Egon Willighagen
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/rWikiPathways |
| git_branch: master |
| git_last_commit: 5c7ce0e |
| git_last_commit_date: 2021-10-26 12:43:34 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:34 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1692/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rWikiPathways 1.15.0 (landing page) Egon Willighagen
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: rWikiPathways |
| Version: 1.15.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rWikiPathways.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings rWikiPathways_1.15.0.tar.gz |
| StartedAt: 2022-03-17 20:09:43 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:12:03 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 139.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: rWikiPathways.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rWikiPathways.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings rWikiPathways_1.15.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/rWikiPathways.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rWikiPathways/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rWikiPathways' version '1.15.0'
* 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 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 0.25 0.05 6.53
findPathwayUrlsByLiterature 0.17 0.00 7.39
findPathwayNamesByLiterature 0.14 0.00 7.66
findPathwaysByLiterature 0.13 0.00 6.39
listPathwayIds 0.02 0.00 5.44
listPathways 0.02 0.00 8.74
listPathwayUrls 0.01 0.00 6.61
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/rWikiPathways.Rcheck/00check.log'
for details.
rWikiPathways.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL rWikiPathways
###
##############################################################################
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'rWikiPathways' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'rWikiPathways'
finding HTML links ... done
downloadPathwayArchive html
findPathwayIdsByLiterature html
findPathwayIdsByText html
findPathwayIdsByXref html
findPathwayNamesByLiterature html
findPathwayNamesByText html
findPathwayNamesByXref html
findPathwayUrlsByLiterature html
findPathwayUrlsByText html
findPathwayUrlsByXref html
findPathwaysByLiterature html
findPathwaysByText html
findPathwaysByXref html
getCurationTagNames html
getCurationTags html
getEveryCurationTag html
getOntologyTermIds html
getOntologyTermNames html
getOntologyTerms html
getPathway html
getPathwayHistory html
getPathwayIdsByCurationTag html
getPathwayIdsByOntologyTerm html
getPathwayIdsByParentOntologyTerm html
getPathwayInfo html
getPathwaysByCurationTag html
getPathwaysByOntologyTerm html
getPathwaysByParentOntologyTerm html
getRecentChanges html
getRecentChangesIds html
getRecentChangesNames html
getXrefList html
listOrganisms html
listPathwayIds html
listPathwayNames html
listPathwayUrls html
listPathways html
readGMT html
readGMTnames html
readPathwayGMT html
wikipathwaysAPI html
wikipathwaysGET html
writeGMT html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'Dune' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'spicyR' is missing or broken
done
rWikiPathways.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
2.17 0.18 30.32
rWikiPathways.Rcheck/rWikiPathways-Ex.timings
| name | user | system | elapsed | |
| downloadPathwayArchive | 0 | 0 | 0 | |
| findPathwayIdsByLiterature | 0.25 | 0.05 | 6.53 | |
| findPathwayIdsByText | 0.00 | 0.00 | 1.11 | |
| findPathwayIdsByXref | 0.02 | 0.00 | 0.83 | |
| findPathwayNamesByLiterature | 0.14 | 0.00 | 7.66 | |
| findPathwayNamesByText | 0.03 | 0.00 | 1.34 | |
| findPathwayNamesByXref | 0.02 | 0.00 | 0.95 | |
| findPathwayUrlsByLiterature | 0.17 | 0.00 | 7.39 | |
| findPathwayUrlsByText | 0.01 | 0.00 | 1.11 | |
| findPathwayUrlsByXref | 0.03 | 0.00 | 0.80 | |
| findPathwaysByLiterature | 0.13 | 0.00 | 6.39 | |
| findPathwaysByText | 0.02 | 0.00 | 1.13 | |
| findPathwaysByXref | 0.01 | 0.01 | 0.79 | |
| getCurationTagNames | 0.00 | 0.00 | 0.08 | |
| getCurationTags | 0.00 | 0.00 | 0.08 | |
| getEveryCurationTag | 0.02 | 0.06 | 1.28 | |
| getOntologyTermIds | 0.00 | 0.00 | 0.17 | |
| getOntologyTermNames | 0.00 | 0.00 | 0.17 | |
| getOntologyTerms | 0.00 | 0.00 | 1.16 | |
| getPathway | 0.02 | 0.00 | 0.15 | |
| getPathwayHistory | 0.01 | 0.00 | 0.16 | |
| getPathwayIdsByCurationTag | 0.03 | 0.00 | 0.78 | |
| getPathwayIdsByOntologyTerm | 0.02 | 0.00 | 0.09 | |
| getPathwayIdsByParentOntologyTerm | 0.03 | 0.00 | 0.10 | |
| getPathwayInfo | 0.00 | 0.00 | 0.06 | |
| getPathwaysByCurationTag | 0.02 | 0.04 | 0.75 | |
| getPathwaysByOntologyTerm | 0.00 | 0.00 | 0.08 | |
| getPathwaysByParentOntologyTerm | 0.01 | 0.00 | 0.09 | |
| getRecentChanges | 0.00 | 0.01 | 0.33 | |
| getRecentChangesIds | 0.00 | 0.00 | 0.22 | |
| getRecentChangesNames | 0.00 | 0.00 | 0.22 | |
| getXrefList | 0.0 | 0.0 | 0.3 | |
| listOrganisms | 0.00 | 0.00 | 0.06 | |
| listPathwayIds | 0.02 | 0.00 | 5.44 | |
| listPathwayNames | 0.00 | 0.01 | 4.20 | |
| listPathwayUrls | 0.01 | 0.00 | 6.61 | |
| listPathways | 0.02 | 0.00 | 8.74 | |
| readGMT | 0 | 0 | 0 | |
| readGMTnames | 0 | 0 | 0 | |
| readPathwayGMT | 0 | 0 | 0 | |
| wikipathwaysAPI | 0 | 0 | 0 | |
| wikipathwaysGET | 0.00 | 0.00 | 0.06 | |
| writeGMT | 0 | 0 | 0 | |