Package: rWikiPathways

Version: 1.3.4

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_1.3.4.tar.gz

StartedAt: 2019-04-09 03:32:33 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:34:01 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 88.9 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_1.3.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/rWikiPathways.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.3.4’
* 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 0.237  0.037   6.127
* 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-3.9-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’ ...
** 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)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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 
  1.635   0.204  21.218 

name	user	system	elapsed
downloadPathwayArchive	0.001	0.000	0.000
findPathwayIdsByLiterature	0.155	0.022	3.047
findPathwayIdsByText	0.013	0.001	0.216
findPathwayIdsByXref	0.026	0.002	0.219
findPathwayNamesByLiterature	0.093	0.008	2.569
findPathwayNamesByText	0.015	0.001	0.251
findPathwayNamesByXref	0.034	0.003	0.252
findPathwayUrlsByLiterature	0.106	0.009	2.500
findPathwayUrlsByText	0.015	0.001	0.201
findPathwayUrlsByXref	0.033	0.002	0.234
findPathwaysByLiterature	0.346	0.087	2.625
findPathwaysByText	0.041	0.015	0.259
findPathwaysByXref	0.135	0.060	0.394
getColoredPathway	0.237	0.037	6.127
getCurationTagNames	0.009	0.001	0.079
getCurationTags	0.009	0.001	0.076
getEveryCurationTag	0.111	0.052	0.899
getOntologyTermIds	0.009	0.002	0.070
getOntologyTermNames	0.009	0.001	0.077
getOntologyTerms	0.009	0.001	0.068
getPathway	0.039	0.002	0.100
getPathwayHistory	0.009	0.002	0.069
getPathwayIdsByCurationTag	0.020	0.004	0.395
getPathwayIdsByOntologyTerm	0.009	0.002	0.088
getPathwayIdsByParentOntologyTerm	0.013	0.006	0.097
getPathwayInfo	0.009	0.001	0.072
getPathwaysByCurationTag	0.065	0.023	0.465
getPathwaysByOntologyTerm	0.011	0.002	0.087
getPathwaysByParentOntologyTerm	0.012	0.002	0.081
getRecentChanges	0.026	0.008	0.202
getRecentChangesIds	0.010	0.000	0.146
getRecentChangesNames	0.012	0.002	0.150
getXrefList	0.006	0.000	0.073
listOrganisms	0.006	0.001	0.063
listPathwayIds	0.015	0.001	3.619
listPathwayNames	0.022	0.003	3.593
listPathwayUrls	0.020	0.002	3.722
listPathways	0.046	0.020	3.680
wikipathwaysAPI	0.003	0.002	0.006
wikipathwaysGET	0.008	0.000	0.073