Johannes Griss
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/ReactomeGSA |
| Branch: RELEASE_3_12 |
| Last Commit: 5752d7f |
| Last Changed Date: 2021-04-16 07:43:14 -0400 (Fri, 16 Apr 2021) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:33:09 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the ReactomeGSA package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1481/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReactomeGSA 1.4.2 (landing page) Johannes Griss
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ReactomeGSA |
| Version: 1.4.2 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ReactomeGSA.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ReactomeGSA_1.4.2.tar.gz |
| StartedAt: 2021-05-06 06:02:59 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 06:30:41 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 1662.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReactomeGSA.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ReactomeGSA.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ReactomeGSA_1.4.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ReactomeGSA.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.4.2'
* 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
plot_gsva_pathway-ReactomeAnalysisResult-method 46.90 0.36 99.63
analyse_sc_clusters-Seurat-method 45.55 1.57 88.10
plot_gsva_heatmap 44.39 0.42 85.01
plot_gsva_heatmap-ReactomeAnalysisResult-method 43.11 1.17 83.85
plot_gsva_pathway 42.86 0.23 90.44
analyse_sc_clusters 38.83 0.28 79.36
analyse_sc_clusters-SingleCellExperiment-method 38.58 0.44 78.65
plot_gsva_pca-ReactomeAnalysisResult-method 34.81 0.28 75.69
plot_gsva_pca 34.11 0.32 74.55
ReactomeAnalysisRequest 5.56 0.57 6.41
perform_reactome_analysis 2.69 0.05 13.92
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_gsva_heatmap 53.67 0.37 94.10
plot_gsva_pathway-ReactomeAnalysisResult-method 50.13 0.49 90.79
plot_gsva_heatmap-ReactomeAnalysisResult-method 44.86 0.48 84.75
analyse_sc_clusters 41.30 0.49 80.58
plot_gsva_pathway 41.26 0.44 82.03
analyse_sc_clusters-SingleCellExperiment-method 40.34 0.41 81.06
plot_gsva_pca-ReactomeAnalysisResult-method 39.86 0.45 80.86
plot_gsva_pca 38.02 0.47 79.16
analyse_sc_clusters-Seurat-method 37.61 0.48 77.11
perform_reactome_analysis 2.79 0.05 14.19
* 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-3.12-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://172.29.0.3/BBS/3.12/bioc/src/contrib/ReactomeGSA_1.4.2.tar.gz && rm -rf ReactomeGSA.buildbin-libdir && mkdir ReactomeGSA.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ReactomeGSA.buildbin-libdir ReactomeGSA_1.4.2.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ReactomeGSA_1.4.2.zip && rm ReactomeGSA_1.4.2.tar.gz ReactomeGSA_1.4.2.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
100 40156 100 40156 0 0 2279k 0 --:--:-- --:--:-- --:--:-- 2450k
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_1.4.2.zip
* DONE (ReactomeGSA)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'ReactomeGSA' successfully unpacked and MD5 sums checked
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ReactomeGSA.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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
1.37 0.06 1.42
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ReactomeGSA.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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
1.87 0.09 1.95
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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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