Package: esetVis

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:esetVis.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings esetVis_1.8.0.tar.gz

StartedAt: 2019-04-15 23:49:33 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:52:40 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 186.4 seconds

RetCode: 0

Status:  OK

CheckDir: esetVis.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:esetVis.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings esetVis_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/esetVis.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 ‘esetVis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘esetVis’ version ‘1.8.0’
* 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 ‘esetVis’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getMethodsInputObjectEsetVis: no visible binding for global variable
  ‘rowData’
getMethodsInputObjectEsetVis: no visible binding for global variable
  ‘colData’
getMethodsInputObjectEsetVis: no visible binding for global variable
  ‘assay’
getMethodsInputObjectEsetVis : <anonymous>: no visible global function
  definition for ‘colData’
getMethodsInputObjectEsetVis : <anonymous>: no visible global function
  definition for ‘rowData’
ggvisPlotEset: no visible global function definition for ‘:=’
ggvisPlotEset: no visible binding for global variable ‘fill’
ggvisPlotEset: no visible binding for global variable ‘shape’
ggvisPlotEset: no visible binding for global variable ‘size’
ggvisPlotEset: no visible binding for global variable ‘opacity’
ggvisPlotEset: no visible global function definition for ‘%>%’
ggvisPlotEset: no visible global function definition for
  ‘scale_ordinal’
ggvisPlotEset: no visible global function definition for ‘set_options’
Undefined global functions or variables:
  %>% := assay colData fill opacity rowData scale_ordinal set_options
  shape size
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
getGeneSetsForPlot 72.006  7.594  80.240
esetLda             6.195  0.260   6.500
esetPlotWrapper     5.908  0.311   6.282
esetSpectralMap     4.970  0.286   5.301
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/esetVis.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 esetVis
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘esetVis’ ...
** R
** 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 (esetVis)

name	user	system	elapsed
esetLda	6.195	0.260	6.500
esetPlotWrapper	5.908	0.311	6.282
esetSpectralMap	4.970	0.286	5.301
esetTsne	4.617	0.137	4.797
getGeneSetsForPlot	72.006	7.594	80.240