Package: divergence

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:divergence.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings divergence_1.2.0.tar.gz

StartedAt: 2020-04-15 01:53:24 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 01:56:34 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 189.7 seconds

RetCode: 0

Status:  OK

CheckDir: divergence.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:divergence.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings divergence_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/divergence.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘divergence/DESCRIPTION’ ... OK
* this is package ‘divergence’ version ‘1.2.0’
* package encoding: UTF-8
* 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 ‘divergence’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
check_SE: no visible binding for global variable ‘data’
computeSingleFeaturesetBinaryVector: no visible global function
  definition for ‘dist’
computeSingleFeaturesetSupport: no visible global function definition
  for ‘dist’
computeSingleFeaturesetSupport: no visible global function definition
  for ‘quantile’
computeSingleRange: no visible global function definition for
  ‘quantile’
getRangesBySections: no visible global function definition for
  ‘detectCores’
rowChiSq: no visible global function definition for ‘chisq.test’
rowChiSq: no visible global function definition for ‘xtabs’
Undefined global functions or variables:
  chisq.test data detectCores dist quantile xtabs
Consider adding
  importFrom("stats", "chisq.test", "dist", "quantile", "xtabs")
  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 ... OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
computeChiSquaredTest           44.421 30.607   8.193
findUnivariateGammaWithSupport  40.243 26.954   5.667
computeUnivariateDigitization   39.719 25.020   6.025
computeUnivariateSupport         4.152  3.182   0.725
computeMultivariateDigitization  6.834  0.339   7.305
computeUnivariateTernaryMatrix   4.179  1.884   1.473
* 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-3.10-bioc/meat/divergence.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 divergence
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘divergence’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (divergence)

name	user	system	elapsed
computeChiSquaredTest	44.421	30.607	8.193
computeMultivariateBinaryMatrix	2.061	0.133	2.210
computeMultivariateDigitization	6.834	0.339	7.305
computeMultivariateSupport	0.482	0.030	0.521
computeQuantileMatrix	0.068	0.001	0.070
computeUnivariateDigitization	39.719	25.020	6.025
computeUnivariateSupport	4.152	3.182	0.725
computeUnivariateTernaryMatrix	4.179	1.884	1.473
findMultivariateGammaWithSupport	0.919	0.079	1.013
findUnivariateGammaWithSupport	40.243	26.954	5.667