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CHECK report for divergence on merida2

This page was generated on 2019-04-09 13:39:10 -0400 (Tue, 09 Apr 2019).

Package 436/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
divergence 0.99.07
Wikum Dinalankara , Luigi Marchionni
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/divergence
Branch: master
Last Commit: e7c789c
Last Changed Date: 2019-02-15 13:13:00 -0400 (Fri, 15 Feb 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: divergence
Version: 0.99.07
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_0.99.07.tar.gz
StartedAt: 2019-04-09 00:31:01 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 00:33:56 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 174.9 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_0.99.07.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/divergence.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘0.99.07’
* 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           41.374 25.770   7.935
findUnivariateGammaWithSupport  38.232 24.704   5.434
computeUnivariateDigitization   36.847 19.608   5.417
computeMultivariateDigitization  6.262  0.410   6.734
computeUnivariateTernaryMatrix   3.483  1.818   0.738
computeUnivariateSupport         3.371  1.781   0.624
* 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:
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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’ ...
** 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
* DONE (divergence)

Tests output


Example timings

divergence.Rcheck/divergence-Ex.timings

nameusersystemelapsed
computeChiSquaredTest41.37425.770 7.935
computeMultivariateBinaryMatrix2.1250.2402.391
computeMultivariateDigitization6.2620.4106.734
computeMultivariateSupport0.4830.0230.513
computeQuantileMatrix0.0600.0020.062
computeUnivariateDigitization36.84719.608 5.417
computeUnivariateSupport3.3711.7810.624
computeUnivariateTernaryMatrix3.4831.8180.738
findMultivariateGammaWithSupport0.8590.1150.987
findUnivariateGammaWithSupport38.23224.704 5.434