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CHECK report for rWikiPathways on merida1

This page was generated on 2019-04-16 12:08:31 -0400 (Tue, 16 Apr 2019).

Package 1375/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rWikiPathways 1.2.1
Egon Willighagen , Alexander Pico
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/rWikiPathways
Branch: RELEASE_3_8
Last Commit: 01cdd36
Last Changed Date: 2019-02-06 19:28:57 -0400 (Wed, 06 Feb 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: rWikiPathways
Version: 1.2.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rWikiPathways.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rWikiPathways_1.2.1.tar.gz
StartedAt: 2019-04-16 02:34:49 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:36:46 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 117.2 seconds
RetCode: 0
Status:  OK 
CheckDir: rWikiPathways.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rWikiPathways.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rWikiPathways_1.2.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/rWikiPathways.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 ‘rWikiPathways/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rWikiPathways’ version ‘1.2.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rWikiPathways’ 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
getColoredPathway          0.216  0.042   8.229
findPathwayIdsByLiterature 0.165  0.021   5.443
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/rWikiPathways.Rcheck/00check.log’
for details.



Installation output

rWikiPathways.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rWikiPathways
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘rWikiPathways’ ...
** 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 (rWikiPathways)

Tests output

rWikiPathways.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(rWikiPathways)
> 
> test_check("rWikiPathways")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 30 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  1.718   0.200  30.971 

Example timings

rWikiPathways.Rcheck/rWikiPathways-Ex.timings

nameusersystemelapsed
downloadPathwayArchive000
findPathwayIdsByLiterature0.1650.0215.443
findPathwayIdsByText0.0130.0010.654
findPathwayIdsByXref0.0290.0020.555
findPathwayNamesByLiterature0.0910.0094.620
findPathwayNamesByText0.0140.0020.617
findPathwayNamesByXref0.0330.0020.523
findPathwayUrlsByLiterature0.1330.0074.577
findPathwayUrlsByText0.0170.0020.621
findPathwayUrlsByXref0.0350.0030.524
findPathwaysByLiterature0.3230.1004.856
findPathwaysByText0.0310.0110.648
findPathwaysByXref0.1310.0650.682
getColoredPathway0.2160.0428.229
getCurationTagNames0.0060.0000.060
getCurationTags0.0100.0010.061
getEveryCurationTag0.1050.0480.889
getOntologyTermIds0.0090.0000.056
getOntologyTermNames0.0080.0010.051
getOntologyTerms0.0060.0000.049
getPathway0.0370.0000.085
getPathwayHistory0.0080.0010.054
getPathwayIdsByCurationTag0.0200.0020.592
getPathwayIdsByOntologyTerm0.0090.0010.077
getPathwayIdsByParentOntologyTerm0.0090.0000.071
getPathwayInfo0.0080.0010.053
getPathwaysByCurationTag0.0580.0200.656
getPathwaysByOntologyTerm0.0110.0020.074
getPathwaysByParentOntologyTerm0.0100.0010.068
getRecentChanges0.0320.0120.251
getRecentChangesIds0.0130.0010.187
getRecentChangesNames0.0130.0020.185
getXrefList0.0090.0010.194
listOrganisms0.0080.0010.051
listPathwayIds0.0170.0034.650
listPathwayNames0.0190.0054.729
listPathwayUrls0.0240.0044.844
listPathways0.0420.0164.865
wikipathwaysAPI0.0020.0020.006
wikipathwaysGET0.010.000.05