BioC 2.12: CHECK report for aroma.light on petty

Package: aroma.light

Version: 1.30.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch aroma.light_1.30.5.tar.gz

StartedAt: 2013-10-08 21:35:39 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 21:37:32 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 113.2 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 version 3.0.1 (2013-05-16)
* 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 '1.30.5'
* 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

 [56s/57s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
normalizeCurveFit.matrix 22.676  0.129  23.065
normalizeAffine.matrix   22.412  0.118  22.662
* 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	0.089	0.002	0.092
backtransformPrincipalCurve.matrix	1.079	0.035	1.128
calibrateMultiscan.matrix	0.005	0.001	0.005
callNaiveGenotypes.numeric	0.986	0.025	1.012
distanceBetweenLines	0.061	0.003	0.065
findPeaksAndValleys.density	0.101	0.004	0.106
fitPrincipalCurve.matrix	0.745	0.029	0.780
fitXYCurve.matrix	0.129	0.007	0.139
iwpca.matrix	0.048	0.004	0.052
likelihood.smooth.spline	0.272	0.019	0.293
medianPolish.matrix	0.023	0.003	0.026
normalizeAffine.matrix	22.412	0.118	22.662
normalizeCurveFit.matrix	22.676	0.129	23.065
normalizeDifferencesToAverage.list	0.381	0.018	0.403
normalizeFragmentLength	1.334	0.063	1.408
normalizeQuantileRank.list	0.347	0.014	0.373
normalizeQuantileRank.matrix	0.192	0.005	0.199
normalizeQuantileSpline.matrix	1.786	0.031	1.818
normalizeTumorBoost.numeric	0.291	0.019	0.315
robustSmoothSpline	0.142	0.012	0.157
sampleCorrelations.matrix	0.946	0.008	0.956
sampleTuples	0.009	0.003	0.012
wpca.matrix	0.102	0.024	0.127