Egon Willighagen
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/rWikiPathways |
| Branch: RELEASE_3_12 |
| Last Commit: 8b32421 |
| Last Changed Date: 2021-04-24 12:56:14 -0400 (Sat, 24 Apr 2021) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:36:37 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the rWikiPathways package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1607/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rWikiPathways 1.10.2 (landing page) Egon Willighagen
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: rWikiPathways |
| Version: 1.10.2 |
| 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_1.10.2.tar.gz |
| StartedAt: 2021-05-06 05:47:32 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 05:53:19 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 346.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: rWikiPathways.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running 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_1.10.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/rWikiPathways.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.10.2’
* 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
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 3.259 0.087 7.397
listPathwayNames 0.028 0.009 10.014
listPathwayUrls 0.021 0.007 5.491
wikipathwaysGET 0.017 0.003 15.769
listPathways 0.014 0.002 6.080
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
── Error (test-listPathways.R:5:3): pathways are found ─────────────────────────
Error: Timeout was reached: [webservice.wikipathways.org] Connection timed out after 10008 milliseconds
Backtrace:
█
1. └─rWikiPathways::listPathways() test-listPathways.R:5:2
2. └─rWikiPathways::wikipathwaysGET("listPathways", list(organism = organism))
3. └─httr::GET(url = URLencode(q.url))
4. └─httr:::request_perform(req, hu$handle$handle)
5. ├─httr:::request_fetch(req$output, req$url, handle)
6. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
7. └─curl::curl_fetch_memory(url, handle = handle)
[ FAIL 8 | WARN 0 | SKIP 0 | PASS 18 ]
Error: Test failures
Execution halted
* 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 ERROR, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.12-bioc/meat/rWikiPathways.Rcheck/00check.log’
for details.
rWikiPathways.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rWikiPathways ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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)
rWikiPathways.Rcheck/tests/testthat.Rout.fail
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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")
══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test-findPathwaysByLiterature.R:5:5): find by keyword ────────────────
Error: Timeout was reached: [webservice.wikipathways.org] Connection timed out after 10009 milliseconds
Backtrace:
█
1. └─rWikiPathways::findPathwaysByLiterature("cancer") test-findPathwaysByLiterature.R:5:4
2. └─rWikiPathways::wikipathwaysGET("findPathwaysByLiterature", list(query = query))
3. └─httr::GET(url = URLencode(q.url))
4. └─httr:::request_perform(req, hu$handle$handle)
5. ├─httr:::request_fetch(req$output, req$url, handle)
6. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
7. └─curl::curl_fetch_memory(url, handle = handle)
── Error (test-findPathwaysByLiterature.R:10:5): find by pmid (again) ──────────
Error: Timeout was reached: [webservice.wikipathways.org] Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
Backtrace:
█
1. └─rWikiPathways::findPathwaysByLiterature(query = "10423528") test-findPathwaysByLiterature.R:10:4
2. └─rWikiPathways::wikipathwaysGET("findPathwaysByLiterature", list(query = query))
3. └─httr::GET(url = URLencode(q.url))
4. └─httr:::request_perform(req, hu$handle$handle)
5. ├─httr:::request_fetch(req$output, req$url, handle)
6. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
7. └─curl::curl_fetch_memory(url, handle = handle)
── Error (test-findPathwaysByXref.R:5:3): find by Xref ─────────────────────────
Error: Timeout was reached: [webservice.wikipathways.org] Connection timed out after 10458 milliseconds
Backtrace:
█
1. └─rWikiPathways::findPathwaysByXref("ENSG00000232810", "En") test-findPathwaysByXref.R:5:2
2. └─rWikiPathways::wikipathwaysGET(...)
3. └─httr::GET(url = URLencode(q.url))
4. └─httr:::request_perform(req, hu$handle$handle)
5. ├─httr:::request_fetch(req$output, req$url, handle)
6. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
7. └─curl::curl_fetch_memory(url, handle = handle)
── Error (test-findPathwaysByXref.R:10:3): find by Xref (again) ────────────────
Error: Timeout was reached: [webservice.wikipathways.org] Operation timed out after 10113 milliseconds with 0 out of 0 bytes received
Backtrace:
█
1. └─rWikiPathways::findPathwaysByXref(...) test-findPathwaysByXref.R:10:2
2. └─rWikiPathways::wikipathwaysGET(...)
3. └─httr::GET(url = URLencode(q.url))
4. └─httr:::request_perform(req, hu$handle$handle)
5. ├─httr:::request_fetch(req$output, req$url, handle)
6. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
7. └─curl::curl_fetch_memory(url, handle = handle)
── Error (test-getCurationTags.R:5:5): get by WPID ─────────────────────────────
Error: Timeout was reached: [webservice.wikipathways.org] Connection timed out after 10022 milliseconds
Backtrace:
█
1. └─rWikiPathways::getCurationTags("WP554") test-getCurationTags.R:5:4
2. └─rWikiPathways::wikipathwaysGET("getCurationTags", list(pwId = pathway))
3. └─httr::GET(url = URLencode(q.url))
4. └─httr:::request_perform(req, hu$handle$handle)
5. ├─httr:::request_fetch(req$output, req$url, handle)
6. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
7. └─curl::curl_fetch_memory(url, handle = handle)
── Error (test-getCurationTags.R:15:5): find by tag name ───────────────────────
Error: Timeout was reached: [webservice.wikipathways.org] Connection timed out after 10847 milliseconds
Backtrace:
█
1. └─rWikiPathways::getPathwaysByCurationTag("Curation:FeaturedPathway") test-getCurationTags.R:15:4
2. ├─base::lapply(...)
