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 05:14:25 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 05:16:13 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 108.5 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) (2019-03-18 r76245)
* 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 0.217  0.059   6.512
* 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’ ...
** 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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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 
  2.056   0.429  23.240 

name	user	system	elapsed
downloadPathwayArchive	0	0	0
findPathwayIdsByLiterature	0.240	0.053	4.190
findPathwayIdsByText	0.015	0.002	0.242
findPathwayIdsByXref	0.030	0.006	0.483
findPathwayNamesByLiterature	0.100	0.014	2.587
findPathwayNamesByText	0.018	0.004	0.234
findPathwayNamesByXref	0.035	0.008	0.287
findPathwayUrlsByLiterature	0.122	0.017	2.941
findPathwayUrlsByText	0.017	0.003	0.254
findPathwayUrlsByXref	0.102	0.008	0.337
findPathwaysByLiterature	0.421	0.236	3.196
findPathwaysByText	0.044	0.024	0.316
findPathwaysByXref	0.173	0.128	0.545
getColoredPathway	0.217	0.059	6.512
getCurationTagNames	0.007	0.001	0.113
getCurationTags	0.012	0.003	0.129
getEveryCurationTag	0.124	0.088	0.958
getOntologyTermIds	0.009	0.003	0.109
getOntologyTermNames	0.008	0.002	0.112
getOntologyTerms	0.008	0.002	0.104
getPathway	0.038	0.003	0.143
getPathwayHistory	0.011	0.003	0.118
getPathwayIdsByCurationTag	0.031	0.008	0.599
getPathwayIdsByOntologyTerm	0.009	0.002	0.126
getPathwayIdsByParentOntologyTerm	0.010	0.003	0.120
getPathwayInfo	0.010	0.002	0.110
getPathwaysByCurationTag	0.081	0.049	0.618
getPathwaysByOntologyTerm	0.012	0.003	0.126
getPathwaysByParentOntologyTerm	0.011	0.003	0.131
getRecentChanges	0.036	0.024	0.267
getRecentChangesIds	0.024	0.015	0.206
getRecentChangesNames	0.016	0.004	0.191
getXrefList	0.007	0.000	0.133
listOrganisms	0.009	0.001	0.103
listPathwayIds	0.017	0.003	3.591
listPathwayNames	0.020	0.005	3.688
listPathwayUrls	0.027	0.005	3.774
listPathways	0.054	0.031	3.688
wikipathwaysAPI	0.006	0.007	0.012
wikipathwaysGET	0.009	0.002	0.104