############################################################################## ############################################################################## ### ### 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_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ReactomeGSA.Rcheck’ * using R version 4.5.0 RC (2025-04-04 r88126) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ReactomeGSA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ReactomeGSA’ version ‘1.22.0’ * 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: load_public_dataset > ### Title: load_public_dataset > ### Aliases: load_public_dataset > > ### ** Examples > > # As a first step, you need to find available datasets > available_datasets <- find_public_datasets("psoriasis tnf") > > # have a quick look at the found datasets > available_datasets[, c("id", "title")] id 1 E-MTAB-6555 2 E-MTAB-6556 title 1 RNA-sequencing of the mRNA transcriptome in blood, across three time-points in severe psoriasis patients treated with the tumor necrosis factor (TNF) inhibitor, etanercept 2 RNA-sequencing of the mRNA transcriptome in lesional and non-lesional skin, across three time-points in severe psoriasis patients treated with the tumor necrosis factor (TNF) inhibitor, etanercept > > # load the first one, use the whole row of the found datasets > # data.frame as the parameter > dataset_1 <- load_public_dataset(available_datasets[1,], verbose = TRUE) Fetching available files No encoding supplied: defaulting to UTF-8. Error in fetch_public_data(dataset_entry, reactome_url) : Request failed (404 - Not Found): Failed to retrieve dataset. Make sure the dataset was successfully loaded beforehand. Calls: load_public_dataset -> fetch_public_data Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed analyse_sc_clusters-Seurat-method 35.698 1.488 73.305 analyse_sc_clusters 33.483 1.465 64.697 analyse_sc_clusters-SingleCellExperiment-method 32.942 1.408 65.070 generate_pseudo_bulk_data 15.004 1.798 16.982 ReactomeAnalysisRequest 5.626 0.396 6.079 * 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-3.21-bioc/meat/ReactomeGSA.Rcheck/00check.log’ for details.