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This page was generated on 2021-10-15 15:06:34 -0400 (Fri, 15 Oct 2021).

CHECK results for divergence on machv2

To the developers/maintainers of the divergence package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/divergence.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 512/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
divergence 1.8.0  (landing page)
Wikum Dinalankara , Luigi Marchionni
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/divergence
git_branch: RELEASE_3_13
git_last_commit: e13dfb8
git_last_commit_date: 2021-05-19 12:40:49 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: divergence
Version: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2021-10-14 18:28:04 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 18:31:21 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 196.3 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_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/divergence.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘divergence/DESCRIPTION’ ... OK
* this is package ‘divergence’ version ‘1.8.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 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
computeChiSquaredTest           77.574 67.553  13.192
computeUnivariateDigitization   40.155 22.923   5.695
findUnivariateGammaWithSupport  38.382 19.910   5.000
computeMultivariateDigitization  6.525  0.377   6.906
computeUnivariateSupport         3.642  1.948   0.545
computeUnivariateTernaryMatrix   3.775  1.609   0.787
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-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/4.1/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
computeChiSquaredTest77.57467.55313.192
computeMultivariateBinaryMatrix2.0420.2482.291
computeMultivariateDigitization6.5250.3776.906
computeMultivariateSupport0.5790.0300.613
computeQuantileMatrix0.1130.0030.116
computeUnivariateDigitization40.15522.923 5.695
computeUnivariateSupport3.6421.9480.545
computeUnivariateTernaryMatrix3.7751.6090.787
findMultivariateGammaWithSupport0.8740.0760.950
findUnivariateGammaWithSupport38.38219.910 5.000