Package: RUVnormalize

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RUVnormalize.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RUVnormalize_1.16.0.tar.gz

StartedAt: 2019-04-16 02:34:32 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:35:22 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 49.2 seconds

RetCode: 0

Status:  OK

CheckDir: RUVnormalize.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RUVnormalize.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RUVnormalize_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/RUVnormalize.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RUVnormalize/DESCRIPTION’ ... OK
* this is package ‘RUVnormalize’ version ‘1.16.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘spams’
* 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 ‘RUVnormalize’ 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
'library' or 'require' call to ‘spams’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
iterativeRUV: no visible global function definition for ‘kmeans’
myPalette: no visible global function definition for ‘col2rgb’
myPalette: no visible global function definition for ‘rgb’
svdPlot: no visible global function definition for ‘pdf’
svdPlot: no visible global function definition for ‘par’
svdPlot: no visible global function definition for ‘plot’
svdPlot: no visible global function definition for ‘points’
svdPlot: no visible global function definition for ‘text’
svdPlot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  col2rgb dev.off kmeans par pdf plot points rgb text
Consider adding
  importFrom("grDevices", "col2rgb", "dev.off", "pdf", "rgb")
  importFrom("graphics", "par", "plot", "points", "text")
  importFrom("stats", "kmeans")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
clScore      4.995  0.229   5.249
naiveRandRUV 4.961  0.257   5.251
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/RUVnormalize.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RUVnormalize
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘RUVnormalize’ ...
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RUVnormalize)

name	user	system	elapsed
clScore	4.995	0.229	5.249
iterativeRUV	0.139	0.004	0.145
naiveRandRUV	4.961	0.257	5.251
naiveReplicateRUV	3.740	0.242	4.001
svdPlot	4.589	0.289	4.899