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

##############################################################################
##############################################################################
###
### Running 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
###
##############################################################################
##############################################################################


* 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.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ARRmNormalization
###
##############################################################################
##############################################################################


* 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)

name	user	system	elapsed
ProbesType	1.366	0.093	1.459
getBackground	0.043	0.011	0.055
getCoefficients	18.359	3.354	21.717
getDesignInfo	0.008	0.004	0.012
getQuantiles	14.401	3.348	17.765
normalizeARRm	36.406	14.349	50.756
positionPlots	14.449	3.608	18.060
quantilePlots	13.972	3.428	17.401