############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FLAMES.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FLAMES_2.4.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/FLAMES.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FLAMES/DESCRIPTION’ ... OK * this is package ‘FLAMES’ version ‘2.4.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 47 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 ... NOTE Found the following hidden files and directories: .dockerignore 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 ‘FLAMES’ can be installed ... NOTE Found the following notes/warnings: Non-staged installation was used See ‘/Users/biocbuild/bbs-3.22-bioc/meat/FLAMES.Rcheck/00install.out’ for details. * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.1.sdk’ * checking C++ specification ... OK * checking installed package size ... INFO installed size is 11.0Mb sub-directories of 1Mb or more: bin 6.1Mb data 1.8Mb libs 1.6Mb * 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 dependencies in R code ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: 'blaze' 'find_barcode' 'gene_quantification' 'isoform_identification' 'minimap2_align' 'transcript_quantification' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE BulkPipeline: no visible global function definition for ‘new’ BulkPipeline: no visible global function definition for ‘setNames’ MultiSampleSCPipeline: no visible global function definition for ‘new’ MultiSampleSCPipeline: no visible global function definition for ‘setNames’ SingleCellPipeline: no visible global function definition for ‘new’ SingleCellPipeline: no visible global function definition for ‘setNames’ addRowRanges: no visible global function definition for ‘head’ addRowRanges: no visible global function definition for ‘as’ add_gene_counts: no visible global function definition for ‘as’ cache_dir: no visible global function definition for ‘packageVersion’ chisq_test_by_gene: no visible global function definition for ‘chisq.test’ create_sce_from_dir: no visible global function definition for ‘setNames’ create_spe: no visible binding for global variable ‘barcode’ create_spe: no visible binding for global variable ‘in_tissue’ download_oarfish: no visible global function definition for ‘download.file’ download_oarfish: no visible global function definition for ‘unzip’ filter_coverage: no visible global function definition for ‘starts_with’ filter_coverage: no visible binding for global variable ‘filter_res’ find_variants: no visible global function definition for ‘setNames’ find_variants_grange: no visible binding for global variable ‘which_label’ find_variants_grange: no visible binding for global variable ‘nucleotide’ find_variants_grange: no visible binding for global variable ‘pos’ find_variants_grange: no visible binding for global variable ‘count’ find_variants_grange: no visible binding for global variable ‘counts_no_ins’ find_variants_grange: no visible binding for global variable ‘ref’ generate_sc_sce: no visible binding for global variable ‘FSM_match’ get_coverage: no visible binding for global variable ‘Freq’ homopolymer_pct : : no visible binding for global variable ‘Freq’ homopolymer_pct : : no visible binding for global variable ‘pct’ plot_coverage: no visible binding for global variable ‘tr_length’ plot_coverage: no visible binding for global variable ‘read_counts’ plot_coverage: no visible binding for global variable ‘total_counts’ plot_coverage: no visible binding for global variable ‘cumpct’ plot_coverage: no visible binding for global variable ‘length_bin’ plot_coverage: no visible binding for global variable ‘min_length’ plot_coverage: no visible binding for global variable ‘max_length’ plot_coverage: no visible global function definition for ‘head’ plot_coverage: no visible binding for global variable ‘transcript’ plot_demultiplex_raw: no visible binding for global variable ‘Sample’ plot_demultiplex_raw: no visible binding for global variable ‘CellBarcode’ plot_demultiplex_raw: no visible binding for global variable ‘UMI’ plot_demultiplex_raw: no visible binding for global variable ‘UMI_count’ plot_demultiplex_raw: no visible binding for global variable ‘barcode_rank’ plot_demultiplex_raw: no visible binding for global variable ‘FlankEditDist’ plot_demultiplex_raw: no visible