Package: aroma.light

Version: 1.30.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch aroma.light_1.30.1.tar.gz

StartedAt: 2013-05-01 02:21:40 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 02:23:34 -0700 (Wed, 01 May 2013)

EllapsedTime: 113.9 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 version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'aroma.light/DESCRIPTION' ... OK
* this is package 'aroma.light' version '1.30.1'
* 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 ... [4s/4s] 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

 [63s/63s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
normalizeCurveFit.matrix 25.810  0.145  25.983
normalizeAffine.matrix   25.573  0.105  25.693
* 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	0.055	0.011	0.066
backtransformPrincipalCurve.matrix	1.053	0.052	1.133
calibrateMultiscan.matrix	0.009	0.000	0.009
callNaiveGenotypes.numeric	0.984	0.029	1.022
distanceBetweenLines	0.065	0.004	0.068
findPeaksAndValleys.density	0.120	0.006	0.129
fitPrincipalCurve.matrix	0.783	0.031	0.824
fitXYCurve.matrix	0.143	0.007	0.157
iwpca.matrix	0.061	0.010	0.074
likelihood.smooth.spline	0.261	0.014	0.278
medianPolish.matrix	0.026	0.002	0.028
normalizeAffine.matrix	25.573	0.105	25.693
normalizeCurveFit.matrix	25.810	0.145	25.983
normalizeDifferencesToAverage.list	0.394	0.022	0.423
normalizeFragmentLength	1.502	0.084	1.623
normalizeQuantileRank.list	0.340	0.016	0.375
normalizeQuantileRank.matrix	0.196	0.006	0.212
normalizeQuantileSpline.matrix	2.316	0.028	2.362
normalizeTumorBoost.numeric	0.277	0.023	0.309
robustSmoothSpline	0.139	0.010	0.178
sampleCorrelations.matrix	0.720	0.007	0.733
sampleTuples	0.011	0.005	0.016
wpca.matrix	0.098	0.031	0.132