Johannes Griss
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/ReactomeGSA |
| git_branch: master |
| git_last_commit: 67b778a |
| git_last_commit_date: 2021-11-05 15:55:56 -0400 (Fri, 05 Nov 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:26 -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 ReactomeGSA package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ReactomeGSA.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 1566/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReactomeGSA 1.9.1 (landing page) Johannes Griss
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: ReactomeGSA |
| Version: 1.9.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ReactomeGSA.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ReactomeGSA_1.9.1.tar.gz |
| StartedAt: 2022-03-17 20:01:48 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:13:29 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 700.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ReactomeGSA.Rcheck |
| Warnings: 1 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ReactomeGSA.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ReactomeGSA_1.9.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/ReactomeGSA.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 'ReactomeGSA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ReactomeGSA' version '1.9.1'
* 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 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_gsva_pathway,ReactomeAnalysisResult: no visible binding for global
variable 'cluster_id'
plot_gsva_pathway,ReactomeAnalysisResult: no visible binding for global
variable 'expr'
plot_gsva_pca,ReactomeAnalysisResult: no visible binding for global
variable 'gsva_result'
plot_gsva_pca,ReactomeAnalysisResult: no visible binding for global
variable 'PC1'
plot_gsva_pca,ReactomeAnalysisResult: no visible binding for global
variable 'PC2'
plot_heatmap,ReactomeAnalysisResult: no visible global function
definition for 'desc'
plot_heatmap,ReactomeAnalysisResult: no visible binding for global
variable 'n_sig'
plot_heatmap,ReactomeAnalysisResult: no visible binding for global
variable 'dataset'
plot_heatmap,ReactomeAnalysisResult: no visible binding for global
variable 'Name'
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 Name PC1 PC2 alpha av_foldchange cluster_id combined_sig dataset
desc expr gsva_result n_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 ... WARNING
Codoc mismatches from documentation object 'plot_heatmap,ReactomeAnalysisResult-method':
\S4method{plot_heatmap}{ReactomeAnalysisResult}
Code: function(x, fdr = 0.01, max_pathways = 30, break_long_names =
TRUE, return_data = FALSE)
Docs: function(x, fdr = 0.05, max_pathways = 30, break_long_names =
TRUE, return_data = FALSE)
Mismatches in argument default values:
Name: 'fdr' Code: 0.01 Docs: 0.05
* 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_gsva_pca 35.84 1.03 72.94
plot_gsva_pca-ReactomeAnalysisResult-method 32.60 1.35 68.25
plot_gsva_pathway 31.72 1.47 69.25
plot_gsva_heatmap-ReactomeAnalysisResult-method 30.47 2.10 67.00
plot_gsva_pathway-ReactomeAnalysisResult-method 29.75 1.54 68.53
plot_gsva_heatmap 28.37 1.97 71.11
analyse_sc_clusters-Seurat-method 25.53 3.16 63.37
analyse_sc_clusters-SingleCellExperiment-method 23.77 2.48 68.19
analyse_sc_clusters 23.42 2.22 63.82
perform_reactome_analysis 1.70 0.05 16.15
* 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 WARNING, 1 NOTE
See
'D:/biocbuild/bbs-3.15-bioc/meat/ReactomeGSA.Rcheck/00check.log'
for details.
ReactomeGSA.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL ReactomeGSA
###
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##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'ReactomeGSA' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
in method for 'analyse_sc_clusters' with signature 'object="Seurat"': no definition for class "Seurat"
in method for 'analyse_sc_clusters' with signature 'object="SingleCellExperiment"': no definition for class "SingleCellExperiment"
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
converting help for package 'ReactomeGSA'
finding HTML links ... done
ReactomeAnalysisRequest html
ReactomeAnalysisResult-class html
add_dataset-ReactomeAnalysisRequest-DGEList-method
html
add_dataset-ReactomeAnalysisRequest-EList-method
html
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method
html
add_dataset-ReactomeAnalysisRequest-data.frame-method
html
add_dataset-ReactomeAnalysisRequest-matrix-method
html
add_dataset html
analyse_sc_clusters-Seurat-method html
analyse_sc_clusters-SingleCellExperiment-method
html
