############################################################################## ############################################################################## ### ### 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_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/ChromSCape.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ChromSCape/DESCRIPTION’ ... OK * this is package ‘ChromSCape’ version ‘1.6.0’ * 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 * 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 R 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 dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘GenomeInfoDb’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE CompareWilcox: no visible binding for global variable ‘annot.’ 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 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’ rawfile_ToBigWig: no visible binding for global variable ‘filename’ rebin_matrix: no visible global function definition for ‘head’ rebin_matrix: no visible binding for global variable ‘new_row’ rebin_matrix: no visible binding for global variable ‘origin_value’ 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 annot. cluster clusterConsensus cytoBand filename 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 documentation object 'count_coverage': count_coverage Code: function(input, format = "BAM", bins, canonical_chr, n_smoothBin = 5, ref = "hg38", read_size = 101, original_bins = NULL) Docs: function(filename, format = "BAM", bins, canonical_chr, n_smoothBin = 5, ref = "hg38", read_size = 101) Argument names in code not in docs: input original_bins Argument names in docs not in code: filename Mismatches in argument names: Position: 1 Code: input Docs: filename Codoc mismatches from documentation object 'find_clusters_louvain_scExp': find_clusters_louvain_scExp Code: function(scExp, k = 10, resolution = 1, use.dimred = "PCA", type = c("rank", "number", "jaccard")[3], BPPARAM = BiocParallel::bpparam()) Docs: function(scExp, k = 10, use.dimred = "PCA", type = c("rank", "number", "jaccard")[3], BPPARAM = BiocParallel::bpparam()) Argument names in code not in docs: resolution Mismatches in argument names: Position: 3 Code: resolution Docs: use.dimred Position: 4 Code: use.dimred Docs: type Position: 5 Code: type Docs: BPPARAM Codoc mismatches from documentation object 'generate_coverage_tracks': generate_coverage_tracks Code: function(scExp_cf, input, odir, format = "scBED", ref_genome = c("hg38", "mm10")[1], bin_width = 150, n_smoothBin = 5, read_size = 101, progress = NULL) Docs: function(scExp_cf, input, odir, input_type = "scBED", ref_genome = c("hg38", "mm10")[1], bin_width = 150, n_smoothBin = 5, read_size = 101, progress = NULL) Argument names in code not in docs: format Argument names in docs not in code: input_type Mismatches in argument names: Position: 4 Code: format Docs: input_type Codoc mismatches from documentation object 'rawfile_ToBigWig': rawfile_ToBigWig Code: function(input, BigWig_filename, format = "BAM", bin_width = 150, n_smoothBin = 5, ref = "hg38", read_size = 101, original_bins = NULL) Docs: function(input, BigWig_filename, format = "BAM", bin_width = 150, n_smoothBin = 5, ref = "hg38", read_size = 101) Argument names in code not in docs: original_bins * checking Rd \usage sections ... WARNING Undocumented arguments in documentation object 'generate_coverage_tracks' ‘input_type’ 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 99.426 0.459 105.833 calculate_CNA 47.532 1.693 50.019 plot_reduced_dim_scExp_CNA 48.215 0.195 51.213 calculate_cyto_mat 46.453 0.567 48.983 get_most_variable_cyto 46.056 0.395 48.396 calculate_gain_or_loss 45.143 0.499 45.897 calculate_logRatio_CNA 43.280 0.495 43.855 get_cyto_features 41.166 0.398 41.683 num_cell_after_cor_filt_scExp 11.393 0.555 12.465 filter_correlated_cell_scExp 10.799 0.576 11.367 preprocessing_filtering_and_reduction 11.132 0.118 11.796 differential_activation 11.055 0.060 11.135 create_scDataset_raw 9.961 0.494 10.470 CompareedgeRGLM 9.411 0.380 9.804 CompareWilcox 7.524 1.053 6.487 plot_reduced_dim_scExp 8.337 0.063 9.146 import_scExp 6.987 0.115 7.415 choose_cluster_scExp 6.031 0.658 6.715 differential_analysis_scExp 5.788 0.023 5.818 consensus_clustering_scExp 5.181 0.612 5.812 plot_violin_feature_scExp 5.237 0.038 5.557 enrich_TF_ChEA3_scExp 1.999 0.089 7.919 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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-3.15-bioc/meat/ChromSCape.Rcheck/00check.log’ for details.