############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ReactomeGSA_1.8.0.tar.gz && rm -rf ReactomeGSA.buildbin-libdir && mkdir ReactomeGSA.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ReactomeGSA.buildbin-libdir ReactomeGSA_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ReactomeGSA_1.8.0.zip && rm ReactomeGSA_1.8.0.tar.gz ReactomeGSA_1.8.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 44222 100 44222 0 0 283k 0 --:--:-- --:--:-- --:--:-- 284k install for i386 * installing *source* package 'ReactomeGSA' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading in method for 'analyse_sc_clusters' with signature 'object="Seurat"': no definition for class "Seurat" in method for 'analyse_sc_clusters' with signature 'object="SingleCellExperiment"': no definition for class "SingleCellExperiment" in method for 'add_dataset' with signature 'request="ReactomeAnalysisRequest",expression_values="EList"': no definition for class "EList" in method for 'add_dataset' with signature 'request="ReactomeAnalysisRequest",expression_values="DGEList"': no definition for class "DGEList" in method for 'add_dataset' with signature 'request="ReactomeAnalysisRequest",expression_values="ExpressionSet"': no definition for class "ExpressionSet" ** help *** installing help indices converting help for package 'ReactomeGSA' finding HTML links ... done ReactomeAnalysisRequest html ReactomeAnalysisResult-class html add_dataset-ReactomeAnalysisRequest-DGEList-method html add_dataset-ReactomeAnalysisRequest-EList-method html add_dataset-ReactomeAnalysisRequest-ExpressionSet-method html add_dataset-ReactomeAnalysisRequest-data.frame-method html add_dataset-ReactomeAnalysisRequest-matrix-method html add_dataset html analyse_sc_clusters-Seurat-method html analyse_sc_clusters-SingleCellExperiment-method html analyse_sc_clusters html break_names html checkRequestValidity html check_reactome_url html convert_reactome_result html data_frame_as_string html get_fc_for_dataset html get_is_sig_dataset html get_reactome_analysis_result html get_reactome_analysis_status html get_reactome_data_types html get_reactome_methods html get_result-ReactomeAnalysisResult-method html get_result html is_gsva_result html names-ReactomeAnalysisResult-method html open_reactome-ReactomeAnalysisResult-method html open_reactome html pathways-ReactomeAnalysisResult-method html pathways html perform_reactome_analysis html plot_correlations-ReactomeAnalysisResult-method html plot_correlations html plot_gsva_heatmap-ReactomeAnalysisResult-method html plot_gsva_heatmap html plot_gsva_pathway-ReactomeAnalysisResult-method html plot_gsva_pathway html plot_gsva_pca-ReactomeAnalysisResult-method html plot_gsva_pca html plot_heatmap-ReactomeAnalysisResult-method html plot_heatmap html plot_volcano-ReactomeAnalysisResult-method html plot_volcano html print-ReactomeAnalysisRequest-method html print-ReactomeAnalysisResult-method html reactome_links-ReactomeAnalysisResult-method html reactome_links html remove_dataset-ReactomeAnalysisRequest-method html remove_dataset html result_types-ReactomeAnalysisResult-method html result_types html set_method-ReactomeAnalysisRequest-method html set_method html set_parameters-ReactomeAnalysisRequest-method html set_parameters html show-ReactomeAnalysisRequest-method html show-ReactomeAnalysisResult-method html start_reactome_analysis html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'ReactomeGSA' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'ReactomeGSA' as ReactomeGSA_1.8.0.zip * DONE (ReactomeGSA) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'ReactomeGSA' successfully unpacked and MD5 sums checked