Package: savR

Version: 1.16.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings savR_1.16.0.tar.gz

StartedAt: 2018-04-12 02:44:23 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:45:31 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 68.0 seconds

RetCode: 0

Status:  OK

CheckDir: savR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings savR_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/savR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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 ‘1.16.0’
* 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 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 ... 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 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/savR.Rcheck/00check.log’
for details.

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

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  5.116   0.036   5.147 

name	user	system	elapsed
buildReports	0	0	0
clusterQualityGtN	0.000	0.000	0.002
clusters	0	0	0
correctedIntensities	3.148	0.028	3.202
cycles	2.868	0.000	2.887
directions	2.756	0.004	2.784
errorMetrics	2.936	0.000	2.969
extractionMetrics	1.764	0.004	1.772
flowcellLayout	1.736	0.000	1.737
location	1.744	0.008	1.753
pfClusters	0	0	0
qualityMetrics	1.980	0.008	1.994
reads	1.592	0.000	1.595
run	1.904	0.004	1.911
savR	2.444	0.000	2.449
tileMetrics	1.580	0.000	1.579