BioC 3.4: CHECK report for spkTools on morelia

Package: spkTools

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings spkTools_1.30.0.tar.gz

StartedAt: 2017-04-15 08:25:40 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 08:27:01 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 81.0 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 --no-vignettes --timings spkTools_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/spkTools.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spkTools/DESCRIPTION’ ... OK
* this is package ‘spkTools’ version ‘1.30.0’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
spkTools 13.543  1.273  14.829
spkAll   12.441  0.725  13.202
* 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-3.4-bioc/meat/spkTools.Rcheck/00check.log’
for details.

* installing *source* package ‘spkTools’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (spkTools)

name	user	system	elapsed
SpikeInExpressSet-class	0.233	0.004	0.237
plotSpkBox	0.818	0.029	0.848
spkAccSD	0.300	0.013	0.315
spkAll	12.441	0.725	13.202
spkAnova	0.150	0.004	0.154
spkBal	0.096	0.002	0.097
spkBox	0.730	0.123	0.853
spkDensity	0.139	0.003	0.143
spkGNN	3.718	0.466	4.184
spkMA	1.330	0.021	1.356
spkPair	0.145	0.006	0.151
spkPairNS	0.125	0.004	0.130
spkPot	0.870	0.021	0.895
spkQuantile	0.103	0.002	0.106
spkSlope	0.097	0.003	0.099
spkTools	13.543	1.273	14.829
spkVar	0.053	0.001	0.055
summarySpkBox	0.724	0.017	0.745