############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scPipe.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scPipe_2.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/scPipe.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scPipe/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘scPipe’ version ‘2.5.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘scPipe’ can be installed ... OK * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... NOTE installed size is 15.9Mb sub-directories of 1Mb or more: extdata 12.1Mb libs 2.5Mb * 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 ... NOTE Namespaces in Imports field not imported from: ‘flexmix’ ‘vctrs’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE sc_atac_feature_counting: warning in sc_atac_create_sce(input_folder = output_folder, organism = organism, sample = sample_name, feature_type = feature_type, pheno_data = pheno_data, report = create_report): partial argument match of 'sample' to 'sample_name' sc_aligning: no visible binding for global variable ‘Var1’ sc_aligning: no visible binding for global variable ‘Freq’ sc_atac_bam_tagging: no visible binding for global variable ‘.N’ sc_atac_bam_tagging: no visible binding for global variable ‘count’ sc_atac_bam_tagging: no visible binding for global variable ‘.SD’ sc_atac_create_cell_qc_metrics: no visible binding for global variable ‘seqnames’ sc_atac_create_cell_qc_metrics: no visible binding for global variable ‘start’ sc_atac_create_cell_qc_metrics: no visible binding for global variable ‘end’ sc_atac_create_cell_qc_metrics: no visible binding for global variable ‘barcode’ sc_atac_create_cell_qc_metrics: no visible binding for global variable ‘count’ sc_atac_feature_counting: no visible binding for global variable ‘start’ sc_atac_feature_counting: no visible binding for global variable ‘end’ sc_atac_feature_counting: no visible global function definition for ‘write.csv’ sc_atac_plot_cells_per_feature: no visible binding for global variable ‘log_cells_per_feature’ sc_atac_plot_cells_per_feature: no visible binding for global variable ‘..count..’ sc_atac_plot_features_per_cell: no visible binding for global variable ‘log_features_per_cell’ sc_atac_plot_features_per_cell: no visible binding for global variable ‘..count..’ sc_atac_plot_fragments_cells_per_feature: no visible binding for global variable ‘log_counts_per_feature’ sc_atac_plot_fragments_cells_per_feature: no visible binding for global variable ‘log_cells_per_feature’ sc_atac_plot_fragments_features_per_cell: no visible binding for global variable ‘log_counts_per_cell’ sc_atac_plot_fragments_features_per_cell: no visible binding for global variable ‘log_features_per_cell’ sc_atac_plot_fragments_per_cell: no visible binding for global variable ‘log_counts_per_cell’ sc_atac_plot_fragments_per_cell: no visible binding for global variable ‘..count..’ sc_atac_plot_fragments_per_feature: no visible binding for global variable ‘log_counts_per_feature’ sc_atac_plot_fragments_per_feature: no visible binding for global variable ‘..count..’ sc_get_umap_data: no visible global function definition for ‘irlba’ sc_get_umap_data: no visible binding for global variable ‘value’ sc_get_umap_data: no visible binding for global variable ‘cluster’ sc_interactive_umap_plot : server: no visible binding for global variable ‘UMAP1’ sc_interactive_umap_plot : server: no visible binding for global variable ‘UMAP2’ sc_interactive_umap_plot : server: no visible binding for global variable ‘barcode’ sc_mae_plot_umap : : no visible global function definition for ‘irlba’ sc_mae_plot_umap : : no visible binding for global variable ‘value’ sc_mae_plot_umap : : no visible binding for global variable ‘cluster’ sc_mae_plot_umap : : no visible global function definition for ‘experiments’ sc_mae_plot_umap: no visible binding for global variable ‘UMAP1’ sc_mae_plot_umap: no visible binding for global variable ‘UMAP2’ Undefined global functions or variables: ..count.. .N .SD Freq UMAP1 UMAP2 Var1 barcode cluster count end experiments irlba log_cells_per_feature log_counts_per_cell log_counts_per_feature log_features_per_cell seqnames start value write.csv Consider adding importFrom("stats", "end", "start") importFrom("utils", "write.csv") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * 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 line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/scPipe/libs/scPipe.so’: Found ‘___assert_rtn’, possibly from ‘assert’ (C) Found ‘___stderrp’, possibly from ‘stderr’ (C) Found ‘___stdoutp’, possibly from ‘stdout’ (C) Found ‘_abort’, possibly from ‘abort’ (C) Found ‘_exit’, possibly from ‘exit’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed sc_atac_bam_tagging 266.015 346.729 751.987 plot_QC_pairs 17.116 0.429 22.850 sc_sample_data 15.466 0.116 17.446 anno_import 4.920 0.090 6.219 calculate_QC_metrics 4.678 0.321 21.563 convert_geneid 2.472 0.212 5.365 * 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: 6 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/scPipe.Rcheck/00check.log’ for details.