binding for global variable ‘n_reads’ plot_demultiplex_raw: no visible binding for global variable ‘BarcodeEditDist’ plot_demultiplex_raw: no visible binding for global variable ‘total reads’ plot_demultiplex_raw: no visible binding for global variable ‘demultiplexed reads’ plot_demultiplex_raw: no visible binding for global variable ‘single match reads’ plot_demultiplex_raw: no visible binding for global variable ‘undemultiplexted reads’ plot_demultiplex_raw: no visible binding for global variable ‘multi-matching reads’ plot_demultiplex_raw: no visible binding for global variable ‘Type’ plot_demultiplex_raw: no visible binding for global variable ‘Reads’ plot_demultiplex_raw: no visible binding for global variable ‘input’ plot_demultiplex_raw: no visible binding for global variable ‘output’ plot_demultiplex_raw: no visible binding for global variable ‘read1_with_adapter’ plot_demultiplex_raw: no visible binding for global variable ‘Count’ plot_flagstat: no visible global function definition for ‘everything’ plot_flagstat: no visible binding for global variable ‘name’ plot_flagstat: no visible binding for global variable ‘value’ plot_isoform_reduced_dim: no visible binding for global variable ‘x’ plot_isoform_reduced_dim: no visible binding for global variable ‘y’ plot_isoform_reduced_dim: no visible binding for global variable ‘expr’ plot_spatial: no visible binding for global variable ‘imageX’ plot_spatial: no visible binding for global variable ‘imageY’ plot_spatial_feature: no visible binding for global variable ‘imageX’ plot_spatial_feature: no visible binding for global variable ‘imageY’ plot_spatial_feature: no visible binding for global variable ‘x’ plot_spatial_feature: no visible binding for global variable ‘y’ plot_spatial_feature: no visible global function definition for ‘scale_alpha_continuous’ plot_spatial_feature: no visible global function definition for ‘scale_colour_gradient’ plot_spatial_isoform: no visible global function definition for ‘head’ plot_spatial_pie: no visible global function definition for ‘setNames’ plot_spatial_pie: no visible global function definition for ‘head’ plot_spatial_pie: no visible binding for global variable ‘imageX’ plot_spatial_pie: no visible binding for global variable ‘imageY’ sc_gene_entropy: no visible global function definition for ‘as’ sc_genotype: no visible binding for global variable ‘allele’ sc_genotype: no visible binding for global variable ‘allele_count’ sc_genotype: no visible binding for global variable ‘barcode’ sc_genotype: no visible binding for global variable ‘pct’ sc_mutations: no visible binding for global variable ‘mutation_index’ sc_mutations: no visible binding for global variable ‘bam_index’ sc_plot_genotype: no visible global function definition for ‘setNames’ sc_plot_genotype: no visible binding for global variable ‘barcode’ sc_plot_genotype: no visible binding for global variable ‘genotype’ sc_plot_genotype: no visible binding for global variable ‘x’ sc_plot_genotype: no visible binding for global variable ‘y’ sc_transcript_usage_chisq: no visible global function definition for ‘as’ sc_transcript_usage_chisq: no visible binding for global variable ‘p.value’ sc_transcript_usage_chisq: no visible binding for global variable ‘adj.p.value’ sc_transcript_usage_permutation: no visible binding for global variable ‘total’ sc_transcript_usage_permutation: no visible binding for global variable ‘test’ sc_transcript_usage_permutation: no visible global function definition for ‘as’ sc_transcript_usage_permutation : : no visible global function definition for ‘as’ sc_transcript_usage_permutation : : : no visible global function definition for ‘na.omit’ sc_transcript_usage_permutation: no visible binding for global variable ‘transcript’ sc_transcript_usage_permutation: no visible binding for global variable ‘p.value’ sc_transcript_usage_permutation: no visible binding for global variable ‘adj.p.value’ variant_count_tb: no visible binding for global variable ‘barcode’ variant_count_tb: no visible binding for global variable ‘allele_count’ variant_count_tb: no visible binding for global variable ‘cell_total_reads’ barcode_demultiplex,FLAMES.MultiSampleSCPipeline: no visible binding for global variable ‘expect_cell_number’ barcode_demultiplex,FLAMES.MultiSampleSCPipeline: no visible binding