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CHECK report for ARRmNormalization on tokay1

This page was generated on 2020-08-09 12:02:02 -0400 (Sun, 09 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ARRmNormalization PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 82/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ARRmNormalization 1.29.0
Jean-Philippe Fortin
Snapshot Date: 2020-08-08 14:51:01 -0400 (Sat, 08 Aug 2020)
URL: https://git.bioconductor.org/packages/ARRmNormalization
Branch: master
Last Commit: 6e747ff
Last Changed Date: 2020-04-27 14:33:29 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ARRmNormalization
Version: 1.29.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ARRmNormalization.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ARRmNormalization_1.29.0.tar.gz
StartedAt: 2020-08-09 00:46:51 -0400 (Sun, 09 Aug 2020)
EndedAt: 2020-08-09 00:50:43 -0400 (Sun, 09 Aug 2020)
EllapsedTime: 232.0 seconds
RetCode: 0
Status:  OK  
CheckDir: ARRmNormalization.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ARRmNormalization.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ARRmNormalization_1.29.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ARRmNormalization.Rcheck'
* using R version 4.0.2 (2020-06-22)
* 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 '1.29.0'
* 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 : <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 '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 '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 points predict
  quantile smooth.spline
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "axis", "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 (user + system) or elapsed time > 5s
                 user system elapsed
normalizeARRm   33.08   5.03   38.12
getCoefficients 18.47   1.51   21.68
getQuantiles    16.22   1.53   17.89
quantilePlots   14.00   1.48   15.48
positionPlots   13.32   0.83   14.16
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
normalizeARRm   31.06   5.10   36.22
getCoefficients 16.22   1.66   17.88
getQuantiles    11.92   1.20   13.13
quantilePlots   11.47   1.10   12.58
positionPlots   11.66   0.68   12.39
* 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-3.12-bioc/meat/ARRmNormalization.Rcheck/00check.log'
for details.



Installation output

ARRmNormalization.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/ARRmNormalization_1.29.0.tar.gz && rm -rf ARRmNormalization.buildbin-libdir && mkdir ARRmNormalization.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ARRmNormalization.buildbin-libdir ARRmNormalization_1.29.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ARRmNormalization_1.29.0.zip && rm ARRmNormalization_1.29.0.tar.gz ARRmNormalization_1.29.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  824k  100  824k    0     0  26.9M      0 --:--:-- --:--:-- --:--:-- 30.9M

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_1.29.0.zip
* DONE (ARRmNormalization)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'ARRmNormalization' successfully unpacked and MD5 sums checked

Tests output


Example timings

ARRmNormalization.Rcheck/examples_i386/ARRmNormalization-Ex.timings

nameusersystemelapsed
ProbesType1.470.051.52
getBackground0.030.000.37
getCoefficients18.47 1.5121.68
getDesignInfo0.050.020.06
getQuantiles16.22 1.5317.89
normalizeARRm33.08 5.0338.12
positionPlots13.32 0.8314.16
quantilePlots14.00 1.4815.48

ARRmNormalization.Rcheck/examples_x64/ARRmNormalization-Ex.timings

nameusersystemelapsed
ProbesType1.010.031.04
getBackground0.050.010.07
getCoefficients16.22 1.6617.88
getDesignInfo0.020.000.01
getQuantiles11.92 1.2013.13
normalizeARRm31.06 5.1036.22
positionPlots11.66 0.6812.39
quantilePlots11.47 1.1012.58