############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ReactomeGSA_1.21.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ReactomeGSA.Rcheck’ * using R Under development (unstable) (2025-01-20 r87609) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘ReactomeGSA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ReactomeGSA’ version ‘1.21.2’ * 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 loading without being on the library search path ... 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot_gsva_heatmap-ReactomeAnalysisResult-method 37.355 2.860 70.034 plot_gsva_pca-ReactomeAnalysisResult-method 37.656 2.386 100.142 plot_gsva_heatmap 37.089 2.746 100.255 plot_gsva_pathway-ReactomeAnalysisResult-method 33.879 2.138 67.678 plot_gsva_pathway 32.939 1.689 62.590 plot_gsva_pca 32.504 1.943 66.023 analyse_sc_clusters-Seurat-method 33.278 1.147 74.203 analyse_sc_clusters-SingleCellExperiment-method 31.920 1.277 67.862 analyse_sc_clusters 31.836 1.087 66.068 generate_pseudo_bulk_data 15.133 1.962 17.123 perform_reactome_analysis 6.396 0.671 53.752 ReactomeAnalysisRequest 4.821 0.288 5.117 load_public_dataset 3.940 0.263 38.652 * 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 re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘analysing-scRNAseq.Rmd’ using rmarkdown | | | 0% | |= | 2% | |=== | 4% | |==== | 6% | |===== | 8% | |======= | 10% | |======== | 12% | |========= | 13% | |=========== | 15% | |============ | 17% | |============= | 19% | |=============== | 21% | |================ | 23% | |================== | 25% | |=================== | 27% | |==================== | 29% | |====================== | 31% | |======================= | 33% | |======================== | 35% | |========================== | 37% | |=========================== | 38% | |============================ | 40% | |============================== | 42% | |=============================== | 44% | |================================ | 46% | |================================== | 48% | |=================================== | 50% | |==================================== | 52% | |====================================== | 54% | |======================================= | 56% | |======================================== | 58% | |========================================== | 60% | |=========================================== | 62% | |============================================ | 63% | |============================================== | 65% | |=============================================== | 67% | |================================================ | 69% | |================================================== | 71% | |=================================================== | 73% | |==================================================== | 75% | |====================================================== | 77% | |======================================================= | 79% | |========================================================= | 81% | |========================================================== | 83% | |=========================================================== | 85% | |============================================================= | 87% | |============================================================== | 88% | |=============================================================== | 90% | |================================================================= | 92% | |================================================================== | 94% | |=================================================================== | 96% | |===================================================================== | 98% | |======================================================================| 100% | | | 0% | |=== | 4% | |====== | 8% | |========= | 12% | |============ | 17% | |=============== | 21% | |================== | 25% | |==================== | 29% | |======================= | 33% | |========================== | 38% | |============================= | 42% | |================================ | 46% | |=================================== | 50% | |====================================== | 54% | |========================================= | 58% | |============================================ | 62% | |=============================================== | 67% | |================================================== | 71% | |==================================================== | 75% | |======================================================= | 79% | |========================================================== | 83% | |============================================================= | 88% | |================================================================ | 92% | |=================================================================== | 96% | |======================================================================| 100% Quitting from lines 193-199 [unnamed-chunk-11] (analysing-scRNAseq.Rmd) Error: processing vignette 'analysing-scRNAseq.Rmd' failed with diagnostics: unable to find an inherited method for function 'pathways' for signature 'x = "NULL"' --- failed re-building ‘analysing-scRNAseq.Rmd’ --- re-building ‘reanalysing-public-data.Rmd’ using rmarkdown --- finished re-building ‘reanalysing-public-data.Rmd’ --- re-building ‘using-reactomegsa.Rmd’ using rmarkdown --- finished re-building ‘using-reactomegsa.Rmd’ SUMMARY: processing the following file failed: ‘analysing-scRNAseq.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.21-bioc/meat/ReactomeGSA.Rcheck/00check.log’ for details.