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CHECK report for ARRmNormalization on celaya2

This page was generated on 2020-01-16 13:36:37 -0500 (Thu, 16 Jan 2020).

Package 84/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ARRmNormalization 1.27.0
Jean-Philippe Fortin
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/ARRmNormalization
Branch: master
Last Commit: 615bd8d
Last Changed Date: 2019-10-29 13:36:40 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ARRmNormalization
Version: 1.27.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ARRmNormalization.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ARRmNormalization_1.27.0.tar.gz
StartedAt: 2020-01-16 01:48:27 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 01:51:14 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 167.1 seconds
RetCode: 0
Status:  OK 
CheckDir: ARRmNormalization.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ARRmNormalization.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ARRmNormalization_1.27.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ARRmNormalization.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ARRmNormalization/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ARRmNormalization’ version ‘1.27.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ARRmNormalization’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 ... NOTE
Package in Depends field not imported from: ‘ARRmData’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ARRm.regression: no visible global function definition for ‘C’
ARRm.regression: no visible global function definition for ‘lm’
getBackground : <anonymous>: no visible global function definition for
  ‘median’
getQuantiles: no visible global function definition for ‘data’
getQuantiles: no visible binding for global variable ‘ProbesType’
getQuantiles : <anonymous>: no visible global function definition for
  ‘quantile’
normalizeARRm: no visible global function definition for ‘data’
normalizeARRm: no visible binding for global variable ‘ProbesType’
normalizeI: no visible global function definition for ‘C’
normalizeI: no visible global function definition for ‘median’
normalizeI : <anonymous>: no visible global function definition for
  ‘quantile’
normalizeI: no visible global function definition for ‘smooth.spline’
normalizeI: no visible global function definition for ‘predict’
normalizeII: no visible global function definition for ‘C’
normalizeII: no visible global function definition for ‘median’
normalizeII : <anonymous>: no visible global function definition for
  ‘quantile’
normalizeII: no visible global function definition for ‘smooth.spline’
normalizeII: no visible global function definition for ‘predict’
positionPlots: no visible global function definition for ‘pdf’
positionPlots: no visible global function definition for ‘plot’
positionPlots: no visible global function definition for ‘axis’
positionPlots: no visible global function definition for ‘abline’
positionPlots: no visible global function definition for ‘dev.off’
quantilePlots: no visible global function definition for ‘pdf’
quantilePlots: no visible global function definition for ‘plot’
quantilePlots: no visible global function definition for ‘points’
quantilePlots: no visible global function definition for ‘abline’
quantilePlots: no visible global function definition for ‘lm’
quantilePlots: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  C ProbesType abline axis data dev.off lm median pdf plot points
  predict quantile smooth.spline
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "axis", "plot", "points")
  importFrom("stats", "C", "lm", "median", "predict", "quantile",
             "smooth.spline")
  importFrom("utils", "data")
to your NAMESPACE file.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
normalizeARRm   36.406 14.349  50.756
getCoefficients 18.359  3.354  21.717
positionPlots   14.449  3.608  18.060
getQuantiles    14.401  3.348  17.765
quantilePlots   13.972  3.428  17.401
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/ARRmNormalization.Rcheck/00check.log’
for details.



Installation output

ARRmNormalization.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ARRmNormalization
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘ARRmNormalization’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ARRmNormalization)

Tests output


Example timings

ARRmNormalization.Rcheck/ARRmNormalization-Ex.timings

nameusersystemelapsed
ProbesType1.3660.0931.459
getBackground0.0430.0110.055
getCoefficients18.359 3.35421.717
getDesignInfo0.0080.0040.012
getQuantiles14.401 3.34817.765
normalizeARRm36.40614.34950.756
positionPlots14.449 3.60818.060
quantilePlots13.972 3.42817.401