############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:scPipe.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings scPipe_2.3.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/scPipe.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘scPipe/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘scPipe’ version ‘2.3.1’ * 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: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... NOTE installed size is 26.8Mb sub-directories of 1Mb or more: extdata 11.6Mb libs 13.9Mb * 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 loading without being on the library search path ... 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 ‘/home/biocbuild/bbs-3.19-bioc/R/site-library/scPipe/libs/scPipe.so’: Found ‘abort’, possibly from ‘abort’ (C) Found ‘exit’, possibly from ‘exit’ (C) Found ‘stderr’, possibly from ‘stderr’ (C) Found ‘stdout’, possibly from ‘stdout’ (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 32.202 15.604 47.120 plot_QC_pairs 6.259 0.220 6.479 sc_sample_data 5.276 0.060 5.336 calculate_QC_metrics 2.208 0.158 21.718 convert_geneid 1.234 0.136 21.251 get_genes_by_GO 0.757 0.044 16.648 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 6 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/scPipe.Rcheck/00check.log’ for details.