Package: aroma.light

Version: 1.18.4

Command: /Library/Frameworks/R.framework/Versions/2.12/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch aroma.light_1.18.4.tar.gz

StartedAt: 2011-03-31 04:27:38 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 04:29:38 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 119.4 seconds

RetCode: 0

Status:  OK

CheckDir: aroma.light.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.7-bioc/meat/aroma.light.Rcheck’
* using R version 2.12.2 Patched (2011-02-25 r54591)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘aroma.light/DESCRIPTION’ ... OK
* this is package ‘aroma.light’ version ‘1.18.4’
* 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 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 ... OK
* checking PDF version of manual ... OK

* 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

* DONE (aroma.light)

name	user	system	elapsed
backtransformAffine.matrix	0.007	0.001	0.009
backtransformPrincipalCurve.matrix	1.292	0.028	1.334
calibrateMultiscan.matrix	0.000	0.001	0.000
callNaiveGenotypes.numeric	0.700	0.105	0.813
distanceBetweenLines	0.094	0.002	0.097
findPeaksAndValleys.density	0.097	0.016	0.119
fitPrincipalCurve.matrix	0.830	0.025	0.864
fitXYCurve.matrix	0.101	0.004	0.111
iwpca.matrix	0.069	0.002	0.071
likelihood.smooth.spline	0.514	0.023	0.544
medianPolish.matrix	0.010	0.000	0.011
normalizeAffine.matrix	28.539	0.596	29.453
normalizeCurveFit.matrix	28.473	0.591	29.307
normalizeDifferencesToAverage.list	0.029	0.002	0.032
normalizeFragmentLength	1.380	0.052	1.435
normalizeQuantileRank.list	0.235	0.060	0.297
normalizeQuantileRank.matrix	0.105	0.031	0.137
normalizeQuantileSpline.matrix	2.997	0.226	3.223
normalizeTumorBoost.numeric	0.138	0.019	0.156
robustSmoothSpline	0.078	0.002	0.210
sampleCorrelations.matrix	0.234	0.004	0.237
sampleTuples	0.002	0.000	0.002
weightedMedian	5.380	0.436	5.819
wpca.matrix	0.143	0.004	0.148