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CHECK report for divergence on celaya2

This page was generated on 2019-10-16 13:04:14 -0400 (Wed, 16 Oct 2019).

Package 444/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
divergence 1.0.0
Wikum Dinalankara , Luigi Marchionni
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/divergence
Branch: RELEASE_3_9
Last Commit: 79e5724
Last Changed Date: 2019-05-02 11:54:14 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: divergence
Version: 1.0.0
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_1.0.0.tar.gz
StartedAt: 2019-10-16 02:16:39 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:20:56 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 256.4 seconds
RetCode: 0
Status:  OK 
CheckDir: divergence.Rcheck
Warnings: 0

Command output

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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_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/divergence.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.0.0’
* 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           71.315 64.115  15.339
findUnivariateGammaWithSupport  63.061 56.043  11.596
computeUnivariateDigitization   62.339 49.211  11.107
computeUnivariateSupport         6.968  7.304   1.446
computeMultivariateDigitization  8.252  0.999   9.275
computeUnivariateTernaryMatrix   5.507  3.510   1.445
* 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-3.9-bioc/meat/divergence.Rcheck/00check.log’
for details.



Installation output

divergence.Rcheck/00install.out

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### Running command:
###
###   /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)

Tests output


Example timings

divergence.Rcheck/divergence-Ex.timings

nameusersystemelapsed
computeChiSquaredTest71.31564.11515.339
computeMultivariateBinaryMatrix2.9540.3473.301
computeMultivariateDigitization8.2520.9999.275
computeMultivariateSupport0.5870.0610.649
computeQuantileMatrix0.1060.0190.125
computeUnivariateDigitization62.33949.21111.107
computeUnivariateSupport6.9687.3041.446
computeUnivariateTernaryMatrix5.5073.5101.445
findMultivariateGammaWithSupport1.0310.1711.202
findUnivariateGammaWithSupport63.06156.04311.596