* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’ * installing *source* package ‘IOBR’ ... ** this is package ‘IOBR’ version ‘2.2.3’ ** package ‘IOBR’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package ‘IOBR’ finding HTML links ... done BinomialAUC html BinomialModel html CIBERSORT html CalculatePref html CalculateTimeROC html Construct_con html ConvertRownameToLoci html CoreAlg html DClsei html DCrr html DrawQQPlot html EPIC html Enet html GetFractions.Abbas html GetOutlierGenes html IPS_calculation html LR_cal html MCPcounter.estimate html ParseInputExpression html PlotAUC html PlotTimeROC html ProcessingData html PrognosticAUC html PrognosticModel html PrognosticResult html RegressionResult html RemoveBatchEffect html SplitTrainTest html Top_probe html add_iobr_mirror html add_riskscore html anno_eset html assimilate_data html batch_cor html batch_kruskal html batch_pcc html batch_sig_surv_plot html batch_surv html batch_wilcoxon html best_cutoff html best_cutoff2 html calculate_break_month html calculate_sig_score html calculate_sig_score_integration html calculate_sig_score_pca html calculate_sig_score_ssgsea html calculate_sig_score_zscore html cell_bar_plot html check_cancer_types html check_eset html clear_iobr_cache html combine_pd_eset html count2tpm html creat_folder html deconvo_cibersort html deconvo_epic html deconvo_estimate html deconvo_ips html deconvo_mcpcounter html deconvo_quantiseq html deconvo_ref html deconvo_timer html deconvo_tme html deconvo_xcell html deconvolute_quantiseq.default html deconvolute_timer.default html design_mytheme html doPerm html dot-appendSignatures html dot-build_mut_matrices html dot-create_mut_matrix html download_iobr_data html enrichment_barplot html eset_distribution html estimateScore html exact_pvalue html extract_sc_data html feature_manipulation html feature_select html filterCommonGenes html find_markers_in_bulk html find_mutations html find_outlier_samples html find_variable_genes html fixMixture html format_msigdb html format_signatures html generateRef html generateRef_DEseq2 html generateRef_limma html generateRef_rnaseq html generateRef_seurat html getHRandCIfromCoxph html get_cols html get_cor html get_cor_matrix html get_default_mirrors html get_iobr_cache_dir html get_sig_sc html gsva_use_new_api html high_var_fea html imvigor210_pdata html iobr_cor_plot html iobr_deconvo_pipeline html iobr_deg html iobr_pca html ipsmap html lasso_select html limma.dif html list_github_datasets html list_iobr_mirrors html load_data html log2eset html makeQN html make_mut_matrix html mapGenes html mapbw html mapcolors html merge_duplicate html merge_duplicates html merge_eset html microenvironmentScores html mouse2human_eset html null_models html outputGCT html output_sig html palettes html parallel_doperm html patterns_to_na html pdata_stad html percent_bar_plot html pie_chart html plotPurity html quanTIseq html quantiseq_helper html random_strata_cells html rawEnrichmentAnalysis html rbind_iobr html remove_batcheffect html remove_duplicate_genes html remove_names html reset_iobr_cache_dir html reset_iobr_mirrors html roc_time html scaleCounts html scale_matrix html select_method html set_iobr_cache_dir html sigScore html sig_box html sig_box_batch html sig_forest html sig_group html sig_gsea html sig_heatmap html sig_pheatmap html sig_roc html sig_surv_plot html signature_collection html signature_score_calculation_methods html spillOver html stad_group html subgroup_data html subgroup_survival html surv_group html tcga_rna_preps html tcga_stad_pdata html test_for_infiltration html timer_available_cancers html timer_info html tme_cluster html tme_deconvolution_methods html transformScores html transform_data html xCellAnalysis html xCellSignifcanceBetaDist html xCellSignifcanceRandomMatrix html *** copying figures ** 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 (IOBR)