2.020.082.09
histpvalueplotter1.980.102.08
lassoReg2.000.092.09
logReg000
nlcvTT000
plot1gene2.210.082.33
plotComb2Samples1.950.202.24
plotCombMultSamples2.110.412.53
plotCombination2genes1.890.041.94
plotLogRatio8.320.058.36
probabilitiesPlot000
probe2gene1.720.081.80
profilesPlot1.870.122.03
propdegenescalculation2.280.082.36
replicates000

a4Base.Rcheck/examples_x64/a4Base-Ex.timings

nameusersystemelapsed
a4palette0.040.000.04
addQuantilesColors2.100.182.27
boxPlot2.460.092.55
combineTwoExpressionSet000
computeLogRatio9.390.149.53
createExpressionSet0.040.000.05
filterVarInt2.140.032.17
heatmap.expressionSet000
histPvalue1.740.031.77
histpvalueplotter1.720.071.78
lassoReg1.790.011.81
logReg000
nlcvTT000
plot1gene1.990.082.06
plotComb2Samples1.560.221.78
plotCombMultSamples1.780.372.16
plotCombination2genes1.610.031.64
plotLogRatio8.850.088.92
probabilitiesPlot000
probe2gene1.450.021.47
profilesPlot1.560.091.66
propdegenescalculation1.630.101.72
replicates000
spectralMap 9.76 1.0310.79
tTest1.770.201.97
volcanoPlot1.790.171.97