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BioC 3.1: CHECK report for aroma.light on moscato2

This page was generated on 2015-10-09 09:27:43 -0700 (Fri, 09 Oct 2015).

Package 50/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
aroma.light 2.4.0
Henrik Bengtsson
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/aroma.light
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: aroma.light
Version: 2.4.0
Command: rm -rf aroma.light.buildbin-libdir aroma.light.Rcheck && mkdir aroma.light.buildbin-libdir aroma.light.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=aroma.light.buildbin-libdir aroma.light_2.4.0.tar.gz >aroma.light.Rcheck\00install.out 2>&1 && cp aroma.light.Rcheck\00install.out aroma.light-install.out && E:\biocbld\bbs-3.1-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_2.4.0.tar.gz
StartedAt: 2015-10-08 23:22:38 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:26:02 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 203.5 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 && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=aroma.light.buildbin-libdir aroma.light_2.4.0.tar.gz >aroma.light.Rcheck\00install.out 2>&1 && cp aroma.light.Rcheck\00install.out aroma.light-install.out  && E:\biocbld\bbs-3.1-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_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/aroma.light.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '2.4.0'
* 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 15.46   0.03   15.49
normalizeAffine   14.88   0.02   14.89
** running examples for arch 'x64' ... [35s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
normalizeCurveFit 14.57   0.05   14.63
normalizeAffine   14.53   0.00   14.54
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'backtransformAffine.matrix.R' [0s]
  Running 'backtransformPrincipalCurve.matrix.R' [1s]
  Running 'callNaiveGenotypes.R' [1s]
  Running 'distanceBetweenLines.R' [0s]
  Running 'findPeaksAndValleys.R' [1s]
  Running 'fitPrincipalCurve.matrix.R' [1s]
  Running 'fitXYCurve.matrix.R' [1s]
  Running 'iwpca.matrix.R' [0s]
  Running 'likelihood.smooth.spline.R' [1s]
  Running 'medianPolish.matrix.R' [0s]
  Running 'normalizeAffine.matrix.R' [5s]
  Running 'normalizeCurveFit.matrix.R' [15s]
  Running 'normalizeDifferencesToAverage.R' [1s]
  Running 'normalizeFragmentLength-ex1.R' [1s]
  Running 'normalizeFragmentLength-ex2.R' [1s]
  Running 'normalizeQuantileRank.list.R' [1s]
  Running 'normalizeQuantileRank.matrix.R' [1s]
  Running 'normalizeQuantileSpline.matrix.R' [2s]
  Running 'normalizeTumorBoost,flavors.R' [1s]
  Running 'normalizeTumorBoost.R' [1s]
  Running 'robustSmoothSpline.R' [1s]
  Running 'sampleCorrelations.matrix.R' [1s]
  Running 'sampleTuples.R' [1s]
  Running 'wpca.matrix.R' [1s]
  Running 'wpca2.matrix.R' [1s]
 [39s] OK
** running tests for arch 'x64' ...
  Running 'backtransformAffine.matrix.R' [0s]
  Running 'backtransformPrincipalCurve.matrix.R' [1s]
  Running 'callNaiveGenotypes.R' [1s]
  Running 'distanceBetweenLines.R' [0s]
  Running 'findPeaksAndValleys.R' [1s]
  Running 'fitPrincipalCurve.matrix.R' [1s]
  Running 'fitXYCurve.matrix.R' [1s]
  Running 'iwpca.matrix.R' [1s]
  Running 'likelihood.smooth.spline.R' [1s]
  Running 'medianPolish.matrix.R' [0s]
  Running 'normalizeAffine.matrix.R' [5s]
  Running 'normalizeCurveFit.matrix.R' [15s]
  Running 'normalizeDifferencesToAverage.R' [1s]
  Running 'normalizeFragmentLength-ex1.R' [1s]
  Running 'normalizeFragmentLength-ex2.R' [1s]
  Running 'normalizeQuantileRank.list.R' [1s]
  Running 'normalizeQuantileRank.matrix.R' [1s]
  Running 'normalizeQuantileSpline.matrix.R' [2s]
  Running 'normalizeTumorBoost,flavors.R' [2s]
  Running 'normalizeTumorBoost.R' [1s]
  Running 'robustSmoothSpline.R' [1s]
  Running 'sampleCorrelations.matrix.R' [2s]
  Running 'sampleTuples.R' [0s]
  Running 'wpca.matrix.R' [1s]
  Running 'wpca2.matrix.R' [1s]
 [40s] OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'E:/biocbld/bbs-3.1-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_2.4.0.zip
* DONE (aroma.light)

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

nameusersystemelapsed
backtransformAffine0.020.000.02
backtransformPrincipalCurve0.450.000.45
calibrateMultiscan000
callNaiveGenotypes0.540.000.54
distanceBetweenLines0.020.000.02
findPeaksAndValleys0.090.000.09
fitPrincipalCurve0.330.030.36
fitXYCurve0.060.020.08
iwpca0.020.000.01
likelihood.smooth.spline0.110.010.13
medianPolish0.010.000.02
normalizeAffine14.88 0.0214.89
normalizeCurveFit15.46 0.0315.49
normalizeDifferencesToAverage0.360.000.36
normalizeFragmentLength0.980.021.00
normalizeQuantileRank0.250.000.25
normalizeQuantileRank.matrix0.070.000.06
normalizeQuantileSpline0.870.000.88
normalizeTumorBoost0.220.000.36
robustSmoothSpline0.050.010.06
sampleCorrelations0.470.000.47
sampleTuples000
wpca0.080.020.11

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

nameusersystemelapsed
backtransformAffine000
backtransformPrincipalCurve0.450.000.45
calibrateMultiscan000
callNaiveGenotypes0.500.000.49
distanceBetweenLines0.010.000.02
findPeaksAndValleys0.050.000.04
fitPrincipalCurve0.340.000.35
fitXYCurve0.060.000.06
iwpca0.020.000.02
likelihood.smooth.spline0.110.010.12
medianPolish000
normalizeAffine14.53 0.0014.54
normalizeCurveFit14.57 0.0514.63
normalizeDifferencesToAverage0.220.010.24
normalizeFragmentLength0.880.000.89
normalizeQuantileRank0.210.000.20
normalizeQuantileRank.matrix0.080.000.08
normalizeQuantileSpline0.980.001.84
normalizeTumorBoost0.230.000.23
robustSmoothSpline0.060.000.06
sampleCorrelations0.530.000.53
sampleTuples000
wpca0.090.000.11