Package: graphite

Version: 1.29.2

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:graphite.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings graphite_1.29.2.tar.gz

StartedAt: 2019-04-09 01:03:05 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:18:23 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 917.9 seconds

RetCode: 0

Status:  OK

CheckDir: graphite.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:graphite.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings graphite_1.29.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/graphite.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
runClipper          59.406  0.806  61.472
runSPIA             53.400  0.224  53.980
as.list.PathwayList 48.432  0.662  49.419
convertIdentifiers  46.766  0.083  47.167
pathwayGraph        45.112  0.083  51.807
pathways            44.783  0.040  45.230
runTopologyGSA      43.421  0.028  43.758
* 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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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL graphite
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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.

> library(testthat)
> library(graphite)
> 
> test_check("graphite")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 95 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
363.052   7.317 468.556 

name	user	system	elapsed
as.list.PathwayList	48.432	0.662	49.419
buildPathway	0.017	0.000	0.016
convertIdentifiers	46.766	0.083	47.167
cytoscapePlot	0.000	0.000	0.001
pathwayDatabases	0.013	0.000	0.012
pathwayGraph	45.112	0.083	51.807
pathways	44.783	0.040	45.230
runClipper	59.406	0.806	61.472
runSPIA	53.400	0.224	53.980
runTopologyGSA	43.421	0.028	43.758