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: 2013-03-25 00:55:56 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:01:52 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 355.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: a4Base.Rcheck

Warnings: 3

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/a4Base.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-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 ... [27s/27s] WARNING
Found the following significant warnings:
  Warning: '.path.package' is deprecated.
  Warning: '.path.package' is deprecated.
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 ... [119s/120s] WARNING
Found the following significant warnings:

  Warning: '.path.package' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                  user system elapsed
spectralMap     21.655  3.207  24.992
computeLogRatio 12.946  0.465  13.537
plotLogRatio    12.074  0.401  12.534
* checking PDF version of manual ... OK

WARNING: There were 3 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: '.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
Warning: '.path.package' is deprecated.
Use 'path.package' instead.
See help("Deprecated")
* DONE (a4Base)

name	user	system	elapsed
a4palette	0.220	0.008	0.228
addQuantilesColors	3.555	0.229	3.805
boxPlot	4.134	0.259	4.405
combineTwoExpressionSet	0.013	0.008	0.021
computeLogRatio	12.946	0.465	13.537
createExpressionSet	0.075	0.011	0.086
filterVarInt	3.150	0.166	3.323
heatmap.expressionSet	0.051	0.067	0.124
histPvalue	3.950	0.264	4.292
histpvalueplotter	3.688	0.253	3.961
lassoReg	3.153	0.225	3.438
logReg	0.018	0.011	0.029
nlcvTT	0.010	0.007	0.019
plot1gene	3.553	0.221	3.837
plotComb2Samples	3.104	0.214	3.367
plotCombMultSamples	3.628	0.296	4.184
plotCombination2genes	3.032	0.198	3.243
plotLogRatio	12.074	0.401	12.534
probabilitiesPlot	0.012	0.009	0.021
probe2gene	3.398	0.129	3.536
profilesPlot	2.844	0.177	3.041
propdegenescalculation	3.255	0.216	3.482
replicates	0.230	0.014	0.245
spectralMap	21.655	3.207	24.992
tTest	4.064	0.322	4.403
volcanoPlot	4.075	0.274	4.365