Multiple platform build/check report for BioC 3.14 - CHECK results for ReactomeGSA on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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*

Package: ReactomeGSA

Version: 1.8.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ReactomeGSA.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ReactomeGSA_1.8.0.tar.gz

StartedAt: 2022-04-13 01:22:20 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 01:46:24 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 1444.0 seconds

RetCode: 0

Status: OK

CheckDir: ReactomeGSA.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ReactomeGSA.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ReactomeGSA_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ReactomeGSA.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.8.0'
* 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 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_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 ... 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                             39.78   0.55   72.55
plot_gsva_pca                                   38.07   0.31   78.78
plot_gsva_heatmap                               37.88   0.42   78.92
plot_gsva_heatmap-ReactomeAnalysisResult-method 35.98   0.88   68.38
plot_gsva_pathway-ReactomeAnalysisResult-method 35.67   0.89   69.17
analyse_sc_clusters-SingleCellExperiment-method 35.42   0.67   75.89
plot_gsva_pathway                               35.09   0.28   75.02
plot_gsva_pca-ReactomeAnalysisResult-method     34.74   0.41   67.22
analyse_sc_clusters-Seurat-method               34.42   0.66   67.25
ReactomeAnalysisRequest                          4.78   0.50    5.47
perform_reactome_analysis                        2.96   0.04   13.29
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                 user system elapsed
analyse_sc_clusters-Seurat-method               37.95   0.47   69.20
plot_gsva_heatmap-ReactomeAnalysisResult-method 36.98   0.32   69.17
plot_gsva_pathway-ReactomeAnalysisResult-method 35.16   0.28   67.86
plot_gsva_pca                                   34.98   0.29   73.47
plot_gsva_pathway                               34.97   0.26   73.61
analyse_sc_clusters-SingleCellExperiment-method 34.88   0.30   73.55
analyse_sc_clusters                             34.43   0.29   66.90
plot_gsva_heatmap                               34.25   0.36   76.17
plot_gsva_pca-ReactomeAnalysisResult-method     33.09   0.39   65.63
perform_reactome_analysis                        2.57   0.03   14.45
* 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-3.14-bioc/meat/ReactomeGSA.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ReactomeGSA_1.8.0.tar.gz && rm -rf ReactomeGSA.buildbin-libdir && mkdir ReactomeGSA.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ReactomeGSA.buildbin-libdir ReactomeGSA_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ReactomeGSA_1.8.0.zip && rm ReactomeGSA_1.8.0.tar.gz ReactomeGSA_1.8.0.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 44222  100 44222    0     0   283k      0 --:--:-- --:--:-- --:--:--  284k

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  
    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

install for x64

* installing *source* package 'ReactomeGSA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ReactomeGSA' as ReactomeGSA_1.8.0.zip
* DONE (ReactomeGSA)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'ReactomeGSA' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 
   1.79    0.18    1.96


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 
   1.84    0.06    1.89

name	user	system	elapsed
ReactomeAnalysisRequest	4.78	0.50	5.47
ReactomeAnalysisResult-class	1.72	0.00	1.75
add_dataset-ReactomeAnalysisRequest-DGEList-method	0.92	0.00	0.92
add_dataset-ReactomeAnalysisRequest-EList-method	0.91	0.01	0.92
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method	0.89	0.00	0.89
add_dataset-ReactomeAnalysisRequest-data.frame-method	0.97	0.02	0.98
add_dataset-ReactomeAnalysisRequest-matrix-method	1.22	0.01	1.24
add_dataset	0.97	0.00	0.96
analyse_sc_clusters-Seurat-method	34.42	0.66	67.25
analyse_sc_clusters-SingleCellExperiment-method	35.42	0.67	75.89
analyse_sc_clusters	39.78	0.55	72.55
get_reactome_data_types	0.00	0.00	0.85
get_reactome_methods	0.05	0.01	1.29
get_result-ReactomeAnalysisResult-method	0.31	0.00	0.31
get_result	0.28	0.00	0.28
names-ReactomeAnalysisResult-method	0.20	0.02	0.22
open_reactome-ReactomeAnalysisResult-method	0.20	0.01	0.21
open_reactome	0.19	0.02	0.21
pathways-ReactomeAnalysisResult-method	1.51	0.00	1.52
pathways	1.45	0.02	1.47
perform_reactome_analysis	2.96	0.04	13.29
plot_correlations-ReactomeAnalysisResult-method	1.61	0.11	1.72
plot_correlations	1.25	0.00	1.25
plot_gsva_heatmap-ReactomeAnalysisResult-method	35.98	0.88	68.38
plot_gsva_heatmap	37.88	0.42	78.92
plot_gsva_pathway-ReactomeAnalysisResult-method	35.67	0.89	69.17
plot_gsva_pathway	35.09	0.28	75.02
plot_gsva_pca-ReactomeAnalysisResult-method	34.74	0.41	67.22
plot_gsva_pca	38.07	0.31	78.78
plot_heatmap-ReactomeAnalysisResult-method	1.52	0.02	1.53
plot_heatmap	1.86	0.00	1.86
plot_volcano-ReactomeAnalysisResult-method	0.19	0.01	0.20
plot_volcano	0.2	0.0	0.2
print-ReactomeAnalysisRequest-method	0	0	0
print-ReactomeAnalysisResult-method	0.17	0.02	0.19
reactome_links-ReactomeAnalysisResult-method	0.17	0.01	0.19
reactome_links	0.19	0.00	0.18
result_types-ReactomeAnalysisResult-method	0.18	0.00	0.19
result_types	0.21	0.02	0.22
set_method-ReactomeAnalysisRequest-method	0	0	0
set_method	0	0	0
set_parameters-ReactomeAnalysisRequest-method	0.01	0.00	0.01
set_parameters	0	0	0
show-ReactomeAnalysisRequest-method	0	0	0
show-ReactomeAnalysisResult-method	0.16	0.03	0.19