3. └─rWikiPathways::getEveryCurationTag(tag)
4. └─rWikiPathways::wikipathwaysGET("getCurationTagsByName", list(tagName = tag))
5. └─httr::GET(url = URLencode(q.url))
6. └─httr:::request_perform(req, hu$handle$handle)
7. ├─httr:::request_fetch(req$output, req$url, handle)
8. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
9. └─curl::curl_fetch_memory(url, handle = handle)
── Error (test-listOrganisms.R:5:3): organisms are found ───────────────────────
Error: Timeout was reached: [webservice.wikipathways.org] Connection timed out after 10282 milliseconds
Backtrace:
█
1. └─rWikiPathways::listOrganisms() test-listOrganisms.R:5:2
2. └─rWikiPathways::wikipathwaysGET("listOrganisms")
3. └─httr::GET(url = URLencode(q.url))
4. └─httr:::request_perform(req, hu$handle$handle)
5. ├─httr:::request_fetch(req$output, req$url, handle)
6. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
7. └─curl::curl_fetch_memory(url, handle = handle)
── Error (test-listPathways.R:5:3): pathways are found ─────────────────────────
Error: Timeout was reached: [webservice.wikipathways.org] Connection timed out after 10008 milliseconds
Backtrace:
█
1. └─rWikiPathways::listPathways() test-listPathways.R:5:2
2. └─rWikiPathways::wikipathwaysGET("listPathways", list(organism = organism))
3. └─httr::GET(url = URLencode(q.url))
4. └─httr:::request_perform(req, hu$handle$handle)
5. ├─httr:::request_fetch(req$output, req$url, handle)
6. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
7. └─curl::curl_fetch_memory(url, handle = handle)
[ FAIL 8 | WARN 0 | SKIP 0 | PASS 18 ]
Error: Test failures
Execution halted
rWikiPathways.Rcheck/rWikiPathways-Ex.timings
| name | user | system | elapsed | |
| downloadPathwayArchive | 0.000 | 0.000 | 0.001 | |
| findPathwayIdsByLiterature | 3.259 | 0.087 | 7.397 | |
| findPathwayIdsByText | 0.014 | 0.003 | 0.371 | |
| findPathwayIdsByXref | 0.022 | 0.001 | 0.317 | |
| findPathwayNamesByLiterature | 0.228 | 0.011 | 4.063 | |
| findPathwayNamesByText | 0.016 | 0.002 | 0.283 | |
| findPathwayNamesByXref | 0.026 | 0.003 | 0.315 | |
| findPathwayUrlsByLiterature | 0.216 | 0.012 | 3.803 | |
| findPathwayUrlsByText | 0.058 | 0.002 | 0.285 | |
| findPathwayUrlsByXref | 0.026 | 0.002 | 0.289 | |
| findPathwaysByLiterature | 0.221 | 0.005 | 3.659 | |
| findPathwaysByText | 0.013 | 0.001 | 0.248 | |
| findPathwaysByXref | 0.045 | 0.007 | 0.312 | |
| getCurationTagNames | 0.009 | 0.000 | 0.068 | |
| getCurationTags | 0.011 | 0.003 | 0.075 | |
| getEveryCurationTag | 0.105 | 0.113 | 1.099 | |
| getOntologyTermIds | 0.008 | 0.000 | 0.105 | |
| getOntologyTermNames | 0.007 | 0.000 | 0.104 | |
| getOntologyTerms | 0.009 | 0.001 | 0.106 | |
| getPathway | 0.030 | 0.001 | 0.130 | |
| getPathwayHistory | 0.009 | 0.002 | 0.108 | |
| getPathwayIdsByCurationTag | 0.017 | 0.003 | 0.794 | |
| getPathwayIdsByOntologyTerm | 0.008 | 0.000 | 0.124 | |
| getPathwayIdsByParentOntologyTerm | 0.009 | 0.001 | 0.117 | |
| getPathwayInfo | 0.026 | 0.001 | 0.115 | |
| getPathwaysByCurationTag | 0.051 | 0.039 | 0.840 | |
| getPathwaysByOntologyTerm | 0.008 | 0.003 | 0.097 | |
| getPathwaysByParentOntologyTerm | 0.010 | 0.004 | 0.102 | |
| getRecentChanges | 0.028 | 0.024 | 2.523 | |
| getRecentChangesIds | 0.009 | 0.001 | 2.912 | |
| getRecentChangesNames | 0.015 | 0.004 | 0.265 | |
| getXrefList | 0.008 | 0.001 | 0.087 | |
| listOrganisms | 0.007 | 0.001 | 0.082 | |
| listPathwayIds | 0.014 | 0.002 | 4.684 | |
| listPathwayNames | 0.028 | 0.009 | 10.014 | |
| listPathwayUrls | 0.021 | 0.007 | 5.491 | |
| listPathways | 0.014 | 0.002 | 6.080 | |
| readPathwayGMT | 0.000 | 0.000 | 0.001 | |
| wikipathwaysAPI | 0.002 | 0.002 | 0.004 | |
| wikipathwaysGET | 0.017 | 0.003 | 15.769 | |