Johannes Griss
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/ReactomeGSA |
| Branch: RELEASE_3_10 |
| Last Commit: 16be774 |
| Last Changed Date: 2019-10-29 13:12:03 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:50:03 -0400 (Wed, 15 Apr 2020).
| Package 1396/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ReactomeGSA 1.0.0 Johannes Griss
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: ReactomeGSA |
| Version: 1.0.0 |
| 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_1.0.0.tar.gz |
| StartedAt: 2020-04-15 05:02:51 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:04:24 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 92.6 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_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/ReactomeGSA.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.0.0’
* 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 or elapsed time > 5s
user system elapsed
pathways-ReactomeAnalysisResult-method 5.958 0.014 6.021
plot_correlations-ReactomeAnalysisResult-method 5.944 0.018 6.028
ReactomeAnalysisResult-class 5.925 0.026 6.004
plot_correlations 5.918 0.013 6.000
pathways 5.777 0.017 5.830
perform_reactome_analysis 2.224 0.079 10.077
* 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-3.10-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/3.6/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 version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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
2.081 0.147 2.228
ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings
| name | user | system | elapsed | |
| ReactomeAnalysisRequest | 1.194 | 0.097 | 1.305 | |
| ReactomeAnalysisResult-class | 5.925 | 0.026 | 6.004 | |
| add_dataset-ReactomeAnalysisRequest-DGEList-method | 0.828 | 0.060 | 0.896 | |
| add_dataset-ReactomeAnalysisRequest-EList-method | 0.818 | 0.037 | 0.865 | |
| add_dataset-ReactomeAnalysisRequest-ExpressionSet-method | 0.877 | 0.041 | 0.924 | |
| add_dataset-ReactomeAnalysisRequest-data.frame-method | 0.833 | 0.028 | 0.871 | |
| add_dataset | 0.997 | 0.029 | 1.037 | |
| get_reactome_data_types | 0.082 | 0.010 | 0.174 | |
| get_reactome_methods | 0.051 | 0.006 | 0.170 | |
| get_result-ReactomeAnalysisResult-method | 0.183 | 0.007 | 0.196 | |
| get_result | 0.137 | 0.006 | 0.149 | |
| names-ReactomeAnalysisResult-method | 0.167 | 0.007 | 0.174 | |
| open_reactome-ReactomeAnalysisResult-method | 0.169 | 0.006 | 0.176 | |
| open_reactome | 0.147 | 0.005 | 0.152 | |
| pathways-ReactomeAnalysisResult-method | 5.958 | 0.014 | 6.021 | |
| pathways | 5.777 | 0.017 | 5.830 | |
| perform_reactome_analysis | 2.224 | 0.079 | 10.077 | |
| plot_correlations-ReactomeAnalysisResult-method | 5.944 | 0.018 | 6.028 | |
| plot_correlations | 5.918 | 0.013 | 6.000 | |
| plot_volcano-ReactomeAnalysisResult-method | 0.199 | 0.007 | 0.211 | |
| plot_volcano | 0.190 | 0.005 | 0.200 | |
| print-ReactomeAnalysisRequest-method | 0.001 | 0.000 | 0.002 | |
| print-ReactomeAnalysisResult-method | 0.169 | 0.006 | 0.178 | |
| reactome_links-ReactomeAnalysisResult-method | 0.171 | 0.007 | 0.179 | |
| reactome_links | 0.139 | 0.005 | 0.144 | |
| result_types-ReactomeAnalysisResult-method | 0.150 | 0.005 | 0.157 | |
| result_types | 0.179 | 0.006 | 0.186 | |
| set_method-ReactomeAnalysisRequest-method | 0.003 | 0.002 | 0.004 | |
| set_method | 0.002 | 0.001 | 0.003 | |
| set_parameters-ReactomeAnalysisRequest-method | 0.003 | 0.000 | 0.003 | |
| set_parameters | 0.003 | 0.001 | 0.003 | |
| show-ReactomeAnalysisRequest-method | 0.002 | 0.000 | 0.003 | |
| show-ReactomeAnalysisResult-method | 0.156 | 0.006 | 0.164 | |