############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/tidybulk_1.4.0.tar.gz && rm -rf tidybulk.buildbin-libdir && mkdir tidybulk.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=tidybulk.buildbin-libdir tidybulk_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL tidybulk_1.4.0.zip && rm tidybulk_1.4.0.tar.gz tidybulk_1.4.0.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 21 3549k 21 769k 0 0 1870k 0 0:00:01 --:--:-- 0:00:01 1868k 100 3549k 100 3549k 0 0 3532k 0 0:00:01 0:00:01 --:--:-- 3535k install for i386 * installing *source* package 'tidybulk' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Note: wrong number of arguments to 'floor' Note: wrong number of arguments to 'floor' ** help *** installing help indices converting help for package 'tidybulk' finding HTML links ... done X_cibersort html add_attr html add_class html add_scaled_counts_bulk.calcNormFactor html add_scaled_counts_bulk.get_low_expressed html adjust_abundance-methods html aggregate_duplicated_transcripts_bulk html aggregate_duplicates-methods html arrange-methods html as_SummarizedExperiment-methods html as_matrix html bind-methods html breast_tcga_mini_SE html check_if_counts_is_na html check_if_duplicated_genes html check_if_wrong_input html cluster_elements-methods html counts_SE html counts_ensembl html create_tt_from_bam_sam_bulk html create_tt_from_tibble_bulk html deconvolve_cellularity-methods html describe_transcript-methods html distinct-methods html dplyr-methods html drop_attr html drop_class html ensembl_symbol_mapping html ensembl_to_symbol-methods html error_if_counts_is_na html error_if_duplicated_genes html error_if_log_transformed html error_if_wrong_input html fill_NA_using_formula html fill_NA_using_value html fill_NA_with_row_median html fill_missing_abundance-methods html filter-methods html flybaseIDs html get_abundance_norm_if_exists html get_adjusted_counts_for_unwanted_variation_bulk html get_bibliography-methods html get_cell_type_proportions html get_clusters_SNN_bulk html get_clusters_SNN_bulk_SE html get_clusters_kmeans_bulk html get_clusters_kmeans_bulk_SE html get_differential_transcript_abundance_bulk html get_differential_transcript_abundance_bulk_SE html get_differential_transcript_abundance_bulk_voom html get_differential_transcript_abundance_bulk_voom_SE html get_differential_transcript_abundance_deseq2 html get_differential_transcript_abundance_deseq2_SE html get_elements html get_elements_features html get_elements_features_abundance html get_reduced_dimensions_MDS_bulk html get_reduced_dimensions_MDS_bulk_SE html get_reduced_dimensions_PCA_bulk html get_reduced_dimensions_PCA_bulk_SE html get_reduced_dimensions_TSNE_bulk html get_reduced_dimensions_TSNE_bulk_SE html get_rotated_dimensions html get_sample html get_sample_counts html get_sample_transcript html get_sample_transcript_counts html get_scaled_counts_bulk html get_symbol_from_ensembl html get_transcript html get_x_y_annotation_columns html group_by-methods html identify_abundant-methods html ifelse2_pipe html ifelse_pipe html impute_missing_abundance-methods html join-methods html keep_abundant-methods html keep_variable-methods html keep_variable_transcripts html keep_variable_transcripts_SE html log10_reverse_trans html logit_trans html mutate-methods html nest-methods html parse_formula html parse_formula_survival html pipe html pivot_sample-methods html pivot_transcript-methods html prepend html quo_names html reduce_dimensions-methods html reexports html remove_redundancy-methods html remove_redundancy_elements_though_reduced_dimensions html remove_redundancy_elements_though_reduced_dimensions_SE html remove_redundancy_elements_through_correlation html remove_redundancy_elements_through_correlation_SE html rename-methods html rotate_dimensions-methods html rowwise-methods html run_epic html run_llsr html scale_abundance-methods html scale_design html se html se_mini html select_closest_pairs html summarise-methods html symbol_to_entrez html test_deseq2_df html test_differential_abundance-methods html test_differential_cellularity-methods html test_differential_cellularity_ html test_gene_enrichment-methods html test_gene_enrichment_bulk_EGSEA html test_gene_overrepresentation-methods html test_gene_rank-methods html test_stratification_cellularity-methods html test_stratification_cellularity_ html tidybulk-methods html tidybulk_SAM_BAM-methods html tidybulk_to_SummarizedExperiment html vignette_manuscript_signature_boxplot html vignette_manuscript_signature_tsne html vignette_manuscript_signature_tsne2 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 install for x64 * installing *source* package 'tidybulk' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'tidybulk' as tidybulk_1.4.0.zip * DONE (tidybulk) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'tidybulk' successfully unpacked and MD5 sums checked