############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:scPipe.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scPipe_2.7.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/scPipe.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scPipe/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘scPipe’ version ‘2.7.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 40 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ... WARNING Found the following significant warnings: Warning: program compiled against libxml 212 using older 211 See ‘/home/biocbuild/bbs-3.21-bioc/meat/scPipe.Rcheck/00install.out’ for details. * used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ * used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... INFO installed size is 37.4Mb sub-directories of 1Mb or more: extdata 12.1Mb libs 24.0Mb * 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 ... NOTE Warning: program compiled against libxml 212 using older 211 A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * 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 ... NOTE Warning: program compiled against libxml 212 using older 211 It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * checking dependencies in R code ... NOTE Warning: program compiled against libxml 212 using older 211 Namespaces in Imports field not imported from: ‘flexmix’ ‘vctrs’ All declared Imports should be used. * checking S3 generic/method consistency ... WARNING Warning: program compiled against libxml 212 using older 211 See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... WARNING Warning: program compiled against libxml 212 using older 211 The argument of a replacement function which corresponds to the right hand side must be named ‘value’. * checking foreign function calls ... NOTE Warning: program compiled against libxml 212 using older 211 See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE Warning: program compiled against libxml 212 using older 211 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: QC_metrics.Rd: SingleCellExperiment UMI_dup_info.Rd: SingleCellExperiment create_sce_by_dir.Rd: SingleCellExperiment demultiplex_info.Rd: SingleCellExperiment feature_info.Rd: SingleCellExperiment feature_type.Rd: SingleCellExperiment gene_id_type.Rd: SingleCellExperiment organism.Rd: SingleCellExperiment Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... WARNING Warning: program compiled against libxml 212 using older 211 All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 * checking Rd \usage sections ... NOTE Warning: program compiled against libxml 212 using older 211 The \usage entries for S3 methods should use the \method markup and not their full name. 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 line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... INFO 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/R/R-4.5.0-devel_2024-11-24/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 32.059 16.372 48.123 sc_sample_data 9.915 0.693 10.630 plot_QC_pairs 8.876 0.127 9.030 calculate_QC_metrics 2.875 0.172 10.646 * 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: 5 WARNINGs, 9 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/scPipe.Rcheck/00check.log’ for details.