Multiple platform build/check report for BioC 3.13 - CHECK results for ReactomeGSA on nebbiolo1

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ReactomeGSA_1.6.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/ReactomeGSA.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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_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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                  user system elapsed
plot_gsva_pathway                               32.300  1.476  75.834
plot_gsva_heatmap-ReactomeAnalysisResult-method 32.985  0.705  73.160
plot_gsva_pathway-ReactomeAnalysisResult-method 32.679  0.845  75.763
analyse_sc_clusters-Seurat-method               32.194  1.070  73.308
plot_gsva_pca-ReactomeAnalysisResult-method     31.845  0.859  75.125
plot_gsva_heatmap                               31.641  0.748  73.601
analyse_sc_clusters-SingleCellExperiment-method 30.966  0.797  70.989
analyse_sc_clusters                             30.973  0.728  71.878
plot_gsva_pca                                   30.757  0.735  71.749
perform_reactome_analysis                        2.082  0.060  16.080
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/ReactomeGSA.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL ReactomeGSA
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* installing to library ‘/home/biocbuild/bbs-3.13-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
** 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)

Tests output


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  1.057   0.111   1.150

Example timings

name	user	system	elapsed
ReactomeAnalysisRequest	3.585	0.188	3.779
ReactomeAnalysisResult-class	1.297	0.005	1.305
add_dataset-ReactomeAnalysisRequest-DGEList-method	0.714	0.004	0.719
add_dataset-ReactomeAnalysisRequest-EList-method	0.615	0.020	0.634
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method	0.605	0.000	0.605
add_dataset-ReactomeAnalysisRequest-data.frame-method	0.947	0.008	0.955
add_dataset-ReactomeAnalysisRequest-matrix-method	0.569	0.008	0.577
add_dataset	0.585	0.008	0.593
analyse_sc_clusters-Seurat-method	32.194	1.070	73.308
analyse_sc_clusters-SingleCellExperiment-method	30.966	0.797	70.989
analyse_sc_clusters	30.973	0.728	71.878
get_reactome_data_types	0.079	0.012	1.380
get_reactome_methods	0.136	0.012	2.336
get_result-ReactomeAnalysisResult-method	0.229	0.004	0.233
get_result	0.172	0.008	0.180
names-ReactomeAnalysisResult-method	0.157	0.008	0.165
open_reactome-ReactomeAnalysisResult-method	0.153	0.012	0.165
open_reactome	0.162	0.016	0.178
pathways-ReactomeAnalysisResult-method	1.287	0.032	1.319
pathways	1.362	0.039	1.401
perform_reactome_analysis	2.082	0.060	16.080
plot_correlations-ReactomeAnalysisResult-method	1.377	0.028	1.405
plot_correlations	1.424	0.036	1.460
plot_gsva_heatmap-ReactomeAnalysisResult-method	32.985	0.705	73.160
plot_gsva_heatmap	31.641	0.748	73.601
plot_gsva_pathway-ReactomeAnalysisResult-method	32.679	0.845	75.763
plot_gsva_pathway	32.300	1.476	75.834
plot_gsva_pca-ReactomeAnalysisResult-method	31.845	0.859	75.125
plot_gsva_pca	30.757	0.735	71.749
plot_volcano-ReactomeAnalysisResult-method	0.159	0.004	0.163
plot_volcano	0.189	0.004	0.194
print-ReactomeAnalysisRequest-method	0.000	0.002	0.001
print-ReactomeAnalysisResult-method	0.158	0.001	0.158
reactome_links-ReactomeAnalysisResult-method	0.164	0.003	0.168
reactome_links	0.148	0.007	0.156
result_types-ReactomeAnalysisResult-method	0.157	0.009	0.165
result_types	0.209	0.000	0.209
set_method-ReactomeAnalysisRequest-method	0.003	0.000	0.002
set_method	0.002	0.000	0.001
set_parameters-ReactomeAnalysisRequest-method	0.001	0.000	0.002
set_parameters	0.002	0.000	0.002
show-ReactomeAnalysisRequest-method	0.002	0.000	0.002
show-ReactomeAnalysisResult-method	0.178	0.000	0.178

CHECK results for ReactomeGSA on nebbiolo1

Summary

Command output

Installation output

Tests output

Example timings