BioC 2.13: CHECK report for aroma.light on perceval

Package: aroma.light

Version: 1.32.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch aroma.light_1.32.0.tar.gz

StartedAt: 2014-04-04 23:27:29 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 23:28:55 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 85.5 seconds

RetCode: 0

Status:  OK

CheckDir: aroma.light.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/aroma.light.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘aroma.light/DESCRIPTION’ ... OK
* this is package ‘aroma.light’ version ‘1.32.0’
* 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 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 ... [40s/40s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
normalizeCurveFit 15.486  0.126  15.759
normalizeAffine   15.042  0.106  15.293
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.13-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	0.082	0.003	0.090
backtransformPrincipalCurve	0.808	0.026	0.853
calibrateMultiscan	0.003	0.000	0.003
callNaiveGenotypes	0.807	0.027	0.873
distanceBetweenLines	0.097	0.003	0.105
findPeaksAndValleys	0.146	0.004	0.154
fitPrincipalCurve	0.654	0.029	0.693
fitXYCurve	0.096	0.005	0.101
iwpca	0.080	0.004	0.086
likelihood.smooth.spline	0.260	0.007	0.268
medianPolish	0.021	0.002	0.023
normalizeAffine	15.042	0.106	15.293
normalizeCurveFit	15.486	0.126	15.759
normalizeDifferencesToAverage	0.315	0.017	0.335
normalizeFragmentLength	1.053	0.053	1.112
normalizeQuantileRank	0.316	0.011	0.332
normalizeQuantileRank.matrix	0.100	0.004	0.106
normalizeQuantileSpline	1.442	0.021	1.464
normalizeTumorBoost	0.330	0.021	0.354
robustSmoothSpline	0.149	0.010	0.162
sampleCorrelations	0.814	0.003	0.816
sampleTuples	0.011	0.002	0.014
wpca	0.121	0.016	0.137