BioC 3.5: CHECK report for genotypeeval on toluca2

Package: genotypeeval

Version: 1.6.7

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genotypeeval_1.6.7.tar.gz

StartedAt: 2017-04-23 04:33:01 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 04:38:56 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 354.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: genotypeeval.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genotypeeval_1.6.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/genotypeeval.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 ‘genotypeeval/DESCRIPTION’ ... OK
* this is package ‘genotypeeval’ version ‘1.6.7’
* 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 ‘genotypeeval’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 ... WARNING
Undocumented code objects:
  ‘makeHistogram’ ‘tsnePlot’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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
getPlots 6.34  0.153   6.536
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/genotypeeval.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
GoldDataFromGRanges	0.174	0.015	0.189
GoldDataParam	0.001	0.000	0.001
ReadGoldData	1.344	0.009	1.353
ReadVCFData	3.318	0.184	3.506
ReadVCFDataChunk	4.120	0.292	4.416
VCFEvaluate	3.657	0.168	3.831
VCFQAParam	0.002	0.000	0.001
didSamplePass	3.015	0.131	3.147
didSamplePassOverall	3.407	0.160	3.573
getName	3.713	0.157	3.873
getPlots	6.340	0.153	6.536
getResults	3.617	0.163	3.789
getVR	1.508	0.150	1.660