Package: derfinderPlot

Version: 1.18.1

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:derfinderPlot.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings derfinderPlot_1.18.1.tar.gz

StartedAt: 2019-10-16 01:06:22 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 01:14:39 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 497.1 seconds

RetCode: 0

Status:  OK

CheckDir: derfinderPlot.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:derfinderPlot.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings derfinderPlot_1.18.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/derfinderPlot.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘derfinderPlot/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘derfinderPlot’ version ‘1.18.1’
* 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 ‘derfinderPlot’ 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 ... NOTE
Namespace in Imports field not imported from: 'RefManageR'
  All declared Imports should be used.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
plotCluster        51.254  0.447  51.729
plotRegionCoverage 40.253  0.044  40.345
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.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-3.9-bioc/meat/derfinderPlot.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL derfinderPlot
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘derfinderPlot’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (derfinderPlot)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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.

> ## Disable the tests if the system variable 'R_DISABLE_TESTS' is set to TRUE
> 
> flag <- as.logical(Sys.getenv('R_DISABLE_TESTS'))
> if(is.na(flag) | flag == FALSE) {
+     library('testthat')
+     test_check('derfinderPlot')
+ }
Loading required package: derfinderPlot
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 15 | SKIPPED: 0 | WARNINGS: 7 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
105.941   1.157 107.448 

name	user	system	elapsed
plotCluster	51.254	0.447	51.729
plotOverview	1.865	0.000	1.866
plotRegionCoverage	40.253	0.044	40.345
vennRegions	0.211	0.000	0.211