Package: aroma.light

Version: 1.29.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch aroma.light_1.29.0.tar.gz

StartedAt: 2013-03-25 01:10:47 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:12:27 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 100.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: aroma.light.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/aroma.light.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '1.29.0'
* 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 ... [3s/3s] 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 ... WARNING
checking a package with encoding  'latin1'  in an ASCII locale

 [54s/54s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
normalizeAffine.matrix   23.520  0.424  23.952
normalizeCurveFit.matrix 19.448  0.356  19.824
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  '/Users/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	0.081	0.033	0.114
backtransformPrincipalCurve.matrix	0.756	0.074	0.849
calibrateMultiscan.matrix	0.004	0.004	0.008
callNaiveGenotypes.numeric	0.710	0.105	0.816
distanceBetweenLines	0.055	0.031	0.085
findPeaksAndValleys.density	0.116	0.033	0.149
fitPrincipalCurve.matrix	0.803	0.079	0.883
fitXYCurve.matrix	0.141	0.026	0.169
iwpca.matrix	0.063	0.039	0.102
likelihood.smooth.spline	0.308	0.054	0.364
medianPolish.matrix	0.027	0.016	0.044
normalizeAffine.matrix	23.520	0.424	23.952
normalizeCurveFit.matrix	19.448	0.356	19.824
normalizeDifferencesToAverage.list	0.343	0.037	0.384
normalizeFragmentLength	1.007	0.170	1.188
normalizeQuantileRank.list	0.280	0.060	0.356
normalizeQuantileRank.matrix	0.140	0.034	0.174
normalizeQuantileSpline.matrix	1.627	0.168	1.798
normalizeTumorBoost.numeric	0.265	0.050	0.322
robustSmoothSpline	0.132	0.022	0.158
sampleCorrelations.matrix	0.715	0.012	0.727
sampleTuples	0.007	0.008	0.016
wpca.matrix	0.073	0.058	0.133