for global variable ‘fastq’ barcode_demultiplex,FLAMES.MultiSampleSCPipeline: no visible binding for global variable ‘demultiplexed_fastq’ barcode_demultiplex,FLAMES.MultiSampleSCPipeline: no visible binding for global variable ‘barcodes_file’ barcode_demultiplex,FLAMES.MultiSampleSCPipeline: no visible binding for global variable ‘outdir’ barcode_demultiplex,FLAMES.MultiSampleSCPipeline: no visible global function definition for ‘setNames’ barcode_demultiplex,FLAMES.MultiSampleSCPipeline : : no visible global function definition for ‘setNames’ barcode_demultiplex,FLAMES.SingleCellPipeline: no visible binding for global variable ‘expect_cell_number’ barcode_demultiplex,FLAMES.SingleCellPipeline: no visible binding for global variable ‘fastq’ barcode_demultiplex,FLAMES.SingleCellPipeline: no visible binding for global variable ‘demultiplexed_fastq’ barcode_demultiplex,FLAMES.SingleCellPipeline: no visible binding for global variable ‘barcodes_file’ barcode_demultiplex,FLAMES.SingleCellPipeline: no visible binding for global variable ‘outdir’ barcode_demultiplex,FLAMES.SingleCellPipeline: no visible global function definition for ‘setNames’ genome_alignment_raw,FLAMES.Pipeline: no visible binding for global variable ‘j’ genome_alignment_raw,FLAMES.Pipeline: no visible binding for global variable ‘genome_bam’ genome_alignment_raw,FLAMES.Pipeline: no visible binding for global variable ‘minimap2’ genome_alignment_raw,FLAMES.Pipeline: no visible binding for global variable ‘samtools’ genome_alignment_raw,FLAMES.Pipeline: no visible binding for global variable ‘threads’ genome_alignment_raw,FLAMES.Pipeline: no visible binding for global variable ‘outdir’ plot_durations,FLAMES.Pipeline: no visible binding for global variable ‘step’ plot_durations,FLAMES.Pipeline: no visible binding for global variable ‘duration’ read_realignment_raw,FLAMES.Pipeline: no visible binding for global variable ‘j’ read_realignment_raw,FLAMES.Pipeline: no visible binding for global variable ‘transcriptome_assembly’ read_realignment_raw,FLAMES.Pipeline: no visible binding for global variable ‘transcriptome_bam’ read_realignment_raw,FLAMES.Pipeline: no visible binding for global variable ‘minimap2’ read_realignment_raw,FLAMES.Pipeline: no visible binding for global variable ‘samtools’ read_realignment_raw,FLAMES.Pipeline: no visible binding for global variable ‘outdir’ resume_FLAMES,FLAMES.Pipeline : : no visible global function definition for ‘capture.output’ run_FLAMES,FLAMES.Pipeline : : no visible global function definition for ‘capture.output’ Undefined global functions or variables: BarcodeEditDist CellBarcode Count FSM_match FlankEditDist Freq Reads Sample Type UMI UMI_count adj.p.value allele allele_count as bam_index barcode barcode_rank barcodes_file capture.output cell_total_reads chisq.test count counts_no_ins cumpct demultiplexed reads demultiplexed_fastq download.file duration everything expect_cell_number expr fastq filter_res genome_bam genotype head imageX imageY in_tissue input j length_bin max_length min_length minimap2 multi-matching reads mutation_index n_reads na.omit name new nucleotide outdir output p.value packageVersion pct pos read1_with_adapter read_counts ref samtools scale_alpha_continuous scale_colour_gradient setNames single match reads starts_with step test threads total total reads total_counts tr_length transcript transcriptome_assembly transcriptome_bam undemultiplexted reads unzip value which_label x y Consider adding importFrom("base", "match", "single") importFrom("methods", "as", "new") importFrom("stats", "chisq.test", "na.omit", "setNames", "step") importFrom("utils", "capture.output", "download.file", "head", "packageVersion", "unzip") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 shell scripts ... 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 include directives in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/FLAMES/libs/FLAMES.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 plot_isoform_reduced_dim 10.201 0.094 10.313 sc_long_multisample_pipeline 7.069 1.142 5.135 find_variants 6.214 0.085 5.924 sc_plot_genotype 5.402 0.115 4.719 MultiSampleSCPipeline 4.522 0.589 6.600 * 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 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/FLAMES.Rcheck/00check.log’ for details.