Package: a4Base

Version: 1.7.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch a4Base_1.7.1.tar.gz

StartedAt: 2013-03-24 01:46:14 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 01:53:25 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 431.6 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 beta (2013-03-21 r62346)
* 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 '1.7.1'
* 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 ... [32s/32s] 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 ... [151s/155s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
spectralMap        34.765  2.102  37.472
computeLogRatio    17.223  0.457  18.139
plotLogRatio       16.751  0.421  17.360
addQuantilesColors  4.849  0.345   5.400
* 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
'.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	0.411	0.008	0.563
addQuantilesColors	4.849	0.345	5.400
boxPlot	4.382	0.297	4.874
combineTwoExpressionSet	0.022	0.008	0.030
computeLogRatio	17.223	0.457	18.139
createExpressionSet	0.109	0.020	0.129
filterVarInt	3.580	0.221	3.889
heatmap.expressionSet	0.063	0.065	0.141
histPvalue	3.771	0.227	4.081
histpvalueplotter	3.649	0.215	3.905
lassoReg	3.554	0.188	3.801
logReg	0.021	0.008	0.035
nlcvTT	0.003	0.005	0.008
plot1gene	3.851	0.196	4.312
plotComb2Samples	3.877	0.216	4.259
plotCombMultSamples	4.182	0.235	4.603
plotCombination2genes	3.801	0.185	4.076
plotLogRatio	16.751	0.421	17.360
probabilitiesPlot	0.479	0.044	0.538
probe2gene	3.367	0.135	3.561
profilesPlot	3.757	0.155	4.020
propdegenescalculation	4.270	0.228	4.591
replicates	0.020	0.008	0.030
spectralMap	34.765	2.102	37.472
tTest	3.783	0.222	4.063
volcanoPlot	4.350	0.295	4.715