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BioC 3.5: CHECK report for aroma.light on tokay2

This page was generated on 2017-10-18 14:19:26 -0400 (Wed, 18 Oct 2017).

Package 59/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
aroma.light 3.6.0
Henrik Bengtsson
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/aroma.light
Branch: RELEASE_3_5
Last Commit: 63dcf9a
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: aroma.light
Version: 3.6.0
Command: rm -rf aroma.light.buildbin-libdir aroma.light.Rcheck && mkdir aroma.light.buildbin-libdir aroma.light.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=aroma.light.buildbin-libdir aroma.light_3.6.0.tar.gz >aroma.light.Rcheck\00install.out 2>&1 && cp aroma.light.Rcheck\00install.out aroma.light-install.out && C:\Users\biocbuild\bbs-3.5-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_3.6.0.tar.gz
StartedAt: 2017-10-17 22:03:03 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 22:06:13 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 189.3 seconds
RetCode: 0
Status:  OK  
CheckDir: aroma.light.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf aroma.light.buildbin-libdir aroma.light.Rcheck && mkdir aroma.light.buildbin-libdir aroma.light.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=aroma.light.buildbin-libdir aroma.light_3.6.0.tar.gz >aroma.light.Rcheck\00install.out 2>&1 && cp aroma.light.Rcheck\00install.out aroma.light-install.out  &&  C:\Users\biocbuild\bbs-3.5-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_3.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/aroma.light.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'aroma.light/DESCRIPTION' ... OK
* this is package 'aroma.light' version '3.6.0'
* 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' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
normalizeAffine    7.5   0.02    7.51
normalizeCurveFit  7.2   0.03    7.24
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
normalizeCurveFit 7.60   0.04    7.64
normalizeAffine   7.18   0.02    7.20
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'backtransformAffine.matrix.R'
  Running 'backtransformPrincipalCurve.matrix.R'
  Running 'callNaiveGenotypes.R'
  Running 'distanceBetweenLines.R'
  Running 'findPeaksAndValleys.R'
  Running 'fitPrincipalCurve.matrix.R'
  Running 'fitXYCurve.matrix.R'
  Running 'iwpca.matrix.R'
  Running 'likelihood.smooth.spline.R'
  Running 'medianPolish.matrix.R'
  Running 'normalizeAffine.matrix.R'
  Running 'normalizeAverage.list.R'
  Running 'normalizeAverage.matrix.R'
  Running 'normalizeCurveFit.matrix.R'
  Running 'normalizeDifferencesToAverage.R'
  Running 'normalizeFragmentLength-ex1.R'
  Running 'normalizeFragmentLength-ex2.R'
  Running 'normalizeQuantileRank.list.R'
  Running 'normalizeQuantileRank.matrix.R'
  Running 'normalizeQuantileSpline.matrix.R'
  Running 'normalizeTumorBoost,flavors.R'
  Running 'normalizeTumorBoost.R'
  Running 'robustSmoothSpline.R'
  Running 'rowAverages.matrix.R'
  Running 'sampleCorrelations.matrix.R'
  Running 'sampleTuples.R'
  Running 'wpca.matrix.R'
  Running 'wpca2.matrix.R'
 OK
** running tests for arch 'x64' ...
  Running 'backtransformAffine.matrix.R'
  Running 'backtransformPrincipalCurve.matrix.R'
  Running 'callNaiveGenotypes.R'
  Running 'distanceBetweenLines.R'
  Running 'findPeaksAndValleys.R'
  Running 'fitPrincipalCurve.matrix.R'
  Running 'fitXYCurve.matrix.R'
  Running 'iwpca.matrix.R'
  Running 'likelihood.smooth.spline.R'
  Running 'medianPolish.matrix.R'
  Running 'normalizeAffine.matrix.R'
  Running 'normalizeAverage.list.R'
  Running 'normalizeAverage.matrix.R'
  Running 'normalizeCurveFit.matrix.R'
  Running 'normalizeDifferencesToAverage.R'
  Running 'normalizeFragmentLength-ex1.R'
  Running 'normalizeFragmentLength-ex2.R'
  Running 'normalizeQuantileRank.list.R'
  Running 'normalizeQuantileRank.matrix.R'
  Running 'normalizeQuantileSpline.matrix.R'
  Running 'normalizeTumorBoost,flavors.R'
  Running 'normalizeTumorBoost.R'
  Running 'robustSmoothSpline.R'
  Running 'rowAverages.matrix.R'
  Running 'sampleCorrelations.matrix.R'
  Running 'sampleTuples.R'
  Running 'wpca.matrix.R'
  Running 'wpca2.matrix.R'
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/aroma.light.Rcheck/00check.log'
for details.


aroma.light.Rcheck/00install.out:


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_3.6.0.zip
* DONE (aroma.light)

aroma.light.Rcheck/examples_i386/aroma.light-Ex.timings:

nameusersystemelapsed
backtransformAffine0.050.000.05
backtransformPrincipalCurve0.620.000.89
calibrateMultiscan000
callNaiveGenotypes1.050.001.05
distanceBetweenLines0.110.000.11
findPeaksAndValleys0.060.000.06
fitPrincipalCurve0.590.010.61
fitXYCurve0.070.000.06
iwpca0.060.000.07
likelihood.smooth.spline0.140.000.14
medianPolish000
normalizeAffine7.500.027.51
normalizeCurveFit7.200.037.24
normalizeDifferencesToAverage0.240.000.23
normalizeFragmentLength0.730.000.74
normalizeQuantileRank0.200.020.21
normalizeQuantileRank.matrix0.110.000.11
normalizeQuantileSpline1.330.001.33
normalizeTumorBoost0.300.010.31
robustSmoothSpline0.090.000.10
sampleCorrelations0.240.000.23
sampleTuples0.010.000.02
wpca0.110.000.11

aroma.light.Rcheck/examples_x64/aroma.light-Ex.timings:

nameusersystemelapsed
backtransformAffine0.060.000.06
backtransformPrincipalCurve0.50.00.5
calibrateMultiscan000
callNaiveGenotypes0.840.000.84
distanceBetweenLines0.10.00.1
findPeaksAndValleys0.030.000.03
fitPrincipalCurve0.610.000.61
fitXYCurve0.040.000.05
iwpca0.080.000.07
likelihood.smooth.spline0.130.000.13
medianPolish000
normalizeAffine7.180.027.20
normalizeCurveFit7.600.047.64
normalizeDifferencesToAverage0.200.020.22
normalizeFragmentLength0.720.000.72
normalizeQuantileRank0.180.020.20
normalizeQuantileRank.matrix0.020.030.05
normalizeQuantileSpline1.160.001.16
normalizeTumorBoost0.300.000.29
robustSmoothSpline0.090.000.10
sampleCorrelations0.330.000.33
sampleTuples0.020.000.01
wpca0.120.000.49