BioC 2.12: CHECK report for a4Base on george2

Package: a4Base

Version: 1.7.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings a4Base_1.7.1.tar.gz

StartedAt: 2013-03-24 23:42:48 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 23:51:34 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 526.0 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 3.0.0 beta (2013-03-19 r62328)
* 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 ‘1.7.1’
* 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/39s] 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 ... [186s/197s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
spectralMap         48.667  0.820  51.770
computeLogRatio     25.126  0.624  27.835
plotLogRatio        23.261  0.476  25.611
addQuantilesColors   6.064  0.200   6.912
plotCombMultSamples  5.649  0.064   5.760
volcanoPlot          5.277  0.136   5.737
plot1gene            4.984  0.188   6.372
plotComb2Samples     5.012  0.084   5.170
boxPlot              4.484  0.240   5.210
* 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
'.path.package' is deprecated.
Use 'path.package' instead.
See help("Deprecated")
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
'.path.package' is deprecated.
Use 'path.package' instead.
See help("Deprecated")
* DONE (a4Base)

name	user	system	elapsed
a4palette	0.724	0.004	0.726
addQuantilesColors	6.064	0.200	6.912
boxPlot	4.484	0.240	5.210
combineTwoExpressionSet	0.052	0.000	0.051
computeLogRatio	25.126	0.624	27.835
createExpressionSet	0.144	0.000	0.146
filterVarInt	3.580	0.068	3.650
heatmap.expressionSet	0.112	0.000	0.109
histPvalue	3.396	0.092	3.495
histpvalueplotter	3.397	0.100	3.529
lassoReg	3.268	0.072	3.399
logReg	0.040	0.000	0.039
nlcvTT	0.008	0.000	0.007
plot1gene	4.984	0.188	6.372
plotComb2Samples	5.012	0.084	5.170
plotCombMultSamples	5.649	0.064	5.760
plotCombination2genes	3.736	0.052	3.883
plotLogRatio	23.261	0.476	25.611
probabilitiesPlot	0.800	0.000	0.805
probe2gene	3.045	0.068	3.209
profilesPlot	3.820	0.088	4.261
propdegenescalculation	4.424	0.100	4.907
replicates	0.044	0.000	0.042
spectralMap	48.667	0.820	51.770
tTest	4.544	0.092	4.779
volcanoPlot	5.277	0.136	5.737

Summary

Command output