BioC 2.12: CHECK report for a4Base on petty

Package: a4Base

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch a4Base_1.8.0.tar.gz

StartedAt: 2013-10-08 21:26:57 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 21:35:05 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 487.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: a4Base.Rcheck

Warnings: 2

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/a4Base.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'a4Base/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'a4Base' version '1.8.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'gridSVG'
* 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/37s] WARNING
Found the following significant warnings:
  Warning: package 'KEGG.db' was built under R version 3.1.0
  Warning: package 'KEGG.db' was built under R version 3.1.0
See '/Users/biocbuild/bbs-2.12-bioc/meat/a4Base.Rcheck/00install.out' for details.
* 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... WARNING
Foreign function call with 'PACKAGE' argument in a base package:
  .C("bincode", ..., PACKAGE = "base")
Packages should not make .C/.Call/.Fortran calls to base packages. They
are not part of the API, for use only by R itself and subject to change
without notice.
* 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 ... [167s/172s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
spectralMap            34.128  1.829  36.484
computeLogRatio        20.269  0.401  21.130
plotLogRatio           18.355  0.378  19.654
boxPlot                 5.971  0.262   6.325
addQuantilesColors      5.263  0.355   5.712
histpvalueplotter       4.905  0.224   5.162
propdegenescalculation  4.919  0.209   5.288
histPvalue              4.833  0.260   5.169
plotCombMultSamples     4.712  0.263   5.227
lassoReg                4.725  0.208   5.048
* checking PDF version of manual ... OK

WARNING: There were 2 warnings.
NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/a4Base.Rcheck/00check.log'
for details.

* installing *source* package 'a4Base' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: package 'KEGG.db' was built under R version 3.1.0
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Warning: package 'KEGG.db' was built under R version 3.1.0
* DONE (a4Base)

name	user	system	elapsed
a4palette	0.037	0.006	0.044
addQuantilesColors	5.263	0.355	5.712
boxPlot	5.971	0.262	6.325
combineTwoExpressionSet	0.004	0.005	0.009
computeLogRatio	20.269	0.401	21.130
createExpressionSet	0.135	0.016	0.154
filterVarInt	4.172	0.269	4.486
heatmap.expressionSet	0.060	0.062	0.122
histPvalue	4.833	0.260	5.169
histpvalueplotter	4.905	0.224	5.162
lassoReg	4.725	0.208	5.048
logReg	0.024	0.007	0.032
nlcvTT	0.002	0.004	0.007
plot1gene	3.957	0.196	4.545
plotComb2Samples	4.387	0.219	4.690
plotCombMultSamples	4.712	0.263	5.227
plotCombination2genes	4.291	0.207	4.523
plotLogRatio	18.355	0.378	19.654
probabilitiesPlot	0.522	0.042	0.573
probe2gene	4.189	0.156	4.368
profilesPlot	4.379	0.172	4.663
propdegenescalculation	4.919	0.209	5.288
replicates	0.007	0.004	0.012
spectralMap	34.128	1.829	36.484
tTest	4.515	0.261	4.828
volcanoPlot	4.516	0.235	4.815