analyse_sc_clusters html
break_names html
checkRequestValidity html
check_reactome_url html
convert_reactome_result html
data_frame_as_string html
get_fc_for_dataset html
get_is_sig_dataset html
get_reactome_analysis_result html
get_reactome_analysis_status html
get_reactome_data_types html
get_reactome_methods html
get_result-ReactomeAnalysisResult-method
html
get_result html
is_gsva_result html
names-ReactomeAnalysisResult-method html
open_reactome-ReactomeAnalysisResult-method
html
open_reactome html
pathways-ReactomeAnalysisResult-method
html
pathways html
perform_reactome_analysis html
plot_correlations-ReactomeAnalysisResult-method
html
plot_correlations html
plot_gsva_heatmap-ReactomeAnalysisResult-method
html
plot_gsva_heatmap html
plot_gsva_pathway-ReactomeAnalysisResult-method
html
plot_gsva_pathway html
plot_gsva_pca-ReactomeAnalysisResult-method
html
plot_gsva_pca html
plot_heatmap-ReactomeAnalysisResult-method
html
plot_heatmap html
plot_volcano-ReactomeAnalysisResult-method
html
plot_volcano html
print-ReactomeAnalysisRequest-method html
print-ReactomeAnalysisResult-method html
reactome_links-ReactomeAnalysisResult-method
html
reactome_links html
remove_dataset-ReactomeAnalysisRequest-method
html
remove_dataset html
result_types-ReactomeAnalysisResult-method
html
result_types html
set_method-ReactomeAnalysisRequest-method
html
set_method html
set_parameters-ReactomeAnalysisRequest-method
html
set_parameters html
show-ReactomeAnalysisRequest-method html
show-ReactomeAnalysisResult-method html
start_reactome_analysis 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 (ReactomeGSA)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'perturbatr' is missing or broken
done
ReactomeGSA.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(ReactomeGSA)
>
> test_check("ReactomeGSA")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ]
>
> proc.time()
user system elapsed
1.62 0.17 1.78
ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings
| name | user | system | elapsed | |
| ReactomeAnalysisRequest | 3.52 | 0.46 | 3.97 | |
| ReactomeAnalysisResult-class | 1.15 | 0.04 | 1.22 | |
| add_dataset-ReactomeAnalysisRequest-DGEList-method | 0.74 | 0.06 | 0.79 | |
| add_dataset-ReactomeAnalysisRequest-EList-method | 0.73 | 0.06 | 0.80 | |
| add_dataset-ReactomeAnalysisRequest-ExpressionSet-method | 0.70 | 0.02 | 0.72 | |
| add_dataset-ReactomeAnalysisRequest-data.frame-method | 0.82 | 0.08 | 0.89 | |
| add_dataset-ReactomeAnalysisRequest-matrix-method | 0.53 | 0.15 | 0.69 | |
| add_dataset | 0.64 | 0.11 | 0.75 | |
| analyse_sc_clusters-Seurat-method | 25.53 | 3.16 | 63.37 | |
| analyse_sc_clusters-SingleCellExperiment-method | 23.77 | 2.48 | 68.19 | |
| analyse_sc_clusters | 23.42 | 2.22 | 63.82 | |
| get_reactome_data_types | 0.05 | 0.00 | 1.79 | |
| get_reactome_methods | 0.00 | 0.00 | 2.66 | |
| get_result-ReactomeAnalysisResult-method | 0.16 | 0.00 | 0.17 | |
| get_result | 0.14 | 0.02 | 0.16 | |
| names-ReactomeAnalysisResult-method | 0.14 | 0.01 | 0.19 | |
| open_reactome-ReactomeAnalysisResult-method | 0.12 | 0.00 | 0.12 | |
| open_reactome | 0.13 | 0.00 | 0.13 | |
| pathways-ReactomeAnalysisResult-method | 1.04 | 0.02 | 1.06 | |
| pathways | 0.96 | 0.01 | 0.97 | |
| perform_reactome_analysis | 1.70 | 0.05 | 16.15 | |
| plot_correlations-ReactomeAnalysisResult-method | 1.36 | 0.03 | 1.39 | |
| plot_correlations | 0.97 | 0.03 | 1.00 | |
| plot_gsva_heatmap-ReactomeAnalysisResult-method | 30.47 | 2.10 | 67.00 | |
| plot_gsva_heatmap | 28.37 | 1.97 | 71.11 | |
| plot_gsva_pathway-ReactomeAnalysisResult-method | 29.75 | 1.54 | 68.53 | |
| plot_gsva_pathway | 31.72 | 1.47 | 69.25 | |
| plot_gsva_pca-ReactomeAnalysisResult-method | 32.60 | 1.35 | 68.25 | |
| plot_gsva_pca | 35.84 | 1.03 | 72.94 | |
| plot_heatmap-ReactomeAnalysisResult-method | 1.83 | 0.03 | 1.86 | |
| plot_heatmap | 1.89 | 0.01 | 1.91 | |
| plot_volcano-ReactomeAnalysisResult-method | 0.19 | 0.02 | 0.20 | |
| plot_volcano | 0.21 | 0.02 | 0.23 | |
| print-ReactomeAnalysisRequest-method | 0 | 0 | 0 | |
| print-ReactomeAnalysisResult-method | 0.18 | 0.03 | 0.21 | |
| reactome_links-ReactomeAnalysisResult-method | 0.18 | 0.01 | 0.20 | |
| reactome_links | 0.21 | 0.00 | 0.20 | |
| result_types-ReactomeAnalysisResult-method | 0.18 | 0.02 | 0.21 | |
| result_types | 0.19 | 0.01 | 0.21 | |
| set_method-ReactomeAnalysisRequest-method | 0 | 0 | 0 | |
| set_method | 0.01 | 0.00 | 0.01 | |
| set_parameters-ReactomeAnalysisRequest-method | 0 | 0 | 0 | |
| set_parameters | 0 | 0 | 0 | |
| show-ReactomeAnalysisRequest-method | 0 | 0 | 0 | |
| show-ReactomeAnalysisResult-method | 0.17 | 0.03 | 0.20 | |