Package: spkTools

Version: 1.40.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:spkTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings spkTools_1.40.0.tar.gz

StartedAt: 2019-10-16 07:05:38 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 07:07:51 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 133.3 seconds

RetCode: 0

Status:  OK

CheckDir: spkTools.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:spkTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings spkTools_1.40.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/spkTools.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 ‘spkTools/DESCRIPTION’ ... OK
* this is package ‘spkTools’ version ‘1.40.0’
* 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 ‘spkTools’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* 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 ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
spkTools 28.789  2.920  31.711
spkAll   27.314  2.575  29.893
spkGNN    8.380  0.774   9.155
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/spkTools.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL spkTools
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘spkTools’ ...
** using staged installation
** R
** data
** 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 (spkTools)

name	user	system	elapsed
SpikeInExpressSet-class	0.369	0.060	0.429
plotSpkBox	0.959	0.099	1.059
spkAccSD	0.197	0.022	0.219
spkAll	27.314	2.575	29.893
spkAnova	0.135	0.008	0.142
spkBal	0.091	0.003	0.094
spkBox	1.181	0.386	1.568
spkDensity	0.199	0.023	0.223
spkGNN	8.380	0.774	9.155
spkMA	1.655	0.100	1.757
spkPair	0.079	0.005	0.084
spkPairNS	0.071	0.010	0.081
spkPot	0.995	0.084	1.081
spkQuantile	0.079	0.003	0.083
spkSlope	0.121	0.012	0.134
spkTools	28.789	2.920	31.711
spkVar	0.108	0.008	0.115
summarySpkBox	0.863	0.048	0.911