############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RiboCrypt.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RiboCrypt_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/RiboCrypt.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘RiboCrypt/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RiboCrypt’ version ‘1.13.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' INFO Imports includes 25 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 ‘RiboCrypt’ can be installed ... OK * checking installed package size ... INFO installed size is 6.8Mb sub-directories of 1Mb or more: images 2.2Mb rmd 4.3Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 Unexported objects imported by ':::' calls: ‘ORFik:::name_decider’ ‘ORFik:::remove.file_ext’ See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘distribution_plot’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE DEG_plot: no visible binding for global variable ‘rna’ DEG_plot: no visible binding for global variable ‘rfp’ DEG_plot: no visible binding for global variable ‘Regulation’ DEG_plot: no visible binding for global variable ‘contrast’ DEG_plot: no visible binding for global variable ‘meanCounts’ DEG_plot: no visible binding for global variable ‘LFC’ RiboCrypt_app: no visible global function definition for ‘is’ RiboCrypt_app : server: no visible binding for global variable ‘df’ RiboCrypt_app : server: no visible binding for global variable ‘experiments’ RiboCrypt_app : server: no visible binding for global variable ‘tx’ RiboCrypt_app : server: no visible binding for global variable ‘org’ RiboCrypt_app : server: no visible binding for global variable ‘gene_name_list’ RiboCrypt_app : server: no visible binding for global variable ‘df_with’ RiboCrypt_app_modular: no visible global function definition for ‘is’ RiboCrypt_app_modular : server: no visible binding for global variable ‘df’ RiboCrypt_app_modular : server: no visible binding for global variable ‘experiments’ RiboCrypt_app_modular : server: no visible binding for global variable ‘tx’ RiboCrypt_app_modular : server: no visible binding for global variable ‘org’ RiboCrypt_app_modular : server: no visible binding for global variable ‘gene_name_list’ RiboCrypt_app_modular : server: no visible binding for global variable ‘df_with’ browser_plot_assembler: no visible binding for global variable ‘profiles’ browser_plot_assembler: no visible binding for global variable ‘mainPlotControls’ browser_plot_assembler: no visible global function definition for ‘mainPlotControls’ click_plot_browser_new_controller: no visible binding for global variable ‘extend_trailers’ click_plot_codon: no visible binding for global variable ‘variable’ click_plot_codon: no visible binding for global variable ‘seqs’ click_plot_heatmap_main_controller: no visible global function definition for ‘shifts.load’ click_plot_heatmap_main_controller: no visible binding for global variable ‘fraction’ createSeqPanelPattern: no visible binding for global variable ‘frames’ distribution_plot: no visible binding for global variable ‘RPKM’ dt_fft: no visible global function definition for ‘spec.pgram’ dt_fft: no visible binding for global variable ‘fraction’ extend_all_to: no visible binding for global variable ‘tx_name’ fivePlots: no visible binding for global variable ‘seqType’ fivePlots: no visible global function definition for ‘readLengthMeta’ fivePlots: no visible binding for global variable ‘position’ fivePlots: no visible binding for global variable ‘index’ fivePlots: no visible binding for global variable ‘frames’ fivePlots: no visible binding for global variable ‘ratio’ fourPlots: no visible binding for global variable ‘seqType’ fourPlots: no visible binding for global variable ‘position’ fourPlots: no visible binding for global variable ‘index’ fourPlots: no visible binding for global variable ‘frames’ geneModelPanelPlot: no visible binding for global variable ‘layers’ geneModelPanelPlot: no visible binding for global variable ‘rect_starts’ geneModelPanelPlot: no visible binding for global variable ‘rect_ends’ geneModelPanelPlot: no visible binding for global variable ‘labels_locations’ geneModelPanelPlot: no visible binding for global variable ‘gene_names’ geneTrackLayer: no visible binding for global variable ‘subjectHits’ geneTrackLayer: no visible binding for global variable ‘queryHits’ getCoverageProfile: no visible global function definition for ‘is’ getIndexes: no visible global function definition for ‘nrun’ getMetaCoverage: no visible global function definition for ‘.’ getMetaCoverage: no visible binding for global variable ‘position’ getMetaCoverage: no visible binding for global variable ‘index’ getMetaCoverage: no visible binding for global variable ‘frames’ getPlotAnimate: no visible binding for global variable ‘position’ getPlotAnimate: no visible binding for global variable ‘frame’ getProfileAnimate: no visible global function definition for ‘is’ getRelativeFrames: no visible binding for global variable ‘cum_width’ getRelativeFrames: no visible binding for global variable ‘rel_frame’ getRiboProfile: no visible global function definition for ‘is’ getRiboProfile: no visible binding for global variable ‘frame’ getStartWindow: no visible binding for global variable ‘.’ getStopWindow: no visible binding for global variable ‘.’ get_gene_name_categories: no visible binding for global variable ‘merged_name’ heatmap_data: no visible binding for global variable ‘position’ heatmap_data: no visible binding for global variable ‘readlength’ heatmap_data: no visible binding for global variable ‘fraction’ load_custom_regions: no visible binding for global variable ‘.’ make_summary_track: no visible global function definition for ‘.’ make_summary_track: no visible binding for global variable ‘position’ make_summary_track: no visible binding for global variable ‘frame’ metaPlot: no visible binding for global variable ‘index’ metaPlot: no visible binding for global variable ‘frames’ multiOmicsPlot_internal: no visible global function definition for ‘is’ multiOmicsPlot_internal: no visible binding for global variable ‘ylabels_full_name’ multiOmicsPlot_internal: no visible binding for global variable ‘display_dist’ observed_cds_heatmap: no visible binding for global variable ‘gene_id’ observed_cds_heatmap: no visible binding for global variable ‘cds_len’ observed_cds_heatmap: no visible binding for global variable ‘utr5_len’ periodicity_plot: no visible binding for global variable ‘fraction’ periodicity_plot: no visible binding for global variable ‘frame’ periodicity_plot : : no visible binding for global variable ‘read_length’ periodicity_plot : : no visible binding for global variable ‘periods’ periodicity_plot : : no visible binding for global variable ‘amplitude’ plotSeqPanel: no visible binding for global variable ‘frames’ profilesFetcher: no visible global function definition for ‘is’ quality_server : : no visible binding for global variable ‘frame’ quality_server : : no visible binding for global variable ‘position’ quality_server : : no visible binding for global variable ‘fraction’ singlePlot_select_plot_type: no visible binding for global variable ‘position’ singlePlot_select_plot_type: no visible binding for global variable ‘frame’ singlePlotsFetcher: no visible global function definition for ‘is’ singlePlotsFetcher: no visible binding for global variable ‘BPPARAM’ sra_search_server : : no visible global function definition for ‘capture.output’ sra_search_server : : no visible binding for global variable ‘dt’ startCoverage: no visible binding for global variable ‘position’ stopCoverage: no visible binding for global variable ‘position’ threePlots: no visible binding for global variable ‘seqType’ threePlots: no visible binding for global variable ‘position’ threePlots: no visible binding for global variable ‘index’ tx_update_select: no visible binding for global variable ‘label’ unlistToExtremities: no visible global function definition for ‘.’ valuesToColors: no visible global function definition for ‘colorRampPalette’ Undefined global functions or variables: . BPPARAM LFC RPKM Regulation amplitude capture.output cds_len colorRampPalette contrast cum_width df df_with display_dist dt experiments extend_trailers fraction frame frames gene_id gene_name_list gene_names index is label labels_locations layers mainPlotControls meanCounts merged_name nrun org periods position profiles queryHits ratio readLengthMeta read_length readlength rect_ends rect_starts rel_frame rfp rna seqType seqs shifts.load spec.pgram subjectHits tx tx_name utr5_len variable ylabels_full_name Consider adding importFrom("grDevices", "colorRampPalette") importFrom("graphics", "frame") importFrom("methods", "is") importFrom("stats", "df", "dt", "spec.pgram") importFrom("utils", "capture.output") 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed DEG_plot 12.113 0.38 12.528 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/RiboCrypt.Rcheck/00check.log’ for details.