Egon Willighagen
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/rWikiPathways |
| Branch: RELEASE_3_7 |
| Last Commit: f86fd89 |
| Last Changed Date: 2018-10-06 21:03:47 -0400 (Sat, 06 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:31:30 -0400 (Wed, 17 Oct 2018).
| Package 1304/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| rWikiPathways 1.0.5 Egon Willighagen
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: rWikiPathways |
| Version: 1.0.5 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:rWikiPathways.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings rWikiPathways_1.0.5.tar.gz |
| StartedAt: 2018-10-16 03:31:00 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 03:32:51 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 111.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: rWikiPathways.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:rWikiPathways.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings rWikiPathways_1.0.5.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/rWikiPathways.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.0.5’
* 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 ... NOTE
downloadPathwayArchive: no visible global function definition for
‘readHTMLTable’
Undefined global functions or variables:
readHTMLTable
* 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 0.224 0.012 9.045
findPathwayIdsByLiterature 0.192 0.024 5.738
listPathways 0.032 0.004 5.210
listPathwayUrls 0.016 0.004 5.030
listPathwayIds 0.016 0.000 6.243
listPathwayNames 0.012 0.000 5.094
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.7-bioc/meat/rWikiPathways.Rcheck/00check.log’
for details.
rWikiPathways.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL rWikiPathways ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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)
rWikiPathways.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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
1.332 0.112 33.700
rWikiPathways.Rcheck/rWikiPathways-Ex.timings
| name | user | system | elapsed | |
| downloadPathwayArchive | 0 | 0 | 0 | |
| findPathwayIdsByLiterature | 0.192 | 0.024 | 5.738 | |
| findPathwayIdsByText | 0.008 | 0.004 | 0.294 | |
| findPathwayIdsByXref | 0.024 | 0.000 | 0.363 | |
| findPathwayNamesByLiterature | 0.068 | 0.004 | 3.611 | |
| findPathwayNamesByText | 0.012 | 0.000 | 0.277 | |
| findPathwayNamesByXref | 0.020 | 0.000 | 0.303 | |
| findPathwayUrlsByLiterature | 0.092 | 0.000 | 3.600 | |
| findPathwayUrlsByText | 0.008 | 0.004 | 0.275 | |
| findPathwayUrlsByXref | 0.024 | 0.000 | 0.320 | |
| findPathwaysByLiterature | 0.132 | 0.048 | 3.843 | |
| findPathwaysByText | 0.028 | 0.000 | 0.469 | |
| findPathwaysByXref | 0.076 | 0.020 | 0.425 | |
| getColoredPathway | 0.224 | 0.012 | 9.045 | |
| getCurationTagNames | 0.008 | 0.000 | 0.418 | |
| getCurationTags | 0.008 | 0.000 | 0.124 | |
| getEveryCurationTag | 0.048 | 0.024 | 0.947 | |
| getOntologyTermIds | 0.004 | 0.000 | 0.112 | |
| getOntologyTermNames | 0.004 | 0.000 | 0.119 | |
| getOntologyTerms | 0.008 | 0.000 | 0.114 | |
| getPathway | 0.020 | 0.004 | 0.142 | |
| getPathwayHistory | 0.008 | 0.000 | 0.142 | |
| getPathwayIdsByCurationTag | 0.02 | 0.00 | 0.93 | |
| getPathwayIdsByOntologyTerm | 0.008 | 0.000 | 0.172 | |
| getPathwayIdsByParentOntologyTerm | 0.012 | 0.000 | 0.145 | |
| getPathwayInfo | 0.008 | 0.000 | 0.111 | |
| getPathwaysByCurationTag | 0.020 | 0.012 | 0.741 | |
| getPathwaysByOntologyTerm | 0.008 | 0.000 | 0.136 | |
| getPathwaysByParentOntologyTerm | 0.008 | 0.000 | 0.130 | |
| getRecentChanges | 0.016 | 0.008 | 0.423 | |
| getRecentChangesIds | 0.008 | 0.004 | 0.349 | |
| getRecentChangesNames | 0.012 | 0.000 | 0.323 | |
| getXrefList | 0.004 | 0.000 | 0.134 | |
| listOrganisms | 0.004 | 0.000 | 0.110 | |
| listPathwayIds | 0.016 | 0.000 | 6.243 | |
| listPathwayNames | 0.012 | 0.000 | 5.094 | |
| listPathwayUrls | 0.016 | 0.004 | 5.030 | |
| listPathways | 0.032 | 0.004 | 5.210 | |
| wikipathwaysAPI | 0.000 | 0.008 | 0.011 | |
| wikipathwaysGET | 0.012 | 0.000 | 0.111 | |