############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ReactomeGSA.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ReactomeGSA_1.6.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ReactomeGSA.Rcheck' * using R version 4.1.1 (2021-08-10) * 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 '1.6.1' * 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 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_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 ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed analyse_sc_clusters-Seurat-method 36.15 1.35 74.81 plot_gsva_pca 35.32 0.37 71.79 plot_gsva_pathway-ReactomeAnalysisResult-method 35.30 0.35 71.09 plot_gsva_pca-ReactomeAnalysisResult-method 33.94 0.38 69.93 plot_gsva_pathway 33.66 0.34 70.96 analyse_sc_clusters-SingleCellExperiment-method 33.25 0.54 70.32 analyse_sc_clusters 33.20 0.49 69.14 plot_gsva_heatmap-ReactomeAnalysisResult-method 32.11 1.17 68.04 plot_gsva_heatmap 32.72 0.23 68.28 ReactomeAnalysisRequest 4.37 0.40 7.29 perform_reactome_analysis 2.58 0.06 14.45 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot_gsva_pathway 36.58 0.31 72.49 plot_gsva_heatmap-ReactomeAnalysisResult-method 35.99 0.34 72.52 plot_gsva_heatmap 35.17 0.44 72.56 plot_gsva_pathway-ReactomeAnalysisResult-method 34.95 0.36 70.53 analyse_sc_clusters-Seurat-method 34.18 0.49 70.20 plot_gsva_pca 32.84 0.31 68.58 analyse_sc_clusters-SingleCellExperiment-method 31.82 0.37 69.47 analyse_sc_clusters 31.56 0.39 67.36 plot_gsva_pca-ReactomeAnalysisResult-method 30.92 0.30 68.14 perform_reactome_analysis 2.44 0.06 12.91 * 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-3.13-bioc/meat/ReactomeGSA.Rcheck/00check.log' for details.