############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ORFik.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ORFik_1.25.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ORFik.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘ORFik/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ORFik’ version ‘1.25.3’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * 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 ‘ORFik’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * checking installed package size ... NOTE installed size is 7.3Mb sub-directories of 1Mb or more: R 1.0Mb extdata 1.4Mb 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 ... 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: ‘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. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE detect_ribo_orfs: warning in outputLibs(df, type = "pshifted", output = "envirlist"): partial argument match of 'output' to 'output.mode' 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_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’ DTEG.plot: no visible binding for global variable ‘rfp’ QCplots: no visible binding for global variable ‘leaders’ QCplots: no visible binding for global variable ‘trailers’ 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: no visible binding for global variable ‘sample_id’ STAR.multiQC: no visible binding for global variable ‘value’ 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’ 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’ 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 ‘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’ 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 ‘sd_per_gene’ findPeaksPerGene: no visible binding for global variable ‘zscore’ findPeaksPerGene: no visible binding for global variable ‘gene_id’ find_url_ebi_safe: no visible binding for global variable ‘run_accession’ flankPerGroup: no visible global function definition for ‘.’ flankPerGroup: no visible binding for global variable ‘group_name’ 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 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’ 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’ 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’ pcaExperiment: no visible binding for global variable ‘PC1’ pcaExperiment: no visible binding for global variable ‘PC2’ 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’ 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’ 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’ 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 Hx IR LEADERS LFC LFC_TE LIBRARYTYPE LibraryStrategy N N_AA_of_type_per_gene N_total ORFGrouping ORFScores PC1 PC2 RRS RSS Regulation STAR_index StartCodons StopCodons TE_log2 TOP Transcript Var1 Var2 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 ensembl_gene_id ensembl_transcript_id entropyRFP exon_rank external_gene_name feature forward 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 grnames group_name head id inFrameCDS ioScore isOverlappingCds kozak leaders mRNA meanCounts mean_IR mean_per_gene mean_percentage mean_txNorm mean_txNorm_percentage mean_txNorm_prob median_per_gene median_score merged osVersion pShifted perc_of_counts_per_sample percent percent_length percentage percentage_mrna_aligned percentage_tx_aligned periods phix.url pick position random rankInTx ranks ratio_cds_leader ratio_cds_mrna read length relative_to_max_score rfp rfp_log2 rna rna_log10 rna_log2 rowMin rowSums2 run_accession sample_id sample_total scalingFactor sd_per_gene seq1 seq2 seq3 seq4 seq5 seqs size spec spots start1 start2 startCodonCoverage startRegionRelative subtitle sum.count sum_per_gene sum_txNorm te trailers uniprotswissprot upstream_kozak_strength utr3_len utr5_len value var_txNorm variable widths windowMean 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 ... NOTE checkRd: (-1) STAR.align.folder.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) STAR.align.folder.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) STAR.align.folder.Rd:72: Lost braces in \itemize; meant \describe ? checkRd: (-1) STAR.align.folder.Rd:73: Lost braces in \itemize; meant \describe ? checkRd: (-1) STAR.align.folder.Rd:74: Lost braces in \itemize; meant \describe ? checkRd: (-1) STAR.align.folder.Rd:75: Lost braces in \itemize; meant \describe ? checkRd: (-1) STAR.align.folder.Rd:76: Lost braces in \itemize; meant \describe ? checkRd: (-1) STAR.align.folder.Rd:77-78: Lost braces in \itemize; meant \describe ? checkRd: (-1) STAR.align.folder.Rd:101: Lost braces in \itemize; meant \describe ? checkRd: (-1) STAR.align.folder.Rd:102: Lost braces in \itemize; meant \describe ? checkRd: (-1) STAR.align.folder.Rd:103: Lost braces in \itemize; meant \describe ? checkRd: (-1) STAR.align.folder.Rd:113: Lost braces in \itemize; meant \describe ? checkRd: (-1) STAR.align.folder.Rd:114: Lost braces in \itemize; meant \describe ? checkRd: (-1) STAR.align.single.Rd:61: Lost braces in \itemize; meant \describe ? checkRd: (-1) STAR.align.single.Rd:62: Lost braces in \itemize; meant \describe ? checkRd: (-1) STAR.align.single.Rd:63: Lost braces in \itemize; meant \describe ? checkRd: (-1) STAR.align.single.Rd:64: Lost braces in \itemize; meant \describe ? checkRd: (-1) STAR.align.single.Rd:65: Lost braces in \itemize; meant \describe ? checkRd: (-1) STAR.align.single.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) STAR.align.single.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) STAR.align.single.Rd:68-69: Lost braces in \itemize; meant \describe ? checkRd: (-1) STAR.align.single.Rd:92: Lost braces in \itemize; meant \describe ? checkRd: (-1) STAR.align.single.Rd:93: Lost braces in \itemize; meant \describe ? checkRd: (-1) STAR.align.single.Rd:94: Lost braces in \itemize; meant \describe ? checkRd: (-1) STAR.align.single.Rd:104: Lost braces in \itemize; meant \describe ? checkRd: (-1) STAR.align.single.Rd:105: Lost braces in \itemize; meant \describe ? checkRd: (-1) codon_usage.