Package: graphite

Version: 1.30.0

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_1.30.0.tar.gz

StartedAt: 2019-10-16 03:27:40 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:44:22 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 1001.5 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_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/graphite.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.30.0’
* 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 ‘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          59.303  1.771  77.271
runSPIA             52.279  2.447  54.745
as.list.PathwayList 46.013  2.452  48.838
convertIdentifiers  43.232  0.559  43.792
runTopologyGSA      42.335  0.712  43.058
pathways            40.176  1.437  41.663
pathwayGraph        40.252  0.502  40.754
* 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’ ...
** 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 (graphite)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
471.049  15.525 513.938 

name	user	system	elapsed
as.list.PathwayList	46.013	2.452	48.838
buildPathway	0.019	0.001	0.020
convertIdentifiers	43.232	0.559	43.792
cytoscapePlot	0	0	0
pathwayDatabases	0.013	0.000	0.014
pathwayGraph	40.252	0.502	40.754
pathways	40.176	1.437	41.663
runClipper	59.303	1.771	77.271
runSPIA	52.279	2.447	54.745
runTopologyGSA	42.335	0.712	43.058