Package: aroma.light

Version: 1.29.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings aroma.light_1.29.0.tar.gz

StartedAt: 2013-01-16 00:37:55 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 00:39:14 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 78.5 seconds

RetCode: 0

Status:  OK

CheckDir: aroma.light.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/aroma.light.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘aroma.light/DESCRIPTION’ ... OK
* this is package ‘aroma.light’ version ‘1.29.0’
* package encoding: latin1
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  inst/rsp/.rspPlugins
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘aroma.light’ can be installed ... OK
* 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 ... 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 ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
normalizeCurveFit.matrix 17.625  0.028  17.653
normalizeAffine.matrix   17.537  0.012  17.565
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/aroma.light.Rcheck/00check.log’
for details.

* installing *source* package ‘aroma.light’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

* DONE (aroma.light)

name	user	system	elapsed
backtransformAffine.matrix	0.048	0.000	0.049
backtransformPrincipalCurve.matrix	0.924	0.008	0.933
calibrateMultiscan.matrix	0.004	0.000	0.005
callNaiveGenotypes.numeric	0.780	0.016	0.796
distanceBetweenLines	0.072	0.004	0.075
findPeaksAndValleys.density	0.104	0.008	0.112
fitPrincipalCurve.matrix	0.604	0.016	0.622
fitXYCurve.matrix	0.104	0.000	0.102
iwpca.matrix	0.064	0.000	0.065
likelihood.smooth.spline	0.236	0.000	0.238
medianPolish.matrix	0.028	0.000	0.028
normalizeAffine.matrix	17.537	0.012	17.565
normalizeCurveFit.matrix	17.625	0.028	17.653
normalizeDifferencesToAverage.list	0.308	0.004	0.311
normalizeFragmentLength	0.944	0.012	0.963
normalizeQuantileRank.list	0.308	0.000	0.311
normalizeQuantileRank.matrix	0.100	0.004	0.102
normalizeQuantileSpline.matrix	2.280	0.004	2.288
normalizeTumorBoost.numeric	0.212	0.008	0.221
robustSmoothSpline	0.108	0.008	0.139
sampleCorrelations.matrix	0.664	0.000	0.666
sampleTuples	0.008	0.004	0.012
wpca.matrix	0.092	0.004	0.099