Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:43 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for rWikiPathways on machv2


To the developers/maintainers of the rWikiPathways package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rWikiPathways.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1684/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rWikiPathways 1.14.0  (landing page)
Egon Willighagen
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/rWikiPathways
git_branch: RELEASE_3_14
git_last_commit: b83547a
git_last_commit_date: 2021-10-26 12:43:34 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: rWikiPathways
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rWikiPathways.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rWikiPathways_1.14.0.tar.gz
StartedAt: 2022-04-12 17:59:14 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 18:01:52 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 157.5 seconds
RetCode: 0
Status:   OK  
CheckDir: rWikiPathways.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rWikiPathways.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rWikiPathways_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/rWikiPathways.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.14.0’
* 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 ... NOTE
Found the following non-portable file path:
  rWikiPathways/docs/articles/rWikiPathways-and-BridgeDbR_files/accessible-code-block-0.0.1/empty-anchor.js

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* 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 ... NOTE
readPathwayGMT: no visible binding for global variable ‘pathway’
Undefined global functions or variables:
  pathway
* 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 (user + system) or elapsed time > 5s
                              user system elapsed
findPathwayIdsByLiterature   0.289  0.029   7.876
findPathwaysByLiterature     0.206  0.006   7.939
findPathwayUrlsByLiterature  0.175  0.015   8.067
findPathwayNamesByLiterature 0.166  0.014   7.565
listPathwayNames             0.018  0.009   5.457
listPathwayUrls              0.016  0.009   5.668
listPathwayIds               0.014  0.006   5.341
listPathways                 0.017  0.002   5.423
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/rWikiPathways.Rcheck/00check.log’
for details.



Installation output

rWikiPathways.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rWikiPathways
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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)

Tests output

rWikiPathways.Rcheck/tests/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 27 ]
> 
> proc.time()
   user  system elapsed 
  3.180   0.224  29.270 

Example timings

rWikiPathways.Rcheck/rWikiPathways-Ex.timings

nameusersystemelapsed
downloadPathwayArchive000
findPathwayIdsByLiterature0.2890.0297.876
findPathwayIdsByText0.0130.0031.370
findPathwayIdsByXref0.0350.0030.838
findPathwayNamesByLiterature0.1660.0147.565
findPathwayNamesByText0.0140.0031.364
findPathwayNamesByXref0.0320.0030.838
findPathwayUrlsByLiterature0.1750.0158.067
findPathwayUrlsByText0.0150.0041.384
findPathwayUrlsByXref0.0310.0040.835
findPathwaysByLiterature0.2060.0067.939
findPathwaysByText0.0160.0011.412
findPathwaysByXref0.0430.0090.848
getCurationTagNames0.0090.0000.083
getCurationTags0.0090.0030.084
getEveryCurationTag0.0830.1391.067
getOntologyTermIds0.0080.0000.064
getOntologyTermNames0.0090.0010.065
getOntologyTerms0.0090.0010.067
getPathway0.0290.0010.090
getPathwayHistory0.0110.0030.071
getPathwayIdsByCurationTag0.0230.0040.748
getPathwayIdsByOntologyTerm0.0080.0000.099
getPathwayIdsByParentOntologyTerm0.0070.0000.087
getPathwayInfo0.0120.0010.082
getPathwaysByCurationTag0.0480.0580.899
getPathwaysByOntologyTerm0.0090.0030.096
getPathwaysByParentOntologyTerm0.0110.0050.104
getRecentChanges0.0210.0250.268
getRecentChangesIds0.0090.0010.205
getRecentChangesNames0.0120.0030.218
getXrefList0.0160.0000.321
listOrganisms0.0070.0010.072
listPathwayIds0.0140.0065.341
listPathwayNames0.0180.0095.457
listPathwayUrls0.0160.0095.668
listPathways0.0170.0025.423
readGMT0.0000.0000.001
readGMTnames0.0000.0010.000
readPathwayGMT0.0010.0000.001
wikipathwaysAPI000
wikipathwaysGET0.0080.0020.072
writeGMT000