############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:RiboCrypt.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RiboCrypt_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/RiboCrypt.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * 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-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘RiboCrypt/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RiboCrypt’ version ‘1.14.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 33 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 ... WARNING Found the following significant warnings: Note: possible error in 'outputLibs(dff, type = read_type, ': unused argument (validate_libs = validate_libs) See ‘/home/biocbuild/bbs-3.21-bioc/meat/RiboCrypt.Rcheck/00install.out’ for details. Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’. * checking installed package size ... INFO installed size is 11.4Mb sub-directories of 1Mb or more: images 5.7Mb rmd 5.2Mb * 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 loading without being on the library search path ... 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. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE collection_to_metawindow: warning in rbindlist(output, id = "genes"): partial argument match of 'id' to 'idcol' 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’ DEG_server : : no visible binding for global variable ‘value’ DEG_server : : no visible global function definition for ‘URLencode’ DE_model_results: no visible binding for global variable ‘Regulation’ RiboCrypt_app: no visible binding for global variable ‘names_init’ RiboCrypt_app: no visible binding for global variable ‘libs’ RiboCrypt_app: no visible binding for global variable ‘time_before’ RiboCrypt_app : server: no visible binding for global variable ‘without_readlengths_env’ 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 ‘libs’ 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_meta’ RiboCrypt_app : server: no visible binding for global variable ‘names_init’ RiboCrypt_app : server: no visible binding for global variable ‘with_readlengths_env’ RiboCrypt_app : server: no visible binding for global variable ‘df_with’ RiboCrypt_app : server: no visible binding for global variable ‘exp_init_meta’ RiboCrypt_app : server: no visible binding for global variable ‘time_before’ allsamples_enrich_bar_plot: no visible binding for global variable ‘variable’ allsamples_enrich_bar_plot: no visible binding for global variable ‘rn’ allsamples_enrich_bar_plot: no visible binding for global variable ‘value’ allsamples_meta_stats: no visible binding for global variable ‘index’ allsamples_meta_stats: no visible binding for global variable ‘grouping_numeric_bins’ allsamples_meta_stats: no visible global function definition for ‘chisq.test’ allsamples_metadata_clustering: no visible global function definition for ‘pdf’ allsamples_metadata_clustering: no visible global function definition for ‘dev.off’ allsamples_metadata_clustering: no visible binding for global variable ‘cluster’ allsamples_metadata_clustering: no visible binding for global variable ‘index’ allsamples_metadata_clustering: no visible binding for global variable ‘grouping_numeric_bins_temp’ allsamples_metadata_clustering: no visible binding for global variable ‘grouping_numeric_bins’ allsamples_sidebar : : no visible binding for global variable ‘index’ allsamples_sidebar_ggproto: no visible binding for global variable ‘index’ annotation_controller: no visible global function definition for ‘is’ annotation_controller: no visible global function definition for ‘wmsg’ annotation_track_allsamples: no visible binding for global variable ‘tx_name’ append_gene_symbols: no visible global function definition for ‘is’ append_gene_symbols: no visible binding for global variable ‘id’ append_gene_symbols: no visible binding for global variable ‘external_gene_name’ append_gene_symbols: no visible binding for global variable ‘label’ browseRC: no visible global function definition for ‘browseURL’ browser_allsamp_server : : no visible binding for global variable ‘gene_name_list’ browser_track_panel_shiny: no visible binding for global variable ‘ylabels_full_name’ browser_track_panel_shiny: no visible binding for global variable ‘total_libs’ browser_track_panel_shiny: no visible binding for global variable ‘display_dist’ click_plot_browser_main_controller: no visible global function definition for ‘is’ 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 binding for global variable ‘fraction’ collection_path_from_exp: no visible binding for global variable ‘label’ collection_path_from_exp: no visible binding for global variable ‘value’ collection_to_metawindow: no visible binding for global variable ‘.’ collection_to_metawindow: no visible global function definition for ‘mcmapply’ collection_to_wide: no visible binding for global variable ‘position’ compute_collection_table_grouping: no visible binding for global variable ‘lib_sizes’ compute_collection_table_grouping: no visible global function definition for ‘.’ compute_collection_table_grouping: no visible binding for global variable ‘score’ createSeqPanelPattern: no visible binding for global variable ‘frames’ distribution_plot: no visible binding for global variable ‘RPKM’ distribution_plot: no visible binding for global variable ‘transcript’ 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’ filter_collection_on_count: no visible global function definition for ‘.’ filter_collection_on_count: no visible binding for global variable ‘count’ filter_collection_on_count: no visible binding for global variable ‘valid’ 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’ geneBoxFromRanges: no visible binding for global variable ‘no_ex’ geneBoxFromRanges: no visible global function definition for ‘.’ geneBoxFromRanges: no visible binding for global variable ‘rect_ends’ geneBoxFromRanges: no visible binding for global variable ‘rect_starts’ geneModelPanelPlot: no visible binding for global variable ‘type’ 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 ‘layers’ geneModelPanelPlot: no visible binding for global variable ‘gene_names’ geneModelPanelPlot: no visible global function definition for ‘.’ geneModelPanelPlot: no visible binding for global variable ‘labels_locations’ geneTrackLayer: no visible binding for global variable ‘subjectHits’ geneTrackLayer: no visible binding for global variable ‘queryHits’ genomic_string_to_grl: no visible global function definition for ‘as’ genomic_string_to_grl: no visible global function definition for ‘is’ genomic_string_to_grl: no visible global function definition for ‘seqlevelsStyle<-’ genomic_string_to_grl: no visible global function definition for ‘seqlevelsStyle’ getCoverageProfile: no visible global function definition for ‘is’ getCoverageProfile: no visible binding for global variable ‘position’ 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’ getProfileWrapper: no visible binding for global variable ‘frame’ getProfileWrapper: no visible binding for global variable ‘count’ getRelativeFrames: no visible binding for global variable ‘cum_width’ getRelativeFrames: no visible global function definition for ‘.’ getRelativeFrames: no visible binding for global variable ‘type’ 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’ get_gene_name_categories: no visible binding for global variable ‘uniprot_id’ get_gene_name_categories_collection: no visible binding for global variable ‘value’ 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’ internalGetterSubsetter: no visible binding for global variable ‘position’ load_collection: no visible binding for global variable ‘position’ load_custom_regions: no visible binding for global variable ‘.’ load_reads: possible error in outputLibs(dff, type = read_type, paths = paths, output.mode = "envirlist", naming = "fullexp", validate_libs = validate_libs, BPPARAM = BPPARAM): unused argument (validate_libs = validate_libs) make_rc_url: no visible binding for global variable ‘merged_name’ 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’ metadata_ui: no visible binding for global variable ‘libtypes’ multiLib_to_metaWindow: no visible global function definition for ‘mclapply’ multiLib_to_metaWindow : : no visible binding for global variable ‘position’ multiLib_to_metaWindow : : no visible binding for global variable ‘genes’ multiOmicsPlot_all_profiles: no visible global function definition for ‘is’ multiOmicsPlot_all_track_plots: 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 ‘total_libs’ multiOmicsPlot_internal: no visible binding for global variable ‘display_dist’ normalize_collection: no visible binding for global variable ‘score_tpm’ normalize_collection: no visible binding for global variable ‘count’ normalize_collection: no visible binding for global variable ‘score’ normalize_collection: no visible global function definition for ‘sd’ normalize_collection: no visible binding for global variable ‘logscore’ 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’ phylo_custom_seq_track_panel: no visible global function definition for ‘seqlevelsStyle<-’ phylo_custom_seq_track_panel: no visible global function definition for ‘seqlevelsStyle’ phylo_custom_seq_track_panel: no visible global function definition for ‘relist’ phylo_custom_seq_track_panel: no visible binding for global variable ‘position’ phylo_custom_seq_track_panel: no visible binding for global variable ‘phyloP’ plotSeqPanel: no visible binding for global variable ‘frames’ 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’ smoothenMultiSampCoverage: no visible binding for global variable ‘count’ smoothenMultiSampCoverage: no visible binding for global variable ‘frame’ smoothenMultiSampCoverage: no visible global function definition for ‘.’ smoothenSingleSampCoverage: no visible binding for global variable ‘count’ smoothenSingleSampCoverage: no visible binding for global variable ‘genes’ smoothenSingleSampCoverage: no visible binding for global variable ‘frame’ smoothenSingleSampCoverage: no visible binding for global variable ‘position’ sra_search_server : : no visible global function definition for ‘capture.output’ sra_search_server : : no visible binding for global variable ‘dt’ startCoverage: no visible global function definition for ‘distance’ startCoverage: no visible binding for global variable ‘position’ stopCoverage: no visible global function definition for ‘distance’ stopCoverage: no visible binding for global variable ‘position’ subset_fst_by_interval: no visible global function definition for ‘is’ subset_fst_by_interval: no visible binding for global variable ‘position’ subset_fst_by_region: no visible global function definition for ‘is’ subset_fst_by_region: no visible binding for global variable ‘position’ subset_fst_interval_sum: no visible binding for global variable ‘position’ subset_fst_interval_sum: no visible global function definition for ‘.’ subset_fst_interval_sum: no visible binding for global variable ‘score’ summary_track_allsamples: 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_from_gene_list: no visible binding for global variable ‘value’ tx_from_gene_list: no visible binding for global variable ‘label’ tx_update_select: no visible binding for global variable ‘value’ valuesToColors: no visible global function definition for ‘colorRampPalette’ Undefined global functions or variables: . LFC RPKM Regulation URLencode amplitude as browseURL capture.output cds_len chisq.test cluster colorRampPalette contrast count cum_width dev.off df df_meta df_with display_dist distance dt exp_init_meta experiments extend_trailers external_gene_name fraction frame frames gene_id gene_name_list gene_names genes grouping_numeric_bins grouping_numeric_bins_temp id index is label labels_locations layers lib_sizes libs libtypes logscore mclapply mcmapply meanCounts merged_name names_init no_ex nrun org pdf periods phyloP position queryHits ratio readLengthMeta read_length readlength rect_ends rect_starts rel_frame relist rfp rn rna score score_tpm sd seqType seqlevelsStyle seqlevelsStyle<- seqs spec.pgram subjectHits time_before total_libs transcript tx tx_name type uniprot_id utr5_len valid value variable with_readlengths_env without_readlengths_env wmsg ylabels_full_name Consider adding importFrom("grDevices", "colorRampPalette", "dev.off", "pdf") importFrom("graphics", "frame") importFrom("methods", "as", "is") importFrom("stats", "chisq.test", "df", "dt", "sd", "spec.pgram") importFrom("utils", "URLencode", "browseURL", "capture.output", "relist") 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 ... WARNING Undocumented arguments in Rd file 'compute_collection_table.Rd' ‘decreasing_order’ Undocumented arguments in Rd file 'make_rc_url.Rd' ‘add_translons’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘RiboCrypt-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: multiOmicsPlot_animate > ### Title: Multi-omics animation using list input > ### Aliases: multiOmicsPlot_animate > > ### ** Examples > > library(RiboCrypt) > df <- ORFik.template.experiment()[9:10,] > cds <- loadRegion(df, "cds") Loading required package: GenomicFeatures Loading required package: AnnotationDbi > mrna <- loadRegion(df, "mrna") > multiOmicsPlot_animate(mrna[1], annotation = cds[1], reference_sequence = findFa(df), + frames_type = "columns", leader_extension = 30, trailer_extension = 30, withFrames = c(T, T), + reads = outputLibs(df, type = "pshifted", output.mode = "envirlist", + naming = "full", BPPARAM = BiocParallel::SerialParam())) Outputting libraries from: ORFik 1 : RFP_Mutant_r1 2 : RFP_Mutant_r2 Error in eval(substitute(expr), data, enclos = parent.frame()) : T used instead of TRUE Calls: multiOmicsPlot_animate ... multiOmicsControllerView -> with -> with.default -> eval -> eval Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed DEG_plot 20.995 0.530 23.409 multiOmicsPlot_ORFikExp 6.169 0.152 6.975 * 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: 1 ERROR, 2 WARNINGs, 3 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/RiboCrypt.Rcheck/00check.log’ for details.