BioC 2.14: CHECK report for spkTools on morelia

Package: spkTools

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch spkTools_1.20.0.tar.gz

StartedAt: 2014-10-08 01:43:34 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 01:45:00 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 86.6 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 --no-multiarch spkTools_1.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/spkTools.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spkTools/DESCRIPTION’ ... OK
* this is package ‘spkTools’ version ‘1.20.0’
* 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 ... [3s/3s] 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 ... [45s/45s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
spkTools 15.124  1.009  16.156
spkAll   14.846  0.178  15.079
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-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	0.312	0.003	0.314
plotSpkBox	1.065	0.039	1.119
spkAccSD	0.414	0.011	0.426
spkAll	14.846	0.178	15.079
spkAnova	0.146	0.003	0.149
spkBal	0.147	0.001	0.149
spkBox	1.059	0.141	1.202
spkDensity	0.233	0.003	0.237
spkGNN	4.638	0.255	4.896
spkMA	1.675	0.026	1.705
spkPair	0.217	0.005	0.224
spkPairNS	0.147	0.005	0.153
spkPot	0.960	0.019	0.983
spkQuantile	0.109	0.001	0.111
spkSlope	0.114	0.002	0.117
spkTools	15.124	1.009	16.156
spkVar	0.128	0.002	0.130
summarySpkBox	1.015	0.027	1.049