############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ORFik.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ORFik_1.20.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ORFik.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * checking for file ‘ORFik/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ORFik’ version ‘1.20.2’ * 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 C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... NOTE installed size is 5.1Mb sub-directories of 1Mb or more: libs 1.6Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R 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’ 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 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’ 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’ 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’ 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 ‘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 ‘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 ‘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 ‘.’ 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 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 ‘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 ‘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 ‘difPer’ 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 ‘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’ readLengthTable: no visible binding for global variable ‘counts_per_sample’ 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 ‘feature’ scaledWindowPositions: no visible binding for global variable ‘scalingFactor’ 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 ‘.’ collapseDuplicatedReads,data.table: no visible binding for global variable ‘size’ 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 best_frame browseURL chr cigar1 cigar2 codon codonSums codon_sum 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 grnames group_name head 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 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") to your NAMESPACE file. * 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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... 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 19.869 0.848 34.772 findUORFs_exp 9.859 0.040 10.124 computeFeatures 8.745 0.090 12.124 codon_usage_plot 6.472 0.464 10.404 codon_usage 5.074 0.057 6.603 extendLeaders 2.979 0.030 5.595 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘Annotation_Alignment.Rmd’ using ‘UTF-8’... OK ‘Importing_Data.Rmd’ using ‘UTF-8’... OK ‘ORFikExperiment.Rmd’ using ‘UTF-8’... OK ‘ORFikOverview.Rmd’ using ‘UTF-8’... OK ‘Ribo-seq_pipeline.Rmd’ using ‘UTF-8’... OK ‘Working_with_transcripts.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 5 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/ORFik.Rcheck/00check.log’ for details.