############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * 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.