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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ORFik.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ORFik_1.25.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ORFik.Rcheck’
* using R version 4.4.1 RC (2024-06-06 r86719)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘biomartr:::getENSEMBL.gtf’ ‘biomartr:::getENSEMBL.Seq’
  ‘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
detect_ribo_orfs: warning in outputLibs(df, type = "pshifted", output =
  "envirlist"): partial argument match of 'output' to 'output.mode'
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘percentage_mrna_aligned’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘mRNA’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘percentage_tx_aligned’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘Transcript’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘ratio_cds_mrna’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘CDS’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘ratio_cds_leader’
alignmentFeatureStatistics : <anonymous>: 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’
codonSumsPerGroup: no visible binding for global variable ‘genes’
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’
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’
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’
DEG_model_simple: no visible binding for global variable ‘id’
DEG_model_simple: no visible binding for global variable ‘contrast’
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’
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’
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’
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’
filter_empty_runs: no visible binding for global variable ‘spots’
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’
find_url_ebi_safe: no visible binding for global variable
  ‘run_accession’
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’
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’
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’
get_phix_genome: no visible binding for global variable ‘phix.url’
getNGenesCoverage: no visible global function definition for ‘.’
getNGenesCoverage: no visible binding for global variable ‘genes’
getNGenesCoverage: no visible binding for global variable ‘fraction’
gSort: no visible binding for global variable ‘grnames’
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’
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’
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’
list.genomes: no visible binding for global variable ‘STAR_index’
longestORFs: no visible global function definition for ‘.’
metadata.autnaming: no visible binding for global variable
  ‘LIBRARYTYPE’
metadata.autnaming: no visible binding for global variable
  ‘LibraryStrategy’
metaWindow: no visible binding for global variable ‘position’
metaWindow: no visible binding for global variable ‘frame’
orfFrameDistributions : <anonymous>: 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’
pcaExperiment: no visible binding for global variable ‘PC1’
pcaExperiment: no visible binding for global variable ‘PC2’
pSitePlot: no visible binding for global variable ‘count’
pSitePlot: no visible binding for global variable ‘frame’
pSitePlot: no visible binding for global variable ‘position’
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’
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 : <anonymous>: 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’
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’
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 : <anonymous>: no visible binding for global variable
  ‘frame’
shiftPlots : <anonymous>: no visible binding for global variable
  ‘position’
STAR.multiQC: no visible binding for global variable ‘sample_id’
STAR.multiQC: no visible binding for global variable ‘value’
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’
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’
TOP.Motif.ecdf: no visible binding for global variable ‘seq1’
TOP.Motif.ecdf: no visible binding for global variable ‘TOP’
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,data.table: no visible global function
  definition for ‘.’
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 ‘.’
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 amplitude as_prob_normalized bamTag<-
  bamWhat<- best_frame browseURL CDS CDSGrouping chr cigar1 cigar2
  codon codon_sum codonSums contrast Cor count count_seq_pos_with_count
  countRFP 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_min fraction.x
  fraction.y fractionLengths fractions frame frame_one_RP frame_two_RP
  gene_id gene_sum genes grnames group_name head Hx id inFrameCDS
  ioScore IR isOverlappingCds kozak leaders LEADERS LFC LFC_TE
  LibraryStrategy LIBRARYTYPE mean_IR mean_per_gene mean_percentage
  mean_txNorm mean_txNorm_percentage mean_txNorm_prob meanCounts
  median_per_gene median_score merged mRNA N N_AA_of_type_per_gene
  N_total ORFGrouping ORFScores osVersion PC1 PC2
  perc_of_counts_per_sample percent percent_length percentage
  percentage_mrna_aligned percentage_tx_aligned periods phix.url pick
  position pShifted random rankInTx ranks ratio_cds_leader
  ratio_cds_mrna read length Regulation relative_to_max_score rfp
  rfp_log2 rna rna_log10 rna_log2 rowMin rowSums2 RRS RSS run_accession
  sample_id sample_total scalingFactor sd_per_gene seq1 seq2 seq3 seq4
  seq5 seqs size spec spots STAR_index start1 start2 startCodonCoverage
  StartCodons startRegionRelative StopCodons subtitle sum_per_gene
  sum_txNorm sum.count te TE_log2 TOP trailers Transcript
  uniprotswissprot upstream_kozak_strength utr3_len utr5_len value
  var_txNorm Var1 Var2 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) 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) 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) 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 ?
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 ?
* 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
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/ORFik.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ORFik
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘ORFik’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c findORFsHelpers.cpp -o findORFsHelpers.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c findOrfs.cpp -o findOrfs.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c findOrfsFasta.cpp -o findOrfsFasta.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c pmapFromTranscripts.cpp -o pmapFromTranscripts.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c pmapToTranscripts.cpp -o pmapToTranscripts.o
pmapToTranscripts.cpp:22:7: warning: variable 'currentWidth' set but not used [-Wunused-but-set-variable]
  int currentWidth = 0;
      ^
pmapToTranscripts.cpp:68:7: warning: variable 'currentWidth' set but not used [-Wunused-but-set-variable]
  int currentWidth = 0;
      ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o ORFik.so RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o pmapFromTranscripts.o pmapToTranscripts.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-ORFik/00new/ORFik/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘symbols’ in package ‘ORFik’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ORFik)

R version 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(ORFik)
Loading required package: IRanges
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    anyDuplicated, aperm, append, as.data.frame, basename, cbind,
    colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
    get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    expand.grid, I, unname

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: Rsamtools

Attaching package: 'ORFik'

The following object is masked from 'package:graphics':

    symbols

> 
> test_check("ORFik")
Error in x$.self$finalize() : attempt to apply non-function
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 427 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
 26.420   1.021  27.392