Johannes Griss
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/ReactomeGSA |
| Branch: RELEASE_3_11 |
| Last Commit: bf92742 |
| Last Changed Date: 2020-09-01 14:49:29 -0400 (Tue, 01 Sep 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:34 -0400 (Sat, 17 Oct 2020).
| 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 1445/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ReactomeGSA 1.2.4 Johannes Griss
| malbec2 | Linux (Ubuntu 18.04.4 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: 1.2.4 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ReactomeGSA.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ReactomeGSA_1.2.4.tar.gz |
| StartedAt: 2020-10-17 07:22:19 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 07:48:10 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 1551.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReactomeGSA.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ReactomeGSA.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ReactomeGSA_1.2.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/ReactomeGSA.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.2.4'
* 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-SingleCellExperiment-method 51.94 0.88 78.56
analyse_sc_clusters 50.00 0.47 77.63
plot_gsva_pca-ReactomeAnalysisResult-method 49.66 0.62 115.25
plot_gsva_heatmap-ReactomeAnalysisResult-method 47.84 1.25 75.41
plot_gsva_pathway-ReactomeAnalysisResult-method 48.58 0.50 75.97
plot_gsva_pathway 48.17 0.36 72.83
analyse_sc_clusters-Seurat-method 45.30 0.98 73.36
plot_gsva_heatmap 44.83 0.38 70.17
plot_gsva_pca 42.77 0.48 68.90
ReactomeAnalysisRequest 6.54 0.74 22.63
perform_reactome_analysis 2.92 0.07 13.50
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_gsva_pca 43.90 0.52 69.86
analyse_sc_clusters 42.43 0.62 70.38
plot_gsva_heatmap 40.85 0.39 66.50
analyse_sc_clusters-SingleCellExperiment-method 40.43 0.55 104.34
analyse_sc_clusters-Seurat-method 40.10 0.52 66.48
plot_gsva_pathway-ReactomeAnalysisResult-method 39.47 0.41 66.14
plot_gsva_pathway 37.59 0.62 63.37
plot_gsva_heatmap-ReactomeAnalysisResult-method 37.50 0.31 64.29
plot_gsva_pca-ReactomeAnalysisResult-method 35.83 0.33 61.30
ReactomeAnalysisRequest 5.61 0.45 21.73
perform_reactome_analysis 2.44 0.05 14.64
* 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-3.11-bioc/meat/ReactomeGSA.Rcheck/00check.log'
for details.
ReactomeGSA.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/ReactomeGSA_1.2.4.tar.gz && rm -rf ReactomeGSA.buildbin-libdir && mkdir ReactomeGSA.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ReactomeGSA.buildbin-libdir ReactomeGSA_1.2.4.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL ReactomeGSA_1.2.4.zip && rm ReactomeGSA_1.2.4.tar.gz ReactomeGSA_1.2.4.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 39819 100 39819 0 0 595k 0 --:--:-- --:--:-- --:--:-- 670k
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_1.2.4.zip
* DONE (ReactomeGSA)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'ReactomeGSA' successfully unpacked and MD5 sums checked
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ReactomeGSA.Rcheck/tests_i386/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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")
== testthat results ===========================================================
[ OK: 17 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
1.71 0.17 1.89
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ReactomeGSA.Rcheck/tests_x64/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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")
== testthat results ===========================================================
[ OK: 17 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
2.14 0.07 2.21
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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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