BioC 3.5: CHECK report for geneClassifiers on toluca2

Package: geneClassifiers

Version: 0.99.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings geneClassifiers_0.99.9.tar.gz

StartedAt: 2017-04-23 04:13:56 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 04:14:39 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 43.1 seconds

RetCode: 0

Status:  OK

CheckDir: geneClassifiers.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 geneClassifiers_0.99.9.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/geneClassifiers.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘geneClassifiers/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geneClassifiers’ version ‘0.99.9’
* 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 ‘geneClassifiers’ 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 ... 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 R/sysdata.rda ... 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: OK

* installing *source* package ‘geneClassifiers’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (geneClassifiers)

name	user	system	elapsed
bracket-methods	0.165	0.009	0.175
dim-methods	0.081	0.002	0.082
getBatchCorrection-methods	0.493	0.010	0.508
getCitations-methods	0.003	0.000	0.003
getClassifications-methods	0.151	0.004	0.156
getClassifier-methods	0.003	0.000	0.003
getDecisionBoundaries-methods	0.002	0.000	0.002
getDescription-methods	0.003	0.000	0.002
getEventChain-methods	0.003	0.001	0.002
getIntercept-methods	0.002	0.000	0.002
getMeans-methods	0.004	0.001	0.005
getName-methods	0.003	0.000	0.003
getNormalizationMethod-methods	0.115	0.002	0.117
getProbeNames-methods	0.004	0.001	0.004
getScores-methods	0.047	0.001	0.048
getSds-methods	0.004	0.001	0.005
getTargetValue-methods	0.018	0.000	0.018
getTrainingData-methods	0.084	0.000	0.084
getWeightingType-methods	0.049	0.001	0.050
getWeights-methods	0.003	0.001	0.005
runClassifier-methods	0.049	0.001	0.051
setNormalizationMethod-methods	0.100	0.001	0.103
showClassifierList-methods	0.041	0.002	0.043