Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2024-05-28 11:35:50 -0400 (Tue, 28 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4752
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4517
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 1713/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReactomeGSA 1.18.0  (landing page)
Johannes Griss
Snapshot Date: 2024-05-27 14:00:08 -0400 (Mon, 27 May 2024)
git_url: https://git.bioconductor.org/packages/ReactomeGSA
git_branch: RELEASE_3_19
git_last_commit: 4bfdb0f
git_last_commit_date: 2024-04-30 11:17:23 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    TIMEOUT  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for ReactomeGSA on lconway


To the developers/maintainers of the ReactomeGSA package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: ReactomeGSA
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReactomeGSA_1.18.0.tar.gz
StartedAt: 2024-05-27 23:07:09 -0400 (Mon, 27 May 2024)
EndedAt: 2024-05-27 23:16:12 -0400 (Mon, 27 May 2024)
EllapsedTime: 542.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: ReactomeGSA.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReactomeGSA_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ReactomeGSA.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReactomeGSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ReactomeGSA’ version ‘1.18.0’
* 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 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 code 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 whether startup messages can be suppressed ... 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 ... ERROR
Running examples in ‘ReactomeGSA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_gsva_heatmap
> ### Title: plot_gsva_heatmap
> ### Aliases: plot_gsva_heatmap
> 
> ### ** Examples
> 
> # load the scRNA-seq example data
> library(ReactomeGSA.data)
Loading required package: limma
Loading required package: edgeR
Loading required package: Seurat
Loading required package: SeuratObject
Loading required package: sp

Attaching package: ‘SeuratObject’

The following objects are masked from ‘package:base’:

    intersect, t

> data(jerby_b_cells)
> 
> # perform the GSVA analysis
> gsva_result <- analyse_sc_clusters(jerby_b_cells, verbose = FALSE)
Converting expression data to string... (This may take a moment)
Conversion complete
Compressing request data...
Reactome Analysis submitted succesfully
> 
> # plot the heatmap
> relevant_pathways <- c("R-HSA-983170", "R-HSA-388841", "R-HSA-2132295", 
+                        "R-HSA-983705", "R-HSA-5690714")
> plot_gsva_heatmap(gsva_result, 
+                   pathway_ids = relevant_pathways, # limit to these pathways
+                   margins = c(6,30), # adapt the figure margins in heatmap.2
+                   dendrogram = "col", # only plot column dendrogram
+                   scale = "row", # scale for each pathway
+                   key = FALSE, # don't display the color key
+                   lwid=c(0.1,4)) # remove the white space on the left
Error: C stack usage  7979480 is too close to the limit
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/ReactomeGSA.Rcheck/00check.log’
for details.


Installation output

ReactomeGSA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ReactomeGSA
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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”
** 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

ReactomeGSA.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
  1.793   0.210   2.002 

Example timings

ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings

nameusersystemelapsed
ReactomeAnalysisRequest6.2020.4616.755
ReactomeAnalysisResult-class1.5540.0291.599
add_dataset-ReactomeAnalysisRequest-DGEList-method0.9930.0611.064
add_dataset-ReactomeAnalysisRequest-EList-method0.8400.0490.899
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method0.8540.0360.901
add_dataset-ReactomeAnalysisRequest-data.frame-method1.1950.0541.265
add_dataset-ReactomeAnalysisRequest-matrix-method0.8380.0560.908
add_dataset0.8250.0490.883
analyse_sc_clusters-Seurat-method39.197 1.78185.039
analyse_sc_clusters-SingleCellExperiment-method35.858 1.73982.561
analyse_sc_clusters35.904 1.84586.197
find_public_datasets0.1090.0202.150
get_public_species0.0280.0040.287
get_reactome_data_types0.0550.0080.580
get_reactome_methods0.0970.0151.388
get_result-ReactomeAnalysisResult-method0.2500.0130.266
get_result0.2660.0150.286
load_public_dataset 1.672 0.16634.715
names-ReactomeAnalysisResult-method0.2420.0120.258
open_reactome-ReactomeAnalysisResult-method0.2600.0140.277
open_reactome0.2890.0580.353
pathways-ReactomeAnalysisResult-method1.5470.0291.591
pathways1.5880.0291.634
perform_reactome_analysis 3.158 0.31916.755
plot_correlations-ReactomeAnalysisResult-method1.7050.0511.775
plot_correlations1.5260.0221.560
plot_gsva_heatmap-ReactomeAnalysisResult-method38.374 1.51789.982