Package: graphite

Version: 1.29.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:graphite.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings graphite_1.29.2.tar.gz

StartedAt: 2019-04-09 01:22:04 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:35:44 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 819.8 seconds

RetCode: 0

Status:  OK

CheckDir: graphite.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:graphite.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings graphite_1.29.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/graphite.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 ‘graphite/DESCRIPTION’ ... OK
* this is package ‘graphite’ version ‘1.29.2’
* 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 ‘graphite’ 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
runClipper          48.615  0.767  49.844
runSPIA             44.528  1.411  46.428
pathways            41.106  1.033  50.878
as.list.PathwayList 40.612  1.211  42.245
pathwayGraph        37.241  0.517  39.687
convertIdentifiers  36.185  0.688  37.188
runTopologyGSA      36.133  0.222  36.661
* 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: OK

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL graphite
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘graphite’ ...
** 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 (graphite)

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(graphite)
> 
> test_check("graphite")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 95 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
397.381  10.287 422.365 

name	user	system	elapsed
as.list.PathwayList	40.612	1.211	42.245
buildPathway	0.016	0.000	0.017
convertIdentifiers	36.185	0.688	37.188
cytoscapePlot	0.000	0.000	0.001
pathwayDatabases	0.015	0.000	0.016
pathwayGraph	37.241	0.517	39.687
pathways	41.106	1.033	50.878
runClipper	48.615	0.767	49.844
runSPIA	44.528	1.411	46.428
runTopologyGSA	36.133	0.222	36.661