Package: ARRmNormalization

Version: 1.24.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ARRmNormalization.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ARRmNormalization_1.24.0.tar.gz

StartedAt: 2019-10-16 01:58:34 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:02:18 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 224.1 seconds

RetCode: 0

Status:  OK

CheckDir: ARRmNormalization.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ARRmNormalization.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ARRmNormalization_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ARRmNormalization.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ARRmNormalization/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ARRmNormalization' version '1.24.0'
* 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 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
* 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 ... 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 : : no visible global function definition for
  'median'
getQuantiles: no visible global function definition for 'data'
getQuantiles: no visible binding for global variable 'ProbesType'
getQuantiles : : 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 : : 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 : : 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
normalizeARRm   33.39   3.54   36.93
getCoefficients 15.30   1.33   16.74
positionPlots   14.11   0.76   14.89
quantilePlots   13.47   1.13   14.59
getQuantiles    12.22   0.93   13.15
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
normalizeARRm   27.20   3.49   30.69
getCoefficients 13.19   1.27   14.45
quantilePlots   12.41   1.45   13.86
positionPlots   12.59   0.78   13.40
getQuantiles    12.22   1.07   13.32
* 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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/ARRmNormalization.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ARRmNormalization_1.24.0.tar.gz && rm -rf ARRmNormalization.buildbin-libdir && mkdir ARRmNormalization.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ARRmNormalization.buildbin-libdir ARRmNormalization_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ARRmNormalization_1.24.0.zip && rm ARRmNormalization_1.24.0.tar.gz ARRmNormalization_1.24.0.zip
###
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install for i386

* installing *source* package 'ARRmNormalization' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ARRmNormalization'
    finding HTML links ... done
    ARRmNormalization-internal              html  
    ARRmNormalization-package               html  
    ProbesType                              html  
    getBackground                           html  
    getCoefficients                         html  
    getDesignInfo                           html  
    getQuantiles                            html  
    normalizeARRm                           html  
    positionPlots                           html  
    quantilePlots                           html  
** 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

install for x64

* installing *source* package 'ARRmNormalization' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ARRmNormalization' as ARRmNormalization_1.24.0.zip
* DONE (ARRmNormalization)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ARRmNormalization' successfully unpacked and MD5 sums checked