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) codon_usage.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) codon_usage.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) codon_usage.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) codon_usage.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) codon_usage.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) codon_usage.Rd:62-63: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) codon_usage.Rd:65-68: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) codon_usage.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) codon_usage.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) codon_usage.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) codon_usage_exp.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) codon_usage_exp.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) codon_usage_exp.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) codon_usage_exp.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) codon_usage_exp.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) codon_usage_exp.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) codon_usage_exp.Rd:74-75: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) codon_usage_exp.Rd:77-80: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) codon_usage_exp.Rd:81: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) codon_usage_exp.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) codon_usage_exp.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) computeFeatures.Rd:76: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeFeatures.Rd:77: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeFeatures.Rd:78: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeFeatures.Rd:79: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeFeatures.Rd:80: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeFeatures.Rd:81: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeFeatures.Rd:82: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeFeatures.Rd:83: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeFeatures.Rd:84: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeFeatures.Rd:85: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeFeatures.Rd:86: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeFeatures.Rd:87: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeFeatures.Rd:88: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeFeatures.Rd:89: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeFeatures.Rd:93: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeFeatures.Rd:94: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeFeatures.Rd:95: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeFeatures.Rd:96: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeFeatures.Rd:97: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeFeatures.Rd:101: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeFeatures.Rd:102: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeFeatures.Rd:103: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeFeatures.Rd:104: Lost braces in \itemize; meant \describe ? checkRd: (-1) coverageHeatMap.Rd:64: Lost braces in \itemize; meant \describe ? checkRd: (-1) coverageHeatMap.Rd:65: Lost braces in \itemize; meant \describe ? checkRd: (-1) coverageHeatMap.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) coverageHeatMap.Rd:80: Lost braces in \itemize; meant \describe ? checkRd: (-1) coverageHeatMap.Rd:81: Lost braces in \itemize; meant \describe ? checkRd: (-1) coverageHeatMap.Rd:82: Lost braces in \itemize; meant \describe ? checkRd: (-1) coverageHeatMap.Rd:83: Lost braces in \itemize; meant \describe ? checkRd: (-1) detect_ribo_orfs.Rd:36: Lost braces in \itemize; meant \describe ? checkRd: (-1) detect_ribo_orfs.Rd:37: Lost braces in \itemize; meant \describe ? checkRd: (-1) detect_ribo_orfs.Rd:38: Lost braces in \itemize; meant \describe ? checkRd: (-1) detect_ribo_orfs.Rd:39: Lost braces in \itemize; meant \describe ? checkRd: (-1) detect_ribo_orfs.Rd:40: Lost braces in \itemize; meant \describe ? checkRd: (-1) detect_ribo_orfs.Rd:41: Lost braces in \itemize; meant \describe ? checkRd: (-1) detect_ribo_orfs.Rd:42: Lost braces in \itemize; meant \describe ? checkRd: (-1) detect_ribo_orfs.Rd:43: Lost braces in \itemize; meant \describe ? checkRd: (-1) detect_ribo_orfs.Rd:44: Lost braces in \itemize; meant \describe ? checkRd: (-1) experiment-class.Rd:16-17: Lost braces in \itemize; meant \describe ? checkRd: (-1) experiment-class.Rd:18-19: Lost braces in \itemize; meant \describe ? checkRd: (-1) experiment-class.Rd:20: Lost braces in \itemize; meant \describe ? checkRd: (-1) experiment-class.Rd:21-22: Lost braces in \itemize; meant \describe ? checkRd: (-1) experiment-class.Rd:23-27: Lost braces in \itemize; meant \describe ? checkRd: (-1) experiment-class.Rd:28-29: Lost braces in \itemize; meant \describe ? checkRd: (-1) readBam.Rd:13: Lost braces in \itemize; meant \describe ? checkRd: (-1) readBam.Rd:14-16: Lost braces in \itemize; meant \describe ? checkRd: (-1) readBam.Rd:17-20: Lost braces in \itemize; meant \describe ? * 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 'convertLibs.Rd' ‘library.names’ Undocumented arguments in Rd file 'makeSummarizedExperimentFromBam.Rd' ‘force’ Undocumented arguments in Rd file 'outputLibs.Rd' ‘library.names’ Undocumented arguments in Rd file 'simpleLibs.Rd' ‘library.names’ Undocumented arguments in Rd file 'transcriptWindow.Rd' ‘library.names’ 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 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 codon_usage_exp 19.590 1.006 30.070 detect_ribo_orfs 10.784 1.090 12.873 DEG_model 7.732 1.318 9.273 codon_usage 7.774 0.253 13.550 ribo_fft 5.876 0.467 8.441 * 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: 1 WARNING, 6 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/ORFik.Rcheck/00check.log’ for details.