Package: rWikiPathways

Version: 1.3.4

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:rWikiPathways.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings rWikiPathways_1.3.4.tar.gz

StartedAt: 2019-04-09 03:25:44 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:27:13 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 89.4 seconds

RetCode: 0

Status:  OK

CheckDir: rWikiPathways.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:rWikiPathways.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings rWikiPathways_1.3.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/rWikiPathways.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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 0.213  0.025   6.355
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/rWikiPathways.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL rWikiPathways
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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-pc-linux-gnu (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 
  1.634   0.068  22.419 

name	user	system	elapsed
downloadPathwayArchive	0	0	0
findPathwayIdsByLiterature	0.245	0.012	3.320
findPathwayIdsByText	0.049	0.000	0.293
findPathwayIdsByXref	0.025	0.000	0.255
findPathwayNamesByLiterature	0.084	0.000	2.683
findPathwayNamesByText	0.012	0.000	0.230
findPathwayNamesByXref	0.018	0.004	0.277
findPathwayUrlsByLiterature	0.085	0.004	2.785
findPathwayUrlsByText	0.013	0.000	0.243
findPathwayUrlsByXref	0.029	0.000	0.280
findPathwaysByLiterature	0.210	0.056	2.981
findPathwaysByText	0.020	0.012	0.276
findPathwaysByXref	0.064	0.024	0.315
getColoredPathway	0.213	0.025	6.355
getCurationTagNames	0.008	0.000	0.116
getCurationTags	0.007	0.000	0.106
getEveryCurationTag	0.051	0.028	0.814
getOntologyTermIds	0.007	0.000	0.102
getOntologyTermNames	0.007	0.000	0.101
getOntologyTerms	0.007	0.000	0.104
getPathway	0.029	0.000	0.133
getPathwayHistory	0.008	0.000	0.107
getPathwayIdsByCurationTag	0.021	0.000	0.602
getPathwayIdsByOntologyTerm	0.007	0.000	0.116
getPathwayIdsByParentOntologyTerm	0.009	0.000	0.115
getPathwayInfo	0.013	0.001	0.108
getPathwaysByCurationTag	0.033	0.015	0.615
getPathwaysByOntologyTerm	0.010	0.000	0.122
getPathwaysByParentOntologyTerm	0.007	0.004	0.115
getRecentChanges	0.024	0.000	0.230
getRecentChangesIds	0.008	0.003	0.186
getRecentChangesNames	0.070	0.004	0.248
getXrefList	0.007	0.000	0.103
listOrganisms	0.006	0.000	0.100
listPathwayIds	0.014	0.000	3.491
listPathwayNames	0.013	0.004	3.630
listPathwayUrls	0.018	0.000	3.733
listPathways	0.031	0.004	3.610
wikipathwaysAPI	0.002	0.009	0.011
wikipathwaysGET	0.008	0.000	0.104