Package: savR

Version: 1.21.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:savR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings savR_1.21.0.tar.gz

StartedAt: 2019-04-09 03:34:26 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:35:50 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 84.4 seconds

RetCode: 0

Status:  OK

CheckDir: savR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:savR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings savR_1.21.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/savR.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘savR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘savR’ version ‘1.21.0’
* 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 ‘savR’ 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 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 ... NOTE
buildReports,savProject-character: no visible global function
  definition for ‘dev.off’
qualityHeatmap,savProject-integer-integer-logical: no visible global
  function definition for ‘quantile’
Undefined global functions or variables:
  dev.off quantile
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("stats", "quantile")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/savR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL savR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘savR’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (savR)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(savR)
Loading required package: ggplot2
> 
> test_check("savR")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 8 SKIPPED: 7 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  7.553   0.185   7.753 

name	user	system	elapsed
buildReports	0	0	0
clusterQualityGtN	0.000	0.001	0.001
clusters	0	0	0
correctedIntensities	2.897	0.032	2.948
cycles	2.892	0.029	2.939
directions	3.467	0.036	3.565
errorMetrics	3.174	0.022	3.207
extractionMetrics	2.944	0.025	2.985
flowcellLayout	3.214	0.012	3.250
location	2.938	0.024	2.980
pfClusters	0	0	0
qualityMetrics	3.310	0.018	3.356
reads	3.496	0.020	3.564
run	3.321	0.015	3.375
savR	3.367	0.016	3.405
tileMetrics	3.183	0.013	3.211