BioC 2.12: CHECK report for a4Base on pelham

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: 2013-05-01 01:42:08 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 01:49:27 -0700 (Wed, 01 May 2013)

EllapsedTime: 439.3 seconds

RetCode: 0

Status: WARNINGS

CheckDir: a4Base.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/a4Base.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* 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 ... [32s/33s] 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 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 ... [156s/162s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
spectralMap         35.058  1.995  38.435
computeLogRatio     17.346  0.446  18.573
plotLogRatio        15.671  0.450  16.727
boxPlot              4.847  0.318   5.424
addQuantilesColors   4.745  0.340   5.422
volcanoPlot          4.659  0.300   5.171
plotCombMultSamples  4.581  0.260   5.115
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
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
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (a4Base)

name	user	system	elapsed
a4palette	0.423	0.008	0.438
addQuantilesColors	4.745	0.340	5.422
boxPlot	4.847	0.318	5.424
combineTwoExpressionSet	0.022	0.007	0.031
computeLogRatio	17.346	0.446	18.573
createExpressionSet	0.125	0.019	0.155
filterVarInt	3.507	0.255	3.885
heatmap.expressionSet	0.063	0.070	0.138
histPvalue	4.594	0.237	4.948
histpvalueplotter	4.560	0.226	4.959
lassoReg	4.017	0.189	4.431
logReg	0.021	0.009	0.035
nlcvTT	0.019	0.005	0.024
plot1gene	4.278	0.216	4.673
plotComb2Samples	4.255	0.217	4.651
plotCombMultSamples	4.581	0.260	5.115
plotCombination2genes	4.233	0.211	4.564
plotLogRatio	15.671	0.450	16.727
probabilitiesPlot	0.020	0.013	0.033
probe2gene	4.002	0.175	4.379
profilesPlot	3.758	0.131	4.057
propdegenescalculation	4.621	0.243	4.960
replicates	0.005	0.005	0.009
spectralMap	35.058	1.995	38.435
tTest	4.317	0.275	4.738
volcanoPlot	4.659	0.300	5.171

Summary

Command output