############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChromSCape_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ChromSCape.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ChromSCape/DESCRIPTION’ ... OK * this is package ‘ChromSCape’ version ‘1.16.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ChromSCape’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... WARNING 'library' or 'require' call not declared from: ‘dplyr’ 'library' or 'require' call to ‘dplyr’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE bams_to_matrix_indexes: no visible binding for global variable ‘files_dir_list’ enrich_TF_ChEA3_genes: no visible binding for global variable ‘CheA3_TF_nTargets’ filter_correlated_cell_scExp: no visible binding for global variable ‘run_tsne’ generate_analysis: no visible global function definition for ‘head’ generate_analysis: no visible binding for global variable ‘k’ generate_analysis: no visible binding for global variable ‘clusterConsensus’ get_most_variable_cyto: no visible binding for global variable ‘cytoBand’ get_most_variable_cyto: no visible binding for global variable ‘Fri_cyto’ num_cell_after_QC_filt_scExp: no visible binding for global variable ‘sample_id’ num_cell_after_QC_filt_scExp: no visible binding for global variable ‘total_counts’ num_cell_scExp: no visible binding for global variable ‘sample_id’ num_cell_scExp: no visible binding for global variable ‘total_counts’ plot_correlation_PCA_scExp: no visible binding for global variable ‘Component’ plot_coverage_BigWig: no visible binding for global variable ‘molecule’ plot_coverage_BigWig: no visible binding for global variable ‘orientation’ plot_coverage_BigWig: no visible binding for global variable ‘Gene’ plot_gain_or_loss_barplots: no visible binding for global variable ‘Gain_or_Loss’ plot_gain_or_loss_barplots: no visible binding for global variable ‘ncells’ plot_gain_or_loss_barplots: no visible binding for global variable ‘cytoBand’ plot_most_contributing_features: no visible binding for global variable ‘genes’ plot_percent_active_feature_scExp: no visible binding for global variable ‘group’ plot_percent_active_feature_scExp: no visible binding for global variable ‘percent_active’ plot_pie_most_contributing_chr: no visible binding for global variable ‘absolute_value’ plot_reduced_dim_scExp: no visible binding for global variable ‘V1’ plot_reduced_dim_scExp: no visible binding for global variable ‘V2’ plot_reduced_dim_scExp: no visible binding for global variable ‘cluster’ plot_top_TF_scExp: no visible binding for global variable ‘TF’ rebin_helper: no visible binding for global variable ‘new_row’ rebin_helper: no visible binding for global variable ‘origin_value’ rebin_matrix: no visible binding for global variable ‘group’ subset_bam_call_peaks: no visible binding for global variable ‘merged_bam’ Undefined global functions or variables: CheA3_TF_nTargets Component Fri_cyto Gain_or_Loss Gene TF V1 V2 absolute_value cluster clusterConsensus cytoBand files_dir_list genes group head k merged_bam molecule ncells new_row orientation origin_value percent_active run_tsne sample_id total_counts Consider adding importFrom("utils", "head") to your NAMESPACE file. * checking Rd files ... NOTE prepare_Rd: raw_counts_to_sparse_matrix.Rd:6-8: Dropping empty section \source * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'generate_analysis.Rd': generate_analysis Code: function(input_data_folder, analysis_name = "Analysis_1", output_directory = "./", input_data_type = c("scBED", "DenseMatrix", "SparseMatrix", "scBAM")[1], feature_count_on = c("bins", "genebody", "peaks")[1], feature_count_parameter = 50000, rebin_sparse_matrix = FALSE, ref_genome = c("hg38", "mm10")[1], run = c("filter", "CNA", "cluster", "consensus", "coverage", "DA", "GSA", "report")[c(1, 3, 5, 6, 7, 8)], min_reads_per_cell = 1000, max_quantile_read_per_cell = 99, n_top_features = 40000, norm_type = "CPM", subsample_n = NULL, exclude_regions = NULL, n_clust = NULL, corr_threshold = 99, percent_correlation = 1, maxK = 10, qval.th = 0.1, logFC.th = 1, enrichment_qval = 0.1, doBatchCorr = FALSE, batch_sels = NULL, control_samples_CNA = NULL, genes_to_plot = c("Krt8", "Krt5", "Tgfb1", "Foxq1", "Cdkn2b", "Cdkn2a", "chr7:15000000-20000000")) Docs: function(input_data_folder, analysis_name = "Analysis_1", output_directory = "./", input_data_type = c("scBED", "DenseMatrix", "SparseMatrix", "scBAM")[1], rebin_sparse_matrix = FALSE, feature_count_on = c("bins", "genebody", "peaks")[1], feature_count_parameter = 50000, ref_genome = c("hg38", "mm10")[1], run = c("filter", "CNA", "cluster", "consensus", "peak_call", "coverage", "DA", "GSA", "report")[c(1, 3, 6, 7, 8, 9)], min_reads_per_cell = 1000, max_quantile_read_per_cell = 99, n_top_features = 40000, norm_type = "CPM", subsample_n = NULL, exclude_regions = NULL, n_clust = NULL, corr_threshold = 99, percent_correlation = 1, maxK = 10, qval.th = 0.1, logFC.th = 1, enrichment_qval = 0.1, doBatchCorr = FALSE, batch_sels = NULL, control_samples_CNA = NULL, genes_to_plot = c("Krt8", "Krt5", "Tgfb1", "Foxq1", "Cdkn2b", "Cdkn2a", "chr7:15000000-20000000")) Mismatches in argument names: Position: 5 Code: feature_count_on Docs: rebin_sparse_matrix Position: 6 Code: feature_count_parameter Docs: feature_count_on Position: 7 Code: rebin_sparse_matrix Docs: feature_count_parameter Mismatches in argument default values: Name: 'run' Code: c("filter", "CNA", "cluster", "consensus", "coverage", "DA", "GSA", "report")[c(1, 3, 5, 6, 7, 8)] Docs: c("filter", "CNA", "cluster", "consensus", "peak_call", "coverage", "DA", "GSA", "report")[c(1, 3, 6, 7, 8, 9)] * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'rebin_matrix.Rd' ‘rebin_function’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot_gain_or_loss_barplots 115.366 0.697 138.158 get_pathway_mat_scExp 63.520 7.213 87.491 calculate_CNA 56.517 4.436 64.042 plot_reduced_dim_scExp_CNA 56.580 0.330 63.690 calculate_cyto_mat 54.701 1.845 60.010 calculate_gain_or_loss 54.386 1.708 60.399 calculate_logRatio_CNA 53.006 1.930 59.784 get_most_variable_cyto 52.675 0.281 65.154 get_cyto_features 49.659 0.256 60.240 differential_activation 12.668 0.071 13.648 preprocessing_filtering_and_reduction 12.294 0.236 13.674 num_cell_after_cor_filt_scExp 12.109 0.120 15.433 filter_correlated_cell_scExp 11.460 0.090 14.222 create_scDataset_raw 9.864 0.709 11.631 CompareedgeRGLM 9.293 0.473 10.230 CompareWilcox 7.690 0.769 7.673 import_scExp 7.901 0.556 10.679 rebin_matrix 7.962 0.066 43.417 plot_reduced_dim_scExp 7.235 0.058 7.990 choose_cluster_scExp 6.434 0.449 7.540 differential_analysis_scExp 6.682 0.045 7.423 consensus_clustering_scExp 5.926 0.426 7.051 plot_violin_feature_scExp 5.197 0.054 5.946 plot_percent_active_feature_scExp 4.992 0.053 5.674 enrich_TF_ChEA3_scExp 1.980 0.113 5.957 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 WARNINGs, 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/ChromSCape.Rcheck/00check.log’ for details.