############################################################################## ############################################################################## ### ### 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_2.3.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/FLAMES.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FLAMES/DESCRIPTION’ ... OK * this is package ‘FLAMES’ version ‘2.3.4’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 50 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 ‘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 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... OK * checking installed package size ... INFO installed size is 5.5Mb sub-directories of 1Mb or more: data 1.8Mb libs 1.8Mb * 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’ MultiSampleSCPipeline: no visible global function definition for ‘new’ SingleCellPipeline: no visible global function definition for ‘new’ addRowRanges: no visible global function definition for ‘head’ addRowRanges: 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_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_barcode: no visible binding for global variable ‘Sample’ find_barcode: no visible binding for global variable ‘Outfile’ 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 ‘head’ plot_spatial_pie: no visible binding for global variable ‘imageX’ plot_spatial_pie: no visible binding for global variable ‘imageY’ sc_mutations: no visible binding for global variable ‘mutation_index’ sc_mutations: no visible binding for global variable ‘bam_index’ 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 ‘outdir’ 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.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 ‘outdir’ barcode_demultiplex,FLAMES.SingleCellPipeline: no visible binding for global variable ‘demultiplexed_fastq’ barcode_demultiplex,FLAMES.SingleCellPipeline: no visible binding for global variable ‘barcodes_file’ 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’ 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 Outfile Reads Sample Type UMI UMI_count adj.p.value 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 everything expect_cell_number expr fastq filter_res genome_bam 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 single match reads starts_with 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") 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-x86_64/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 25.024 0.393 25.657 find_variants 24.585 0.597 24.820 sc_long_multisample_pipeline 20.656 2.772 20.006 MultiSampleSCPipeline 18.526 2.142 22.114 sc_DTU_analysis 11.933 1.259 11.830 blaze 8.353 1.259 10.327 plot_isoform_heatmap 8.711 0.479 9.281 create_sce_from_dir 6.840 1.187 6.648 BulkPipeline 6.947 0.792 8.323 SingleCellPipeline 6.797 0.812 6.184 sc_long_pipeline 6.608 0.831 6.056 bulk_long_pipeline 4.519 1.009 4.275 create_se_from_dir 4.238 0.734 5.387 * 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/FLAMES.Rcheck/00check.log’ for details.