############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL ChromSCape ### ############################################################################## ############################################################################## * installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'ChromSCape' ... ** using staged installation ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c as_dist.cpp -o as_dist.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ChromSCape.dll tmp.def RcppExports.o as_dist.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-ChromSCape/00new/ChromSCape/libs/x64 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'ChromSCape' finding HTML links ... done CheA3_TF_nTargets html CompareWilcox html CompareedgeRGLM html DA_custom html DA_one_vs_rest html DA_pairwise html H1proportion html annotToCol2 html annotation_from_merged_peaks html anocol_binary html anocol_categorical html bams_to_matrix_indexes html beds_to_matrix_indexes html calculate_CNA html calculate_cyto_mat html calculate_gain_or_loss html calculate_logRatio_CNA html call_macs2_merge_peaks html changeRange html check_correct_datamatrix html choose_cluster_scExp html choose_perplexity html col2hex html colors_scExp html combine_datamatrix html combine_enrichmentTests html concatenate_scBed_into_clusters html consensus_clustering_scExp html correlation_and_hierarchical_clust_scExp html count_coverage html create_project_folder html create_sample_name_mat html create_scDataset_raw html create_scExp html define_feature html detect_samples html differential_activation html differential_analysis_scExp html distPearson html enrich_TF_ChEA3_genes html enrich_TF_ChEA3_scExp html enrichmentTest html exclude_features_scExp html feature_annotation_scExp html filter_correlated_cell_scExp html filter_genes_with_refined_peak_annotation html filter_scExp html find_clusters_louvain_scExp html find_top_features html gene_set_enrichment_analysis_scExp html generate_analysis html generate_count_matrix html generate_coverage_tracks html generate_feature_names html generate_report html getExperimentNames html getMainExperiment html get_color_dataframe_from_input html get_cyto_features html get_genomic_coordinates html get_most_variable_cyto html gg_fill_hue html groupMat html has_genomic_coordinates html hclustAnnotHeatmapPlot html hg38.GeneTSS html hg38.chromosomes html hg38.cytoBand html imageCol html import_count_input_files html import_scExp html index_peaks_barcodes_to_matrix_indexes html inter_correlation_scExp html intra_correlation_scExp html launchApp html load_MSIGdb html merge_MACS2_peaks html mm10.GeneTSS html mm10.chromosomes html mm10.cytoBand html normalize_scExp html num_cell_after_QC_filt_scExp html num_cell_after_cor_filt_scExp html num_cell_before_cor_filt_scExp html num_cell_in_cluster_scExp html num_cell_scExp html pca_irlba_for_sparseMatrix html peaks_to_bins html plot_cluster_consensus_scExp html plot_coverage_BigWig html plot_differential_summary_scExp html plot_differential_volcano_scExp html plot_distribution_scExp html plot_gain_or_loss_barplots html plot_heatmap_scExp html plot_inter_correlation_scExp html plot_intra_correlation_scExp html plot_most_contributing_features html plot_pie_most_contributing_chr html plot_reduced_dim_scExp html plot_reduced_dim_scExp_CNA html plot_top_TF_scExp html preprocess_CPM html preprocess_RPKM html preprocess_TFIDF html preprocess_TPM html preprocess_feature_size_only html preprocessing_filtering_and_reduction html raw_counts_to_sparse_matrix html rawfile_ToBigWig html read_count_mat_with_separated_chr_start_end html read_sparse_matrix html reduce_dim_batch_correction html reduce_dims_scExp html remove_chr_M_fun html remove_non_canonical_fun html results_enrichmentTest html retrieve_top_bot_features_pca html run_pairwise_tests html run_tsne_scExp html scExp html separate_BAM_into_clusters html separator_count_mat html smoothBin html subsample_scExp html subset_bam_call_peaks html summary_DA html swapAltExp_sameColData html table_enriched_genes_scExp html warning_DA html warning_filter_correlated_cell_scExp html warning_plot_reduced_dim_scExp html warning_raw_counts_to_sparse_matrix html wrapper_Signac_FeatureMatrix 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 (ChromSCape) Making 'packages.html' ... done