Package: divergence

Version: 0.99.07

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:divergence.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings divergence_0.99.07.tar.gz

StartedAt: 2019-04-09 00:07:40 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:10:35 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 174.6 seconds

RetCode: 0

Status:  OK

CheckDir: divergence.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:divergence.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings divergence_0.99.07.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/divergence.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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
computeUnivariateDigitization   23.777 20.197   8.520
findUnivariateGammaWithSupport  22.447 18.129   7.611
computeChiSquaredTest           24.549 14.545   8.223
computeMultivariateDigitization  5.731  0.123   5.853
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/divergence.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL divergence
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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	24.549	14.545	8.223
computeMultivariateBinaryMatrix	1.581	0.066	1.654
computeMultivariateDigitization	5.731	0.123	5.853
computeMultivariateSupport	0.285	0.000	0.286
computeQuantileMatrix	0.050	0.000	0.055
computeUnivariateDigitization	23.777	20.197	8.520
computeUnivariateSupport	1.795	1.198	0.671
computeUnivariateTernaryMatrix	2.279	1.653	0.993
findMultivariateGammaWithSupport	0.530	0.015	0.546
findUnivariateGammaWithSupport	22.447	18.129	7.611