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CHECK report for graphite on merida1

This page was generated on 2019-04-16 11:56:03 -0400 (Tue, 16 Apr 2019).

Package 681/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
graphite 1.28.2
Gabriele Sales
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/graphite
Branch: RELEASE_3_8
Last Commit: 875f94b
Last Changed Date: 2019-01-15 15:47:30 -0400 (Tue, 15 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: graphite
Version: 1.28.2
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_1.28.2.tar.gz
StartedAt: 2019-04-16 00:25:02 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:38:31 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 808.8 seconds
RetCode: 0
Status:  OK 
CheckDir: graphite.Rcheck
Warnings: 0

Command output

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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_1.28.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/graphite.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.28.2’
* 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          52.285  0.888  61.145
runSPIA             45.817  1.153  47.365
as.list.PathwayList 40.929  1.218  42.654
convertIdentifiers  38.688  0.269  39.443
runTopologyGSA      38.081  0.393  38.789
pathways            35.973  0.740  37.017
pathwayGraph        35.416  0.243  35.969
* 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


Installation output

graphite.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL graphite
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/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)

Tests output

graphite.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
391.464   9.097 412.337 

Example timings

graphite.Rcheck/graphite-Ex.timings

nameusersystemelapsed
as.list.PathwayList40.929 1.21842.654
buildPathway0.0150.0000.016
convertIdentifiers38.688 0.26939.443
cytoscapePlot000
pathwayDatabases0.0150.0010.016
pathwayGraph35.416 0.24335.969
pathways35.973 0.74037.017
runClipper52.285 0.88861.145
runSPIA45.817 1.15347.365
runTopologyGSA38.081 0.39338.789