Package: rWikiPathways

Version: 1.6.1

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_1.6.1.tar.gz

StartedAt: 2020-04-15 05:24:59 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:26:53 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 113.3 seconds

RetCode: 0

Status:  OK

CheckDir: rWikiPathways.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:rWikiPathways.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rWikiPathways_1.6.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/rWikiPathways.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.6.1’
* 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
findPathwaysByLiterature   0.313  0.113   5.755
findPathwayIdsByLiterature 0.109  0.019   5.753
* 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-3.10-bioc/meat/rWikiPathways.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rWikiPathways
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘rWikiPathways’ ...
** 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 (rWikiPathways)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 27 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  2.088   0.171  24.042 

name	user	system	elapsed
downloadPathwayArchive	0.000	0.000	0.001
findPathwayIdsByLiterature	0.109	0.019	5.753
findPathwayIdsByText	0.007	0.000	0.733
findPathwayIdsByXref	0.054	0.001	0.702
findPathwayNamesByLiterature	0.061	0.010	4.950
findPathwayNamesByText	0.015	0.002	0.707
findPathwayNamesByXref	0.021	0.002	0.531
findPathwayUrlsByLiterature	0.068	0.006	4.795
findPathwayUrlsByText	0.015	0.001	0.937
findPathwayUrlsByXref	0.023	0.002	0.543
findPathwaysByLiterature	0.313	0.113	5.755
findPathwaysByText	0.035	0.013	0.877
findPathwaysByXref	0.140	0.067	0.713
getColoredPathway	0	0	0
getCurationTagNames	0.008	0.000	0.053
getCurationTags	0.008	0.001	0.071
getEveryCurationTag	0.112	0.049	0.953
getOntologyTermIds	0.007	0.000	0.043
getOntologyTermNames	0.012	0.001	0.045
getOntologyTerms	0.006	0.000	0.038
getPathway	0.040	0.000	0.075
getPathwayHistory	0.009	0.001	0.048
getPathwayIdsByCurationTag	0.020	0.002	0.634
getPathwayIdsByOntologyTerm	0.012	0.000	0.067
getPathwayIdsByParentOntologyTerm	0.007	0.001	0.058
getPathwayInfo	0.008	0.000	0.041
getPathwaysByCurationTag	0.058	0.020	0.772
getPathwaysByOntologyTerm	0.010	0.002	0.057
getPathwaysByParentOntologyTerm	0.010	0.002	0.058
getRecentChanges	0.052	0.021	0.356
getRecentChangesIds	0.013	0.002	0.239
getRecentChangesNames	0.015	0.002	0.244
getXrefList	0.008	0.001	0.190
listOrganisms	0.009	0.001	0.039
listPathwayIds	0.012	0.001	4.455
listPathwayNames	0.014	0.002	4.540
listPathwayUrls	0.019	0.002	4.471
listPathways	0.040	0.016	4.506
wikipathwaysAPI	0.003	0.002	0.006
wikipathwaysGET	0.008	0.000	0.040