BioC 2.14: CHECK report for a4Base on petty

Package: a4Base

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch a4Base_1.12.0.tar.gz

StartedAt: 2014-10-07 20:33:29 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 20:41:47 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 498.9 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_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/a4Base.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.12.0’
* 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 ... [36s/38s] 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.
Packages in Depends field not imported from:
  ‘a4Preproc’ ‘annaffy’ ‘AnnotationDbi’ ‘genefilter’ ‘glmnet’ ‘gplots’
  ‘mpm’ ‘multtest’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotLogRatio: no visible global function definition for ‘JavaGD’
plotLogRatio: no visible global function definition for ‘grid.garnish’
plotLogRatio: no visible global function definition for
  ‘grid.hyperlink’
plotLogRatio: no visible global function definition for ‘grid.script’
plotLogRatio: no visible global function definition for ‘gridToSVG’
* 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 ... [157s/164s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
spectralMap         29.217  1.263  31.073
computeLogRatio     19.088  0.318  19.704
plotLogRatio        17.599  0.310  18.076
boxPlot              5.242  0.209   5.485
addQuantilesColors   5.083  0.278   6.230
volcanoPlot          4.908  0.215   5.230
tTest                4.880  0.182   5.356
plotCombMultSamples  4.838  0.202   6.845
lassoReg             4.823  0.194   5.108
histpvalueplotter    4.594  0.173   5.053
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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	0.030	0.002	0.042
addQuantilesColors	5.083	0.278	6.230
boxPlot	5.242	0.209	5.485
combineTwoExpressionSet	0.001	0.000	0.002
computeLogRatio	19.088	0.318	19.704
createExpressionSet	0.133	0.000	0.134
filterVarInt	4.050	0.186	4.281
heatmap.expressionSet	0.009	0.001	0.010
histPvalue	4.651	0.170	4.974
histpvalueplotter	4.594	0.173	5.053
lassoReg	4.823	0.194	5.108
logReg	0.002	0.000	0.002
nlcvTT	0.001	0.000	0.001
plot1gene	4.149	0.169	4.833
plotComb2Samples	4.210	0.183	4.519
plotCombMultSamples	4.838	0.202	6.845
plotCombination2genes	4.059	0.160	4.233
plotLogRatio	17.599	0.310	18.076
probabilitiesPlot	0.002	0.000	0.001
probe2gene	4.682	0.124	4.843
profilesPlot	4.088	0.134	4.250
propdegenescalculation	4.721	0.168	4.913
replicates	0.005	0.000	0.006
spectralMap	29.217	1.263	31.073
tTest	4.880	0.182	5.356
volcanoPlot	4.908	0.215	5.230