############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ORFik.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ORFik_1.29.7.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ORFik.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘ORFik/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ORFik’ version ‘1.29.7’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 29 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 ... NOTE Found the following non-portable file path: ORFik/inst/extdata/test_processing/contaminants_depletion/LOGS/contaminants_output_template_Log.final.out Tarballs are only required to store paths of up to 100 bytes and cannot store those of more than 256 bytes, with restrictions including to 100 bytes for the final component. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for sufficient/correct file permissions ... OK * checking whether package ‘ORFik’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking installed package size ... INFO installed size is 7.5Mb sub-directories of 1Mb or more: R 1.1Mb extdata 1.5Mb help 1.0Mb libs 3.0Mb * 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 ... NOTE Warning: no function found corresponding to methods exports from ‘ORFik’ for: ‘organism’ 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 dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘GenomicFeatures:::.merge_seqinfo_and_infer_missing_seqlengths’ ‘IRanges:::regroupBySupergroup’ ‘S4Vectors:::normarg_mcols’ ‘biomartr:::getENSEMBL.Seq’ ‘biomartr:::getENSEMBL.gtf’ 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: ‘go_analaysis_gorilla’ ‘pseudoIntronsPerGroup’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE DEG.plot.static: no visible binding for global variable ‘Regulation’ DEG.plot.static: no visible binding for global variable ‘meanCounts’ DEG.plot.static: no visible binding for global variable ‘LFC’ DEG_gorilla: no visible binding for global variable ‘contrast’ DEG_gorilla: no visible binding for global variable ‘Regulation’ DEG_gorilla: no visible binding for global variable ‘external_gene_name’ DEG_model_simple: no visible binding for global variable ‘id’ DEG_model_simple: no visible binding for global variable ‘contrast’ DTEG.plot: no visible binding for global variable ‘Regulation’ DTEG.plot: no visible binding for global variable ‘rna.lfc’ DTEG.plot: no visible binding for global variable ‘rfp.lfc’ DTEG_add_regulation_categories: no visible binding for global variable ‘te.sign’ DTEG_add_regulation_categories: no visible binding for global variable ‘rfp.sign’ DTEG_add_regulation_categories: no visible binding for global variable ‘rna.sign’ DTEG_add_regulation_categories: no visible binding for global variable ‘Regulation’ DTEG_add_regulation_categories: no visible binding for global variable ‘all_models_sign’ DTEG_add_regulation_categories: no visible binding for global variable ‘te.lfc’ DTEG_add_regulation_categories: no visible binding for global variable ‘rna.lfc’ DTEG_pair_results: no visible binding for global variable ‘rna.sign’ DTEG_pair_results: no visible binding for global variable ‘rna.padj’ DTEG_pair_results: no visible binding for global variable ‘rfp.sign’ DTEG_pair_results: no visible binding for global variable ‘rfp.padj’ DTEG_pair_results: no visible binding for global variable ‘te.sign’ DTEG_pair_results: no visible binding for global variable ‘te.padj’ DTEG_pair_results: no visible binding for global variable ‘all_models_sign’ QCstats.plot: no visible binding for global variable ‘variable’ QCstats.plot: no visible binding for global variable ‘sample_total’ QCstats.plot: no visible binding for global variable ‘value’ QCstats.plot: no visible global function definition for ‘.’ QCstats.plot: no visible binding for global variable ‘sample_id’ QCstats.plot: no visible binding for global variable ‘percentage’ QCstats.plot: no visible binding for global variable ‘perc_of_counts_per_sample’ QCstats.plot: no visible binding for global variable ‘read length’ RiboQC.plot: no visible binding for global variable ‘variable’ RiboQC.plot: no visible binding for global variable ‘sample_total’ RiboQC.plot: no visible binding for global variable ‘value’ RiboQC.plot: no visible global function definition for ‘.’ RiboQC.plot: no visible binding for global variable ‘sample_id’ RiboQC.plot: no visible binding for global variable ‘percentage’ RiboQC.plot: no visible binding for global variable ‘percent’ RiboQC.plot: no visible binding for global variable ‘frame’ STAR.multiQC_plot: no visible binding for global variable ‘value’ STAR.multiQC_plot: no visible binding for global variable ‘sample_id’ TOP.Motif.ecdf: no visible binding for global variable ‘seq1’ TOP.Motif.ecdf: no visible binding for global variable ‘TOP’ alignmentFeatureStatistics : : no visible binding for global variable ‘percentage_mrna_aligned’ alignmentFeatureStatistics : : no visible binding for global variable ‘mRNA’ alignmentFeatureStatistics : : no visible binding for global variable ‘percentage_tx_aligned’ alignmentFeatureStatistics : : no visible binding for global variable ‘Transcript’ alignmentFeatureStatistics : : no visible binding for global variable ‘ratio_cds_mrna’ alignmentFeatureStatistics : : no visible binding for global variable ‘CDS’ alignmentFeatureStatistics : : no visible binding for global variable ‘ratio_cds_leader’ alignmentFeatureStatistics : : no visible binding for global variable ‘LEADERS’ allFeaturesHelper: no visible binding for global variable ‘te’ allFeaturesHelper: no visible binding for global variable ‘fpkmRFP’ allFeaturesHelper: no visible binding for global variable ‘fpkmRNA’ allFeaturesHelper: no visible binding for global variable ‘countRFP’ allFeaturesHelper: no visible binding for global variable ‘entropyRFP’ allFeaturesHelper: no visible binding for global variable ‘disengagementScores’ allFeaturesHelper: no visible binding for global variable ‘RRS’ allFeaturesHelper: no visible binding for global variable ‘RSS’ allFeaturesHelper: no visible binding for global variable ‘ORFScores’ allFeaturesHelper: no visible binding for global variable ‘ioScore’ allFeaturesHelper: no visible binding for global variable ‘startCodonCoverage’ allFeaturesHelper: no visible binding for global variable ‘startRegionRelative’ allFeaturesHelper: no visible binding for global variable ‘kozak’ allFeaturesHelper: no visible binding for global variable ‘StartCodons’ allFeaturesHelper: no visible binding for global variable ‘StopCodons’ allFeaturesHelper: no visible binding for global variable ‘fractionLengths’ allFeaturesHelper: no visible binding for global variable ‘distORFCDS’ allFeaturesHelper: no visible binding for global variable ‘inFrameCDS’ allFeaturesHelper: no visible binding for global variable ‘isOverlappingCds’ allFeaturesHelper: no visible binding for global variable ‘rankInTx’ appendZeroes: no visible binding for global variable ‘frame’ appendZeroes: no visible binding for global variable ‘position’ appendZeroes: no visible binding for global variable ‘count’ append_gene_symbols: no visible binding for global variable ‘id_original’ 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’ artificial.orfs: no visible binding for global variable ‘random’ artificial.orfs: no visible binding for global variable ‘pick’ artificial.orfs: no visible global function definition for ‘.’ browseSRA: no visible global function definition for ‘browseURL’ cellTypeNames: missing arguments not allowed in calls to ‘c’ codonSumsPerGroup: no visible binding for global variable ‘genes’ codon_usage: no visible binding for global variable ‘merged’ codon_usage: no visible binding for global variable ‘AA’ codon_usage: no visible binding for global variable ‘codon’ codon_usage_plot: no visible binding for global variable ‘seqs’ collapse.by.scores: no visible global function definition for ‘.’ collapse.fastq.internal: no visible binding for global variable ‘N’ cor_plot: no visible binding for global variable ‘Var2’ cor_plot: no visible binding for global variable ‘Var1’ cor_plot: no visible binding for global variable ‘Cor’ cor_table: no visible binding for global variable ‘Var1’ cor_table: no visible binding for global variable ‘Var2’ cor_table: no visible binding for global variable ‘Cor’ coverageByTranscriptFST: no visible binding for global variable ‘file_forward’ coverageByTranscriptFST: no visible binding for global variable ‘file_reverse’ coverageByTranscriptFST : : no visible binding for global variable ‘chr’ coverageByTranscriptFST : : no visible binding for global variable ‘query_id’ coverageByTranscriptFST : : no visible global function definition for ‘foverlaps’ coverageByTranscriptFST : : no visible binding for global variable ‘start_segment’ coverageByTranscriptFST : : no visible binding for global variable ‘i.start’ coverageByTranscriptFST : : no visible binding for global variable ‘end_segment’ coverageByTranscriptFST : : no visible binding for global variable ‘i.end’ coverageByTranscriptFST : : no visible binding for global variable ‘file_forward’ coverageByTranscriptFST : : no visible binding for global variable ‘file_reverse’ coverageByTranscriptFST : : no visible global function definition for ‘.’ coverageHeatMap: no visible binding for global variable ‘position’ coverageHeatMap: no visible binding for global variable ‘fraction’ coveragePerORFStatistics: no visible global function definition for ‘.’ coveragePerORFStatistics: no visible binding for global variable ‘count’ coveragePerORFStatistics: no visible binding for global variable ‘genes’ coverageScorings: no visible binding for global variable ‘count’ coverageScorings: no visible binding for global variable ‘zscore’ coverageScorings: no visible binding for global variable ‘windowMean’ coverageScorings: no visible binding for global variable ‘windowSD’ coverageScorings: no visible global function definition for ‘.’ coverageScorings: no visible binding for global variable ‘modzscore’ coverageScorings: no visible binding for global variable ‘windowMedian’ coverageScorings: no visible binding for global variable ‘windowMAD’ coverageScorings: no visible binding for global variable ‘gene_sum’ coverageScorings: no visible binding for global variable ‘fraction’ coverage_random_access_file: no visible binding for global variable ‘genes’ coverage_random_access_file: no visible binding for global variable ‘position’ coverage_random_access_file: no visible binding for global variable ‘frame’ coverage_to_dt: no visible binding for global variable ‘frame’ coverage_to_dt: no visible binding for global variable ‘genes’ coverage_to_dt: no visible binding for global variable ‘position’ detectRibosomeShifts: no visible global function definition for ‘.’ detectRibosomeShifts: no visible binding for global variable ‘size’ detectRibosomeShifts: no visible binding for global variable ‘fraction’ detectRibosomeShifts: no visible binding for global variable ‘pShifted’ detectRibosomeShifts: no visible binding for global variable ‘sum.count’ detectRibosomeShifts: no visible binding for global variable ‘count’ detectRibosomeShifts: no visible binding for global variable ‘genes’ detectRibosomeShifts: no visible binding for global variable ‘frac.score’ detect_ribo_orfs: no visible global function definition for ‘organism’ download_gene_homologues: no visible binding for global variable ‘species’ entropy: no visible binding for global variable ‘Hx’ entropy: no visible binding for global variable ‘codonSums’ entropy: no visible global function definition for ‘.’ entropy: no visible binding for global variable ‘genes’ fetch_xml_attributes: no visible binding for global variable ‘..to_keep’ filterExtremePeakGenes: no visible binding for global variable ‘count’ filterExtremePeakGenes: no visible binding for global variable ‘median_per_gene’ filterExtremePeakGenes: no visible binding for global variable ‘genes’ filterExtremePeakGenes: no visible global function definition for ‘.’ filterTranscripts: no visible binding for global variable ‘utr5_len’ filterTranscripts: no visible binding for global variable ‘utr3_len’ filter_empty_runs: no visible binding for global variable ‘spots’ findNGSPairs: no visible global function definition for ‘.’ findNGSPairs: no visible binding for global variable ‘forward’ findPeaksPerGene: no visible binding for global variable ‘sum_per_gene’ findPeaksPerGene: no visible binding for global variable ‘count’ findPeaksPerGene: no visible binding for global variable ‘genes’ findPeaksPerGene: no visible binding for global variable ‘mean_per_gene’ findPeaksPerGene: no visible binding for global variable ‘median_per_gene’ findPeaksPerGene: no visible binding for global variable ‘sd_per_gene’ findPeaksPerGene: no visible binding for global variable ‘mad_per_gene’ findPeaksPerGene: no visible binding for global variable ‘zscore’ findPeaksPerGene: no visible binding for global variable ‘modzscore’ findPeaksPerGene: no visible binding for global variable ‘gene_id’ find_url_ebi_safe: no visible binding for global variable ‘run_accession’ floss: no visible binding for global variable ‘ORFGrouping’ floss: no visible binding for global variable ‘widths’ floss: no visible global function definition for ‘.’ floss: no visible binding for global variable ‘CDSGrouping’ floss: no visible binding for global variable ‘fraction.x’ floss: no visible binding for global variable ‘fraction.y’ gSort: no visible binding for global variable ‘grnames’ geneToSymbol: no visible global function definition for ‘organism’ geneToSymbol: no visible binding for global variable ‘ensembl_gene_id’ geneToSymbol: no visible binding for global variable ‘external_gene_name’ geneToSymbol: no visible binding for global variable ‘ensembl_transcript_id’ geneToSymbol: no visible binding for global variable ‘uniprotswissprot’ getNGenesCoverage: no visible global function definition for ‘.’ getNGenesCoverage: no visible binding for global variable ‘genes’ getNGenesCoverage: no visible binding for global variable ‘fraction’ get_phix_genome: no visible binding for global variable ‘phix.url’ go_analaysis_gorilla: no visible global function definition for ‘browseURL’ grl_has_any_valid_lengths: no visible binding for global variable ‘grl’ initiationScore: no visible global function definition for ‘.’ initiationScore: no visible binding for global variable ‘dif’ initiationScore: no visible binding for global variable ‘fraction’ initiationScore: no visible binding for global variable ‘genes’ initiationScore: no visible binding for global variable ‘difPer’ install.sratoolkit: no visible binding for global variable ‘osVersion’ isPeriodic: no visible binding for global variable ‘spec’ kozakHeatmap: no visible global function definition for ‘.’ kozakHeatmap: no visible binding for global variable ‘variable’ kozakHeatmap: no visible binding for global variable ‘value’ kozakHeatmap: no visible binding for global variable ‘count_seq_pos_with_count’ kozakHeatmap: no visible binding for global variable ‘median_score’ kozak_IR_ranking: no visible global function definition for ‘.’ kozak_IR_ranking: no visible binding for global variable ‘IR’ kozak_IR_ranking: no visible binding for global variable ‘upstream_kozak_strength’ kozak_IR_ranking: no visible binding for global variable ‘count’ kozak_IR_ranking: no visible binding for global variable ‘mean_IR’ list.genomes: no visible binding for global variable ‘STAR_index’ longestORFs: no visible global function definition for ‘.’ metaWindow: no visible binding for global variable ‘position’ metaWindow: no visible binding for global variable ‘frame’ metadata.autnaming: no visible binding for global variable ‘LIBRARYTYPE’ metadata.autnaming: no visible binding for global variable ‘LibraryStrategy’ ofst_merge_internal: no visible binding for global variable ‘file_paths’ orfFrameDistributions : : no visible binding for global variable ‘fraction’ orfFrameDistributions: no visible binding for global variable ‘percent’ orfFrameDistributions: no visible binding for global variable ‘fraction’ orfFrameDistributions: no visible binding for global variable ‘percent_length’ orfFrameDistributions: no visible global function definition for ‘.’ orfFrameDistributions: no visible binding for global variable ‘best_frame’ orfScore: no visible binding for global variable ‘genes’ orfScore: no visible binding for global variable ‘frame’ orfScore: no visible binding for global variable ‘frame_one_RP’ orfScore: no visible binding for global variable ‘frame_two_RP’ pSitePlot: no visible binding for global variable ‘count’ pSitePlot: no visible binding for global variable ‘frame’ pSitePlot: no visible binding for global variable ‘position’ readBam: no visible global function definition for ‘bamTag<-’ readBam: no visible global function definition for ‘bamWhat<-’ readLengthTable: no visible binding for global variable ‘counts_per_sample’ readLengthTable: no visible binding for global variable ‘sample_id’ readLengthTable: no visible binding for global variable ‘perc_of_counts_per_sample’ regionPerReadLength : : no visible binding for global variable ‘fraction’ remakeTxdbExonIds: no visible global function definition for ‘.’ remakeTxdbExonIds: no visible binding for global variable ‘chr’ removeTxdbExons: no visible binding for global variable ‘exon_rank’ removeTxdbExons: no visible binding for global variable ‘ranks’ riboORFsFolder: no visible global function definition for ‘organism’ ribo_fft: no visible binding for global variable ‘fraction’ ribo_fft_plot: no visible binding for global variable ‘periods’ ribo_fft_plot: no visible binding for global variable ‘amplitude’ rnaNormalize: no visible binding for global variable ‘genes’ rnaNormalize: no visible binding for global variable ‘feature’ sample_info_append_SRA: no visible binding for global variable ‘GEO’ scaledWindowPositions: no visible binding for global variable ‘scalingFactor’ scaledWindowPositions: no visible binding for global variable ‘genes’ scaledWindowPositions: no visible binding for global variable ‘position’ scaledWindowPositions: no visible global function definition for ‘.’ scoreSummarizedExperiment: no visible global function definition for ‘rowSums2’ seq_usage: no visible binding for global variable ‘variable’ seq_usage: no visible binding for global variable ‘codon_sum’ seq_usage: no visible global function definition for ‘.’ seq_usage: no visible binding for global variable ‘gene_sum’ seq_usage: no visible binding for global variable ‘N_AA_of_type_per_gene’ seq_usage: no visible binding for global variable ‘as_prob_normalized’ seq_usage: no visible binding for global variable ‘N_total’ seq_usage: no visible binding for global variable ‘N’ seq_usage: no visible binding for global variable ‘mean_txNorm’ seq_usage: no visible binding for global variable ‘sum_txNorm’ seq_usage: no visible binding for global variable ‘dispersion’ seq_usage: no visible binding for global variable ‘dispersion_txNorm’ seq_usage: no visible binding for global variable ‘var_txNorm’ seq_usage: no visible binding for global variable ‘mean_percentage’ seq_usage: no visible binding for global variable ‘mean_txNorm_prob’ seq_usage: no visible binding for global variable ‘mean_txNorm_percentage’ seq_usage: no visible binding for global variable ‘relative_to_max_score’ shiftPlots : : no visible binding for global variable ‘frame’ shiftPlots : : no visible binding for global variable ‘position’ te.plot: no visible global function definition for ‘rowMin’ te.plot: no visible binding for global variable ‘variable’ te.plot: no visible binding for global variable ‘LFC_TE’ te.plot: no visible binding for global variable ‘rfp_log2’ te.plot: no visible binding for global variable ‘rna_log2’ te.plot: no visible binding for global variable ‘rna_log10’ te.table: no visible global function definition for ‘rowMin’ te.table: no visible binding for global variable ‘variable’ te.table: no visible binding for global variable ‘TE_log2’ te.table: no visible binding for global variable ‘rfp_log2’ te.table: no visible binding for global variable ‘rna_log2’ te_rna.plot: no visible binding for global variable ‘subtitle’ te_rna.plot: no visible binding for global variable ‘rna_log10’ te_rna.plot: no visible binding for global variable ‘TE_log2’ topMotif: no visible binding for global variable ‘seq1’ topMotif: no visible binding for global variable ‘seq2’ topMotif: no visible binding for global variable ‘seq3’ topMotif: no visible binding for global variable ‘seq4’ topMotif: no visible binding for global variable ‘seq5’ transcriptWindow: no visible binding for global variable ‘fractions’ transcriptWindow: no visible binding for global variable ‘feature’ unlistToExtremities: no visible binding for global variable ‘group_name’ unlistToExtremities: no visible global function definition for ‘.’ unlistToExtremities: no visible binding for global variable ‘group’ windowCoveragePlot: no visible binding for global variable ‘feature’ windowCoveragePlot: no visible binding for global variable ‘fraction’ windowCoveragePlot: no visible binding for global variable ‘fraction_min’ windowCoveragePlot: no visible binding for global variable ‘position’ collapseDuplicatedReads,GAlignmentPairs: no visible global function definition for ‘.’ collapseDuplicatedReads,GAlignmentPairs: no visible binding for global variable ‘start1’ collapseDuplicatedReads,GAlignmentPairs: no visible binding for global variable ‘start2’ collapseDuplicatedReads,GAlignmentPairs: no visible binding for global variable ‘cigar1’ collapseDuplicatedReads,GAlignmentPairs: no visible binding for global variable ‘cigar2’ collapseDuplicatedReads,GAlignments: no visible global function definition for ‘.’ collapseDuplicatedReads,GRanges: no visible binding for global variable ‘size’ collapseDuplicatedReads,GRanges: no visible global function definition for ‘.’ collapseDuplicatedReads,data.table: no visible global function definition for ‘.’ design,experiment: no visible binding for global variable ‘..formula’ seqlevels,experiment: no visible binding for global variable ‘df’ show,covRleList: no visible global function definition for ‘head’ Undefined global functions or variables: . ..formula ..to_keep AA CDS CDSGrouping Cor GEO Hx IR LEADERS LFC LFC_TE LIBRARYTYPE LibraryStrategy N N_AA_of_type_per_gene N_total ORFGrouping ORFScores RRS RSS Regulation STAR_index StartCodons StopCodons TE_log2 TOP Transcript Var1 Var2 all_models_sign amplitude as_prob_normalized bamTag<- bamWhat<- best_frame browseURL chr cigar1 cigar2 codon codonSums codon_sum contrast count countRFP count_seq_pos_with_count counts_per_sample df dif difPer disengagementScores dispersion dispersion_txNorm distORFCDS end_segment ensembl_gene_id ensembl_transcript_id entropyRFP exon_rank external_gene_name feature file_forward file_paths file_reverse forward foverlaps fpkmRFP fpkmRNA frac.score fraction fraction.x fraction.y fractionLengths fraction_min fractions frame frame_one_RP frame_two_RP gene_id gene_sum genes grl grnames group group_name head i.end i.start id id_original inFrameCDS ioScore isOverlappingCds kozak label mRNA mad_per_gene meanCounts mean_IR mean_per_gene mean_percentage mean_txNorm mean_txNorm_percentage mean_txNorm_prob median_per_gene median_score merged modzscore organism osVersion pShifted perc_of_counts_per_sample percent percent_length percentage percentage_mrna_aligned percentage_tx_aligned periods phix.url pick position query_id random rankInTx ranks ratio_cds_leader ratio_cds_mrna read length relative_to_max_score rfp.lfc rfp.padj rfp.sign rfp_log2 rna.lfc rna.padj rna.sign rna_log10 rna_log2 rowMin rowSums2 run_accession sample_id sample_total scalingFactor sd_per_gene seq1 seq2 seq3 seq4 seq5 seqs size spec species spots start1 start2 startCodonCoverage startRegionRelative start_segment subtitle sum.count sum_per_gene sum_txNorm te te.lfc te.padj te.sign uniprotswissprot upstream_kozak_strength utr3_len utr5_len value var_txNorm variable widths windowMAD windowMean windowMedian windowSD zscore Consider adding importFrom("base", "length") importFrom("graphics", "frame") importFrom("stats", "df") importFrom("utils", "browseURL", "head", "osVersion") 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: DTEG.analysis.Rd: SummarizedExperiment ORFikQC.Rd: SummarizedExperiment QCreport.Rd: SummarizedExperiment allFeaturesHelper.Rd: GRangesList, GAlignments, GRanges, FaFile asTX.Rd: GRangesList assignFirstExonsStartSite.Rd: GRangesList assignLastExonsStopSite.Rd: GRangesList bedToGR.Rd: GRanges codonSumsPerGroup.Rd: GRangesList, GAlignments, GRanges codon_usage_exp.Rd: FaFile computeFeatures.Rd: GRangesList, GAlignments, GRanges, FaFile computeFeaturesCage.Rd: GRangesList, GAlignments, GRanges, FaFile coverageByTranscriptC.Rd: coverageByTranscript, GRangesList coverageByTranscriptW.Rd: coverageByTranscript, GRanges, GAlignments, GRangesList coveragePerTiling.Rd: GRangesList, GAlignments, GRanges