BioC 2.14: CHECK report for aroma.light on moscato2

Package: aroma.light

Version: 2.0.0

Command: rm -rf aroma.light.buildbin-libdir && mkdir aroma.light.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=aroma.light.buildbin-libdir aroma.light_2.0.0.tar.gz >aroma.light-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=aroma.light.buildbin-libdir --install="check:aroma.light-install.out" --force-multiarch --no-vignettes --timings aroma.light_2.0.0.tar.gz

StartedAt: 2014-10-07 22:45:13 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:47:10 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 116.9 seconds

RetCode: 0

Status:  OK

CheckDir: aroma.light.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf aroma.light.buildbin-libdir && mkdir aroma.light.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=aroma.light.buildbin-libdir aroma.light_2.0.0.tar.gz >aroma.light-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=aroma.light.buildbin-libdir --install="check:aroma.light-install.out" --force-multiarch --no-vignettes --timings aroma.light_2.0.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/aroma.light.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'aroma.light/DESCRIPTION' ... OK
* this is package 'aroma.light' version '2.0.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... [36s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
normalizeCurveFit 15.18      0   15.18
normalizeAffine   14.66      0   14.66
** running examples for arch 'x64' ... [35s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
normalizeCurveFit 14.41   0.02   14.43
normalizeAffine   14.15   0.00   14.15
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  'E:/biocbld/bbs-2.14-bioc/meat/aroma.light.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'aroma.light' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'aroma.light' as aroma.light_2.0.0.zip
* DONE (aroma.light)

name	user	system	elapsed
backtransformAffine	0.00	0.00	0.02
backtransformPrincipalCurve	0.5	0.0	0.5
calibrateMultiscan	0	0	0
callNaiveGenotypes	0.66	0.00	0.66
distanceBetweenLines	0.02	0.00	0.02
findPeaksAndValleys	0.08	0.00	0.08
fitPrincipalCurve	0.42	0.00	0.42
fitXYCurve	0.08	0.00	0.08
iwpca	0.01	0.00	0.01
likelihood.smooth.spline	0.14	0.00	0.14
medianPolish	0.02	0.00	0.02
normalizeAffine	14.66	0.00	14.66
normalizeCurveFit	15.18	0.00	15.18
normalizeDifferencesToAverage	0.27	0.01	0.28
normalizeFragmentLength	0.93	0.00	0.94
normalizeQuantileRank	0.24	0.00	0.32
normalizeQuantileRank.matrix	0.08	0.00	0.08
normalizeQuantileSpline	0.99	0.00	1.00
normalizeTumorBoost	0.25	0.03	0.28
robustSmoothSpline	0.07	0.02	0.08
sampleCorrelations	0.43	0.00	0.44
sampleTuples	0	0	0
wpca	0.11	0.00	0.21

name	user	system	elapsed
backtransformAffine	0	0	0
backtransformPrincipalCurve	0.53	0.00	0.61
calibrateMultiscan	0	0	0
callNaiveGenotypes	0.7	0.0	0.7
distanceBetweenLines	0.02	0.00	0.22
findPeaksAndValleys	0.06	0.00	0.07
fitPrincipalCurve	0.45	0.01	0.46
fitXYCurve	0.08	0.00	0.08
iwpca	0.02	0.00	0.02
likelihood.smooth.spline	0.15	0.00	0.15
medianPolish	0	0	0
normalizeAffine	14.15	0.00	14.15
normalizeCurveFit	14.41	0.02	14.43
normalizeDifferencesToAverage	0.24	0.00	0.24
normalizeFragmentLength	0.89	0.00	0.89
normalizeQuantileRank	0.22	0.00	0.21
normalizeQuantileRank.matrix	0.11	0.00	0.11
normalizeQuantileSpline	1.03	0.00	1.03
normalizeTumorBoost	0.23	0.00	0.24
robustSmoothSpline	0.06	0.00	0.06
sampleCorrelations	0.49	0.00	0.48
sampleTuples	0	0	0
wpca	0.09	0.00	0.11