BioC 2.12: CHECK report for a4Base on george2

Package: a4Base

Version: 1.8.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings a4Base_1.8.0.tar.gz

StartedAt: 2013-10-08 23:49:21 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:58:10 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 528.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: a4Base.Rcheck

Warnings: 1

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/a4Base.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.8.0’
* 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 ... [38s/40s] 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 ... [185s/197s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
spectralMap         48.015  0.716  50.945
computeLogRatio     25.162  0.652  27.215
plotLogRatio        23.813  0.448  26.240
addQuantilesColors   6.584  0.192   7.069
plotCombMultSamples  5.901  0.088   6.191
tTest                5.421  0.124   5.781
volcanoPlot          4.484  0.088   5.005
lassoReg             4.120  0.076   5.676
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  ‘/home/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	0.032	0.004	0.037
addQuantilesColors	6.584	0.192	7.069
boxPlot	4.480	0.292	4.771
combineTwoExpressionSet	0.032	0.000	0.035
computeLogRatio	25.162	0.652	27.215
createExpressionSet	0.14	0.00	0.14
filterVarInt	3.584	0.088	3.683
heatmap.expressionSet	0.108	0.000	0.108
histPvalue	4.308	0.072	4.966
histpvalueplotter	3.381	0.072	4.122
lassoReg	4.120	0.076	5.676
logReg	0.036	0.000	0.038
nlcvTT	0.032	0.000	0.032
plot1gene	4.136	0.200	4.510
plotComb2Samples	4.524	0.072	4.834
plotCombMultSamples	5.901	0.088	6.191
plotCombination2genes	3.908	0.084	4.060
plotLogRatio	23.813	0.448	26.240
probabilitiesPlot	0.044	0.000	0.048
probe2gene	3.837	0.084	4.515
profilesPlot	3.008	0.044	3.105
propdegenescalculation	4.140	0.080	4.235
replicates	0.052	0.000	0.052
spectralMap	48.015	0.716	50.945
tTest	5.421	0.124	5.781
volcanoPlot	4.484	0.088	5.005