BioC 3.5: CHECK report for genotypeeval on veracruz2

Package: genotypeeval

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genotypeeval_1.8.0.tar.gz

StartedAt: 2017-10-18 04:11:40 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 04:16:17 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 276.5 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_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/genotypeeval.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genotypeeval/DESCRIPTION’ ... OK
* this is package ‘genotypeeval’ version ‘1.8.0’
* 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 ‘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’ ‘pcaPlot’ ‘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 5.416  0.133   5.689
* 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	0.115	0.002	0.123
GoldDataParam	0	0	0
ReadGoldData	1.142	0.029	1.198
ReadVCFData	2.999	0.182	3.238
ReadVCFDataChunk	2.685	0.215	2.956
VCFEvaluate	3.442	0.156	3.719
VCFQAParam	0.001	0.000	0.001
didSamplePass	2.858	0.147	3.055
didSamplePassOverall	2.382	0.138	2.552
getName	2.681	0.146	2.883
getPlots	5.416	0.133	5.689
getResults	2.408	0.114	2.565
getVR	1.368	0.126	1.547