detectRibosomeShifts.Rd: GAlignments disengagementScore.Rd: GRangesList, TxDb distToCds.Rd: GRangesList distToTSS.Rd: GRangesList downstreamFromPerGroup.Rd: GRangesList downstreamOfPerGroup.Rd: GRangesList entropy.Rd: GRangesList, GRanges, GAlignments experiment-class.Rd: SummarizedExperiment export.ofst-GAlignmentPairs-method.Rd: fst-package export.ofst-GAlignments-method.Rd: fst-package export.ofst-GRanges-method.Rd: fst-package export.ofst.Rd: fst-package extendLeaders.Rd: GRangesList extendTrailers.Rd: GRangesList fimport.Rd: seqlevelsStyle, Seqinfo, GAlignments, GRanges findFa.Rd: FaFile findMapORFs.Rd: GRangesList, FaFile findORFs.Rd: IRanges, IRangesList, FaFile findUORFs.Rd: FaFile firstEndPerGroup.Rd: GRangesList firstExonPerGroup.Rd: GRangesList firstStartPerGroup.Rd: GRangesList flankPerGroup.Rd: GRangesList floss.Rd: GRangesList, GRanges, GAlignments fpkm.Rd: GRangesList, GRanges, GAlignments fractionLength.Rd: GRangesList fread.bed.Rd: import.bed, seqlevelsStyle, Seqinfo, GRanges gSort.Rd: GRangesList hasHits.Rd: GRangesList heatMapL.Rd: GRangesList heatMapRegion.Rd: GRanges, GAlignments heatMap_single.Rd: GRangesList, GAlignments, GRanges import.ofst.Rd: fst-package, GAlignmentPairs initiationScore.Rd: GRangesList, GAlignments insideOutsideORF.Rd: GRangesList, TxDb kozakSequenceScore.Rd: GRangesList, FaFile kozak_IR_ranking.Rd: FaFile lastExonEndPerGroup.Rd: GRangesList lastExonPerGroup.Rd: GRangesList lastExonStartPerGroup.Rd: GRangesList loadTxdb.Rd: seqlevelsStyle, Seqinfo longestORFs.Rd: GRangesList makeExonRanks.Rd: GRangesList makeORFNames.Rd: GRangesList makeSummarizedExperimentFromBam.Rd: GRangesList, SummarizedExperiment mapToGRanges.Rd: GRangesList matchNaming.Rd: GRangesList matchSeqStyle.Rd: seqlevelsStyle, Seqinfo numCodons.Rd: GRangesList numExonsPerGroup.Rd: GRangesList optimizeReads.Rd: GRangesList optimizedTranscriptLengths.Rd: transcriptLengths orfID.Rd: GRangesList orfScore.Rd: GRangesList, GAlignments, GRanges outputLibs.Rd: seqlevelsStyle, Seqinfo rankOrder.Rd: GRangesList readBam.Rd: readGAlignments, seqlevelsStyle, Seqinfo, GAlignments, GAlignmentPairs readBigWig.Rd: seqlevelsStyle, Seqinfo, GRanges readWig.Rd: seqlevelsStyle, Seqinfo, GRanges reduceKeepAttr.Rd: GRangesList, reduce regionPerReadLength.Rd: GRangesList, GAlignments, GRanges reverseMinusStrandPerGroup.Rd: GRangesList ribo_fft.Rd: GAlignments, GRanges, GRangesList ribosomeReleaseScore.Rd: GRangesList, GAlignments, GRanges ribosomeStallingScore.Rd: GRangesList rnaNormalize.Rd: GRangesList scaledWindowPositions.Rd: GRangesList, GAlignments, GRanges seqnamesPerGroup.Rd: GRangesList shiftFootprints.Rd: GAlignments, GRanges sortPerGroup.Rd: sort.GenomicRanges, GRangesList splitIn3Tx.Rd: GRangesList startCodons.Rd: GRangesList startRegion.Rd: GRangesList startRegionCoverage.Rd: GRangesList startRegionString.Rd: GRangesList, FaFile startSites.Rd: GRangesList stopCodons.Rd: GRangesList stopRegion.Rd: GRangesList stopSites.Rd: GRangesList strandBool.Rd: GRangesList strandPerGroup.Rd: GRangesList tile1.Rd: GRangesList transcriptWindow.Rd: GRangesList transcriptWindowPer.Rd: GRangesList translationalEff.Rd: GRangesList, GRanges, GAlignments txNames.Rd: GRangesList txSeqsFromFa.Rd: GRangesList, FaFile, extractTranscriptSeqs, DNAStringSet uniqueGroups.Rd: GRangesList uniqueOrder.Rd: GRangesList, GRanges unlistToExtremities.Rd: GRangesList upstreamFromPerGroup.Rd: GRangesList upstreamOfPerGroup.Rd: GRangesList validSeqlevels.Rd: GRangesList widthPerGroup.Rd: GRangesList windowPerGroup.Rd: GRangesList windowPerReadLength.Rd: GRangesList, GAlignments, GRanges Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed orfFrameDistributions 65.826 7.100 29.397 orfScore 27.464 3.680 4.968 makeTxdbFromGenome 24.872 1.205 26.794 codon_usage_exp 13.644 0.618 14.333 STAR.allsteps.multiQC 7.714 0.329 8.219 shiftPlots 6.022 1.583 1.145 detect_ribo_orfs 5.698 0.358 5.878 codon_usage 5.678 0.071 6.449 shiftFootprintsByExperiment 0.938 0.088 8.121 DEG_model_results 0.637 0.145 5.658 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 7 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/ORFik.Rcheck/00check.log’ for details.