Johannes Griss
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/ReactomeGSA |
| Branch: master |
| Last Commit: d52a97a |
| Last Changed Date: 2019-10-29 13:43:40 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:55:20 -0500 (Thu, 16 Jan 2020).
| Package 1393/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ReactomeGSA 1.1.0 Johannes Griss
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: ReactomeGSA |
| Version: 1.1.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ReactomeGSA_1.1.0.tar.gz |
| StartedAt: 2020-01-16 08:03:16 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 08:05:14 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 117.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReactomeGSA.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ReactomeGSA_1.1.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ReactomeGSA.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReactomeGSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ReactomeGSA’ version ‘1.1.0’
* package encoding: UTF-8
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ReactomeGSA’ 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
plot_correlations,ReactomeAnalysisResult: no visible binding for global
variable ‘combined_sig’
plot_correlations,ReactomeAnalysisResult: no visible binding for global
variable ‘alpha’
plot_volcano,ReactomeAnalysisResult: no visible binding for global
variable ‘av_foldchange’
plot_volcano,ReactomeAnalysisResult: no visible binding for global
variable ‘FDR’
Undefined global functions or variables:
FDR alpha av_foldchange combined_sig
* 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
plot_correlations-ReactomeAnalysisResult-method 6.531 0.042 6.574
plot_correlations 6.450 0.017 6.466
pathways-ReactomeAnalysisResult-method 6.388 0.030 6.422
pathways 6.292 0.031 6.324
ReactomeAnalysisResult-class 6.153 0.041 6.195
perform_reactome_analysis 3.253 0.316 13.039
* 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
‘/Users/biocbuild/bbs-3.11-bioc/meat/ReactomeGSA.Rcheck/00check.log’
for details.
ReactomeGSA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ReactomeGSA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘ReactomeGSA’ ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading in method for ‘add_dataset’ with signature ‘request="ReactomeAnalysisRequest",expression_values="EList"’: no definition for class “EList” in method for ‘add_dataset’ with signature ‘request="ReactomeAnalysisRequest",expression_values="DGEList"’: no definition for class “DGEList” in method for ‘add_dataset’ with signature ‘request="ReactomeAnalysisRequest",expression_values="ExpressionSet"’: no definition for class “ExpressionSet” ** 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 (ReactomeGSA)
ReactomeGSA.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(ReactomeGSA)
>
> test_check("ReactomeGSA")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 17 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
2.521 0.291 2.767
ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings
| name | user | system | elapsed | |
| ReactomeAnalysisRequest | 1.729 | 0.251 | 1.985 | |
| ReactomeAnalysisResult-class | 6.153 | 0.041 | 6.195 | |
| add_dataset-ReactomeAnalysisRequest-DGEList-method | 1.269 | 0.131 | 1.400 | |
| add_dataset-ReactomeAnalysisRequest-EList-method | 1.273 | 0.126 | 1.399 | |
| add_dataset-ReactomeAnalysisRequest-ExpressionSet-method | 1.135 | 0.102 | 1.237 | |
| add_dataset-ReactomeAnalysisRequest-data.frame-method | 1.248 | 0.137 | 1.384 | |
| add_dataset | 1.282 | 0.111 | 1.392 | |
| get_reactome_data_types | 0.111 | 0.022 | 1.070 | |
| get_reactome_methods | 0.049 | 0.015 | 1.405 | |
| get_result-ReactomeAnalysisResult-method | 0.164 | 0.012 | 0.176 | |
| get_result | 0.198 | 0.012 | 0.210 | |
| names-ReactomeAnalysisResult-method | 0.183 | 0.014 | 0.197 | |
| open_reactome-ReactomeAnalysisResult-method | 0.197 | 0.014 | 0.210 | |
| open_reactome | 0.138 | 0.009 | 0.147 | |
| pathways-ReactomeAnalysisResult-method | 6.388 | 0.030 | 6.422 | |
| pathways | 6.292 | 0.031 | 6.324 | |
| perform_reactome_analysis | 3.253 | 0.316 | 13.039 | |
| plot_correlations-ReactomeAnalysisResult-method | 6.531 | 0.042 | 6.574 | |
| plot_correlations | 6.450 | 0.017 | 6.466 | |
| plot_volcano-ReactomeAnalysisResult-method | 0.218 | 0.012 | 0.231 | |
| plot_volcano | 0.266 | 0.011 | 0.277 | |
| print-ReactomeAnalysisRequest-method | 0.003 | 0.001 | 0.003 | |
| print-ReactomeAnalysisResult-method | 0.203 | 0.013 | 0.216 | |
| reactome_links-ReactomeAnalysisResult-method | 0.143 | 0.010 | 0.153 | |
| reactome_links | 0.158 | 0.008 | 0.167 | |
| result_types-ReactomeAnalysisResult-method | 0.200 | 0.014 | 0.214 | |
| result_types | 0.203 | 0.013 | 0.215 | |
| set_method-ReactomeAnalysisRequest-method | 0.004 | 0.003 | 0.006 | |
| set_method | 0.004 | 0.002 | 0.006 | |
| set_parameters-ReactomeAnalysisRequest-method | 0.003 | 0.000 | 0.003 | |
| set_parameters | 0.002 | 0.000 | 0.002 | |
| show-ReactomeAnalysisRequest-method | 0.003 | 0.001 | 0.003 | |
| show-ReactomeAnalysisResult-method | 0.211 | 0.014 | 0.225 | |