name	user	system	elapsed
ReactomeAnalysisRequest	4.20	0.32	4.53
ReactomeAnalysisResult-class	1.35	0.02	1.36
add_dataset-ReactomeAnalysisRequest-DGEList-method	0.89	0.00	0.89
add_dataset-ReactomeAnalysisRequest-EList-method	1.12	0.00	1.55
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method	1.05	0.03	1.07
add_dataset-ReactomeAnalysisRequest-data.frame-method	0.84	0.02	0.86
add_dataset-ReactomeAnalysisRequest-matrix-method	0.85	0.00	0.84
add_dataset	0.84	0.00	0.85
analyse_sc_clusters-Seurat-method	37.95	0.47	69.20
analyse_sc_clusters-SingleCellExperiment-method	34.88	0.30	73.55
analyse_sc_clusters	34.43	0.29	66.90
get_reactome_data_types	0.00	0.00	0.85
get_reactome_methods	0.07	0.02	1.29
get_result-ReactomeAnalysisResult-method	0.25	0.05	0.30
get_result	0.28	0.01	0.30
names-ReactomeAnalysisResult-method	0.25	0.02	0.26
open_reactome-ReactomeAnalysisResult-method	0.20	0.00	0.21
open_reactome	0.15	0.03	0.19
pathways-ReactomeAnalysisResult-method	1.80	0.06	1.86
pathways	1.23	0.02	1.25
perform_reactome_analysis	2.57	0.03	14.45
plot_correlations-ReactomeAnalysisResult-method	1.78	0.00	1.78
plot_correlations	1.25	0.04	1.30
plot_gsva_heatmap-ReactomeAnalysisResult-method	36.98	0.32	69.17
plot_gsva_heatmap	34.25	0.36	76.17
plot_gsva_pathway-ReactomeAnalysisResult-method	35.16	0.28	67.86
plot_gsva_pathway	34.97	0.26	73.61
plot_gsva_pca-ReactomeAnalysisResult-method	33.09	0.39	65.63
plot_gsva_pca	34.98	0.29	73.47
plot_heatmap-ReactomeAnalysisResult-method	1.56	0.01	1.58
plot_heatmap	1.54	0.00	1.53
plot_volcano-ReactomeAnalysisResult-method	0.26	0.02	0.28
plot_volcano	0.28	0.00	0.28
print-ReactomeAnalysisRequest-method	0	0	0
print-ReactomeAnalysisResult-method	0.21	0.01	0.22
reactome_links-ReactomeAnalysisResult-method	0.18	0.02	0.21
reactome_links	0.19	0.00	0.18
result_types-ReactomeAnalysisResult-method	0.19	0.00	0.19
result_types	0.15	0.03	0.19
set_method-ReactomeAnalysisRequest-method	0	0	0
set_method	0.00	0.01	0.01
set_parameters-ReactomeAnalysisRequest-method	0	0	0
set_parameters	0	0	0
show-ReactomeAnalysisRequest-method	0	0	0
show-ReactomeAnalysisResult-method	0.19	0.00	0.19

CHECK results for ReactomeGSA on tokay2

Summary

Command output

Installation output

Tests output

Example timings