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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ORFik.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ORFik_1.26.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/ORFik.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ORFik/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ORFik' version '1.26.0'
* 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 whether package 'ORFik' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking installed package size ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    extdata   1.3Mb
    libs      1.0Mb
* 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 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 : <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'
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 : <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'
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 : <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'
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'
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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/ORFik/libs/x64/ORFik.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
codon_usage_exp             9.36   0.19   29.78
detect_ribo_orfs            8.69   0.12   28.38
findUORFs_exp               6.47   0.11    6.58
computeFeatures             5.08   0.08    5.15
codon_usage_plot            4.82   0.09   23.23
orfFrameDistributions       3.31   0.03   40.46
shiftFootprintsByExperiment 2.82   0.02   27.81
regionPerReadLength         2.74   0.05   38.54
outputLibs                  2.36   0.03   26.16
* 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: 6 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/ORFik.Rcheck/00check.log'
for details.