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This page was generated on 2021-10-15 15:06:18 -0400 (Fri, 15 Oct 2021).
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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 1534/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReactomeGSA 1.6.1 (landing page) Johannes Griss
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ReactomeGSA |
| Version: 1.6.1 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ReactomeGSA.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ReactomeGSA_1.6.1.tar.gz |
| StartedAt: 2021-10-15 04:15:34 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 04:39:14 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 1419.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReactomeGSA.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ReactomeGSA.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ReactomeGSA_1.6.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ReactomeGSA.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.6.1'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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_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 PC1 PC2 alpha av_foldchange cluster_id combined_sig expr
gsva_result
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
analyse_sc_clusters-Seurat-method 36.15 1.35 74.81
plot_gsva_pca 35.32 0.37 71.79
plot_gsva_pathway-ReactomeAnalysisResult-method 35.30 0.35 71.09
plot_gsva_pca-ReactomeAnalysisResult-method 33.94 0.38 69.93
plot_gsva_pathway 33.66 0.34 70.96
analyse_sc_clusters-SingleCellExperiment-method 33.25 0.54 70.32
analyse_sc_clusters 33.20 0.49 69.14
plot_gsva_heatmap-ReactomeAnalysisResult-method 32.11 1.17 68.04
plot_gsva_heatmap 32.72 0.23 68.28
ReactomeAnalysisRequest 4.37 0.40 7.29
perform_reactome_analysis 2.58 0.06 14.45
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_gsva_pathway 36.58 0.31 72.49
plot_gsva_heatmap-ReactomeAnalysisResult-method 35.99 0.34 72.52
plot_gsva_heatmap 35.17 0.44 72.56
plot_gsva_pathway-ReactomeAnalysisResult-method 34.95 0.36 70.53
analyse_sc_clusters-Seurat-method 34.18 0.49 70.20
plot_gsva_pca 32.84 0.31 68.58
analyse_sc_clusters-SingleCellExperiment-method 31.82 0.37 69.47
analyse_sc_clusters 31.56 0.39 67.36
plot_gsva_pca-ReactomeAnalysisResult-method 30.92 0.30 68.14
perform_reactome_analysis 2.44 0.06 12.91
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.13-bioc/meat/ReactomeGSA.Rcheck/00check.log'
for details.
ReactomeGSA.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ReactomeGSA_1.6.1.tar.gz && rm -rf ReactomeGSA.buildbin-libdir && mkdir ReactomeGSA.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ReactomeGSA.buildbin-libdir ReactomeGSA_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ReactomeGSA_1.6.1.zip && rm ReactomeGSA_1.6.1.tar.gz ReactomeGSA_1.6.1.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
9 40687 9 3841 0 0 47484 0 --:--:-- --:--:-- --:--:-- 47419
100 40687 100 40687 0 0 261k 0 --:--:-- --:--:-- --:--:-- 261k
install for i386
* 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
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_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
install for x64
* installing *source* package 'ReactomeGSA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ReactomeGSA' as ReactomeGSA_1.6.1.zip
* DONE (ReactomeGSA)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'ReactomeGSA' successfully unpacked and MD5 sums checked
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ReactomeGSA.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
1.29 0.17 1.45
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ReactomeGSA.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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
1.35 0.20 1.54
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ReactomeGSA.Rcheck/examples_i386/ReactomeGSA-Ex.timings
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ReactomeGSA.Rcheck/examples_x64/ReactomeGSA-Ex.timings
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