############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ReactomeGSA_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ReactomeGSA.Rcheck’ * using R Under development (unstable) (2023-02-14 r83833) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 * running under: Ubuntu 20.04.6 LTS * using session charset: UTF-8 * checking for file ‘ReactomeGSA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ReactomeGSA’ version ‘1.13.0’ * 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 R 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 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 ... WARNING Codoc mismatches from documentation object 'plot_heatmap,ReactomeAnalysisResult-method': \S4method{plot_heatmap}{ReactomeAnalysisResult} Code: function(x, fdr = 0.01, max_pathways = 30, break_long_names = TRUE, return_data = FALSE) Docs: function(x, fdr = 0.05, max_pathways = 30, break_long_names = TRUE, return_data = FALSE) Mismatches in argument default values: Name: 'fdr' Code: 0.01 Docs: 0.05 * 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_pca 35.857 0.876 97.589 plot_gsva_pca-ReactomeAnalysisResult-method 35.194 0.970 94.853 plot_gsva_pathway 33.931 1.267 96.690 analyse_sc_clusters-Seurat-method 33.973 1.021 95.493 analyse_sc_clusters 32.432 1.721 95.598 plot_gsva_heatmap-ReactomeAnalysisResult-method 32.758 1.128 92.171 analyse_sc_clusters-SingleCellExperiment-method 32.579 1.078 95.877 plot_gsva_heatmap 32.541 1.013 93.890 plot_gsva_pathway-ReactomeAnalysisResult-method 31.884 1.285 93.730 perform_reactome_analysis 2.042 0.193 17.425 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘analysing-scRNAseq.Rmd’ using ‘UTF-8’... OK ‘using-reactomegsa.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘analysing-scRNAseq.Rmd’ using rmarkdown Quitting from lines 38-47 (analysing-scRNAseq.Rmd) Error: processing vignette 'analysing-scRNAseq.Rmd' failed with diagnostics: trying to use CRAN without setting a mirror --- failed re-building ‘analysing-scRNAseq.Rmd’ --- re-building ‘using-reactomegsa.Rmd’ using rmarkdown Quitting from lines 42-47 (using-reactomegsa.Rmd) Error: processing vignette 'using-reactomegsa.Rmd' failed with diagnostics: trying to use CRAN without setting a mirror --- failed re-building ‘using-reactomegsa.Rmd’ SUMMARY: processing the following files failed: ‘analysing-scRNAseq.Rmd’ ‘using-reactomegsa.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/ReactomeGSA.Rcheck/00check.log’ for details.