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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:divergence.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings divergence_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/divergence.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘divergence/DESCRIPTION’ ... OK
* this is package ‘divergence’ version ‘1.22.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 code 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 ... NOTE
checkRd: (-1) computeMultivariateDigitization.Rd:26: Lost braces; missing escapes or markup?
    26 | By default gamma = {0.01, 0.02, ... 0.09, 0.1, 0.2, ..., 0.9}.}
       |                    ^
checkRd: (-1) computeUnivariateDigitization.Rd:22: Lost braces; missing escapes or markup?
    22 | By default gamma = {0.01, 0.02, ... 0.09, 0.1, 0.2, ..., 0.9}.}
       |                    ^
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
computeUnivariateDigitization  25.058 96.297   6.010
computeChiSquaredTest          26.494 91.713   6.586
findUnivariateGammaWithSupport 22.440 55.418   4.671
computeUnivariateSupport        2.274  7.045   0.482
computeUnivariateTernaryMatrix  2.554  3.401   1.168
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... NOTE
Package vignette with \VignetteEngine{} not specifying an engine package:
  ‘divergence.Rmd’
Engines should be specified as \VignetteEngine{PKG::ENG}.
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/divergence.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL divergence
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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)