Package: aroma.light

Version: 1.19.4

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch aroma.light_1.19.4.tar.gz

StartedAt: 2011-03-17 15:32:32 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 15:34:05 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 93.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: aroma.light.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/aroma.light.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'aroma.light/DESCRIPTION' ... OK
* this is package 'aroma.light' version '1.19.4'
* package encoding: latin1
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'aroma.light' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... OK
* checking R code for possible problems ... OK
* 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 ... NOTE
'library' or 'require' call not declared from: R.basic
* checking examples ... WARNING
checking a package with encoding  'latin1'  in an ASCII locale

 OK
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  '/Users/biocbuild/bbs-2.8-bioc/meat/aroma.light.Rcheck/00check.log'
for details

* installing *source* package 'aroma.light' ...
** R
** inst
** preparing package for lazy loading
R.methodsS3 v1.2.1 (2010-09-18) successfully loaded. See ?R.methodsS3 for help.
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Warning messages:
1: In value[[3L]](cond) :
  Multiple installations of package 'aroma.light' was found. Using the first. Paths to all installations: /Users/biocbuild/bbs-2.8-bioc/meat/aroma.light.Rcheck, /Library/Frameworks/R.framework/Versions/2.13/Resources/library
2: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible 

* DONE (aroma.light)

name	user	system	elapsed
backtransformAffine.matrix	0.004	0.001	0.005
backtransformPrincipalCurve.matrix	0.828	0.009	0.837
calibrateMultiscan.matrix	0	0	0
callNaiveGenotypes.numeric	0.55	0.02	0.57
distanceBetweenLines	0.017	0.001	0.019
findPeaksAndValleys.density	0.060	0.001	0.061
fitPrincipalCurve.matrix	0.598	0.009	0.606
fitXYCurve.matrix	0.077	0.003	0.080
iwpca.matrix	0.011	0.001	0.013
likelihood.smooth.spline	0.214	0.002	0.217
medianPolish.matrix	0.007	0.000	0.008
normalizeAffine.matrix	18.844	0.071	19.016
normalizeCurveFit.matrix	18.563	0.066	18.630
normalizeDifferencesToAverage.list	0.021	0.001	0.022
normalizeFragmentLength	0.816	0.010	0.827
normalizeQuantileRank.list	0.157	0.004	0.180
normalizeQuantileRank.matrix	0.073	0.006	0.078
normalizeQuantileSpline.matrix	1.974	0.014	1.988
normalizeTumorBoost.numeric	0.099	0.006	0.139
robustSmoothSpline	0.061	0.001	0.081
sampleCorrelations.matrix	0.166	0.003	0.170
sampleTuples	0.001	0.000	0.001
weightedMedian	4.135	0.145	4.280
wpca.matrix	0.074	0.003	0.077