BioC 3.0: CHECK report for a4Base on oaxaca

Package: a4Base

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch a4Base_1.14.0.tar.gz

StartedAt: 2015-04-09 21:06:45 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 21:11:44 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 298.8 seconds

RetCode: 0

Status:  OK

CheckDir: a4Base.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch a4Base_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/a4Base.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘a4Base/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘a4Base’ version ‘1.14.0’
* checking package namespace information ... OK
* checking package dependencies ... 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 for sufficient/correct file permissions ... OK
* checking whether package ‘a4Base’ can be installed ... [23s/24s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 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
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: 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 : <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’
imageGrob: no visible global function definition for ‘gTree’
imageGrob: no visible global function definition for ‘gList’
lassoReg: no visible global function definition for ‘glmnet’
makeImageRect: no visible global function definition for ‘rectGrob’
makeImageRect: no visible global function definition for ‘gpar’
plotLogRatio: no visible global function definition for ‘addGeneInfo’
plotLogRatio: no visible global function definition for ‘JavaGD’
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 ‘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’
probe2gene: no visible global function definition for ‘aafSymbol’
probe2gene: no visible global function definition for ‘getText’
tTest: no visible global function definition for ‘rowttests’
tTest: no visible global function definition for ‘mt.rawp2adjp’
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 ‘grid.points’
volcanoplotter: no visible global function definition for ‘grid.text’
* 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 ... [90s/95s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
spectralMap     16.046  0.766  16.919
computeLogRatio 10.899  0.208  12.693
plotLogRatio     9.063  0.178   9.327
* checking PDF version of manual ... OK
* DONE

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/a4Base.Rcheck/00check.log’
for details.

* installing *source* package ‘a4Base’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (a4Base)

name	user	system	elapsed
a4palette	0.019	0.001	0.020
addQuantilesColors	3.313	0.199	3.584
boxPlot	3.073	0.103	3.216
combineTwoExpressionSet	0.001	0.000	0.001
computeLogRatio	10.899	0.208	12.693
createExpressionSet	0.064	0.000	0.065
filterVarInt	2.675	0.123	2.815
heatmap.expressionSet	0.005	0.001	0.006
histPvalue	2.914	0.095	3.154
histpvalueplotter	2.631	0.091	2.776
lassoReg	2.866	0.106	3.006
logReg	0.001	0.000	0.001
nlcvTT	0.001	0.000	0.001
plot1gene	2.436	0.091	2.667
plotComb2Samples	2.680	0.090	2.978
plotCombMultSamples	2.794	0.098	4.176
plotCombination2genes	2.394	0.080	2.525
plotLogRatio	9.063	0.178	9.327
probabilitiesPlot	0.001	0.000	0.001
probe2gene	2.446	0.072	2.521
profilesPlot	2.204	0.064	2.283
propdegenescalculation	2.583	0.092	2.681
replicates	0.004	0.000	0.004
spectralMap	16.046	0.766	16.919
tTest	2.817	0.121	2.998
volcanoPlot	2.687	0.102	2.861