BioC 3.5: CHECK report for esetVis on veracruz2

Package: esetVis

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings esetVis_1.2.0.tar.gz

StartedAt: 2017-10-18 03:20:05 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 03:22:39 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 153.6 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 --no-vignettes --timings esetVis_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/esetVis.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.2.0’
* 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 ... NOTE
  installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
* 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 loading without being on the library search path ... 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
esetPlotWrapper: no visible global function definition for ‘:=’
esetPlotWrapper: no visible binding for global variable ‘fill’
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’
Undefined global functions or variables:
  := assay colData fill rowData
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
getGeneSetsForPlot 49.661  4.662  56.161
esetLda             6.993  0.181   7.367
esetPlotWrapper     5.792  0.281   6.247
* 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-3.5-bioc/meat/esetVis.Rcheck/00check.log’
for details.

* installing *source* package ‘esetVis’ ...
** R
** inst
** preparing 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	6.993	0.181	7.367
esetPlotWrapper	5.792	0.281	6.247
esetSpectralMap	4.219	0.255	4.619
esetTsne	4.149	0.119	4.384
getGeneSetsForPlot	49.661	4.662	56.161