Package: aroma.light

Version: 1.16.1

Command: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD check --no-vignettes --timings aroma.light_1.16.1.tar.gz

StartedAt: 2010-10-04 15:50:34 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 15:52:21 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 107.8 seconds

RetCode: 0

Status:  OK

CheckDir: aroma.light.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/aroma.light.Rcheck'
* using R version 2.11.1 Patched (2010-05-31 r52167)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'aroma.light/DESCRIPTION' ... OK
* this is package 'aroma.light' version '1.16.1'
* 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 examples ... OK
* checking PDF version of manual ... OK

* install options are ' --no-html'

* 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	0.009
backtransformPrincipalCurve.matrix	1.378	0.028	1.411
calibrateMultiscan.matrix	0	0	0
callNaiveGenotypes.numeric	0.679	0.100	0.787
distanceBetweenLines	0.095	0.003	0.098
findPeaksAndValleys.numeric	0.112	0.021	0.134
fitPrincipalCurve.matrix	0.869	0.021	0.895
fitXYCurve.matrix	0.113	0.003	0.117
iwpca.matrix	0.068	0.002	0.071
likelihood.smooth.spline	0.555	0.023	0.591
medianPolish.matrix	0.014	0.001	0.015
normalizeAffine.matrix	27.007	0.516	27.890
normalizeCurveFit.matrix	26.828	0.504	27.653
normalizeDifferencesToAverage.list	0.063	0.006	0.068
normalizeFragmentLength	1.413	0.049	1.467
normalizeQuantileRank.list	0.240	0.058	0.302
normalizeQuantileRank.matrix	0.107	0.035	0.148
normalizeQuantileSpline.matrix	3.337	0.251	3.636
normalizeTumorBoost.numeric	0.153	0.018	0.172
robustSmoothSpline	0.086	0.002	0.117
sampleCorrelations.matrix	0.227	0.007	0.235
sampleTuples	0.001	0.000	0.002
weightedMedian	5.740	0.491	6.441
wpca.matrix	0.145	0.005	0.153