############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL EWCE ### ############################################################################## ############################################################################## * installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'EWCE' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'EWCE' finding HTML links ... done EWCE-package html add_res_to_merging_list html assign_cores html bin_columns_into_quantiles html bin_specificity_into_quantiles html bootstrap_enrichment_test html bootstrap_plot html calc_quantiles html calculate_meanexp_for_level html calculate_specificity_for_level html cell_list_dist html check_annotLevels html check_args_for_bootstrap_plot_generation html check_bootstrap_args html check_controlled_args html check_ewce_expression_data_args html check_ewce_genelist_inputs html check_full_results html check_generate_controlled_bootstrap_geneset html check_group_name html check_nas html check_numeric html check_percent_hits html check_sce html check_species html controlled_geneset_enrichment html convert_new_ewce_to_old html convert_old_ewce_to_new html create_background_multilist html create_list_network html ctd_to_sce html delayedarray_normalize html drop_nonexpressed_cells html drop_nonexpressed_genes html drop_uninformative_genes html dt_to_df html ewce_expression_data html ewce_plot html example_bootstrap_results html example_transcriptome_results html extract_matrix html filter_ctd_genes html filter_genes_without_1to1_homolog html filter_nonorthologs html filter_variance_quantiles html fix_bad_hgnc_symbols html fix_bad_mgi_symbols html fix_celltype_names html fix_celltype_names_full_results html generate_bootstrap_plots html generate_bootstrap_plots_for_transcriptome html generate_celltype_data html generate_controlled_bootstrap_geneset html get_celltype_table html get_ctd_levels html get_exp_data_for_bootstrapped_genes html get_graph_theme html get_sig_results html get_summed_proportions html is_32bit html is_celltypedataset html is_ctd_standardised html is_delayed_array html is_matrix html is_sparse_matrix html list_species html load_rdata html max_ctd_depth html merge_ctd html merge_sce html merge_sce_list html merge_two_expfiles html merged_ewce html message_parallel html messager html myScalesComma html plot_bootstrap_plots html plot_ctd html plot_log_bootstrap_distributions html plot_with_bootstrap_distributions html prep.dendro html prep_dendro html prepare_genesize_control_network html prepare_tt html report_dge html report_results html run_deseq2 html run_limma html run_mast html sce_lists_apply html sce_merged_apply html sct_normalize html standardise_ctd html to_dataframe html to_delayed_array html to_sparse_matrix 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 * DONE (EWCE) Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") : DESCRIPTION file of package 'GeneStructureTools' is missing or broken Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") : DESCRIPTION file of package 'Pviz' is missing or broken done