Package: graphite

Version: 1.30.0

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_1.30.0.tar.gz

StartedAt: 2019-10-16 02:11:15 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:25:14 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 839.2 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_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/graphite.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 ‘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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
runClipper          50.297  0.825  53.268
as.list.PathwayList 49.672  0.671  50.517
convertIdentifiers  46.982  0.059  47.302
pathwayGraph        44.543  0.060  44.828
pathways            43.249  0.187  52.338
runSPIA             42.336  0.340  71.664
runTopologyGSA      34.561  0.064  36.141
* 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 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.

> library(testthat)
> library(graphite)
> 
> test_check("graphite")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 95 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
367.042   3.805 384.110 

name	user	system	elapsed
as.list.PathwayList	49.672	0.671	50.517
buildPathway	0.011	0.002	0.012
convertIdentifiers	46.982	0.059	47.302
cytoscapePlot	0	0	0
pathwayDatabases	0.011	0.000	0.011
pathwayGraph	44.543	0.060	44.828
pathways	43.249	0.187	52.338
runClipper	50.297	0.825	53.268
runSPIA	42.336	0.340	71.664
runTopologyGSA	34.561	0.064	36.141