Package: aroma.light

Version: 1.19.3

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch aroma.light_1.19.3.tar.gz

StartedAt: 2011-02-24 18:01:38 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 18:03:37 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 118.9 seconds

RetCode: 0

Status:  OK

CheckDir: aroma.light.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.8-bioc/meat/aroma.light.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* 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 ‘1.19.3’
* 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	0.002	0.008
backtransformPrincipalCurve.matrix	1.302	0.029	1.339
calibrateMultiscan.matrix	0.000	0.001	0.000
callNaiveGenotypes.numeric	0.711	0.092	0.805
distanceBetweenLines	0.097	0.002	0.099
findPeaksAndValleys.density	0.075	0.016	0.090
fitPrincipalCurve.matrix	0.818	0.023	1.095
fitXYCurve.matrix	0.102	0.005	0.109
iwpca.matrix	0.072	0.002	0.074
likelihood.smooth.spline	0.546	0.022	0.571
medianPolish.matrix	0.014	0.001	0.016
normalizeAffine.matrix	28.271	0.461	28.749
normalizeCurveFit.matrix	28.205	0.465	28.709
normalizeDifferencesToAverage.list	0.030	0.002	0.032
normalizeFragmentLength	1.459	0.053	1.513
normalizeQuantileRank.list	0.237	0.064	0.303
normalizeQuantileRank.matrix	0.102	0.036	0.138
normalizeQuantileSpline.matrix	3.041	0.242	3.290
normalizeTumorBoost.numeric	0.143	0.021	0.164
robustSmoothSpline	0.085	0.003	0.130
sampleCorrelations.matrix	0.254	0.004	0.258
sampleTuples	0.001	0.000	0.002
weightedMedian	5.949	0.488	6.446
wpca.matrix	0.159	0.004	0.164