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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ORFik.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ORFik_1.29.9.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ORFik.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ORFik/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ORFik’ version ‘1.29.9’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... NOTE
Found the following non-portable file path:
  ORFik/inst/extdata/test_processing/contaminants_depletion/LOGS/contaminants_output_template_Log.final.out

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ORFik’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R         1.2Mb
    extdata   1.5Mb
    help      1.0Mb
    libs      3.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... NOTE
Warning: no function found corresponding to methods exports from ‘ORFik’ for: ‘organism’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘GenomicFeatures:::.merge_seqinfo_and_infer_missing_seqlengths’
  ‘IRanges:::regroupBySupergroup’ ‘S4Vectors:::normarg_mcols’
  ‘biomartr:::getENSEMBL.Seq’ ‘biomartr:::getENSEMBL.gtf’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘go_analaysis_gorilla’ ‘pseudoIntronsPerGroup’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DEG.plot.static: no visible binding for global variable ‘Regulation’
DEG.plot.static: no visible binding for global variable ‘meanCounts’
DEG.plot.static: no visible binding for global variable ‘LFC’
DEG_gorilla: no visible binding for global variable ‘contrast’
DEG_gorilla: no visible binding for global variable ‘Regulation’
DEG_gorilla: no visible binding for global variable
  ‘external_gene_name’
DEG_model_simple: no visible binding for global variable ‘id’
DEG_model_simple: no visible binding for global variable ‘contrast’
DTEG.plot: no visible binding for global variable ‘Regulation’
DTEG.plot: no visible binding for global variable ‘rna.lfc’
DTEG.plot: no visible binding for global variable ‘rfp.lfc’
DTEG_add_regulation_categories: no visible binding for global variable
  ‘te.sign’
DTEG_add_regulation_categories: no visible binding for global variable
  ‘rfp.sign’
DTEG_add_regulation_categories: no visible binding for global variable
  ‘rna.sign’
DTEG_add_regulation_categories: no visible binding for global variable
  ‘Regulation’
DTEG_add_regulation_categories: no visible binding for global variable
  ‘all_models_sign’
DTEG_add_regulation_categories: no visible binding for global variable
  ‘te.lfc’
DTEG_add_regulation_categories: no visible binding for global variable
  ‘rna.lfc’
DTEG_pair_results: no visible binding for global variable ‘rna.sign’
DTEG_pair_results: no visible binding for global variable ‘rna.padj’
DTEG_pair_results: no visible binding for global variable ‘rfp.sign’
DTEG_pair_results: no visible binding for global variable ‘rfp.padj’
DTEG_pair_results: no visible binding for global variable ‘te.sign’
DTEG_pair_results: no visible binding for global variable ‘te.padj’
DTEG_pair_results: no visible binding for global variable
  ‘all_models_sign’
QCstats.plot: no visible binding for global variable ‘variable’
QCstats.plot: no visible binding for global variable ‘sample_total’
QCstats.plot: no visible binding for global variable ‘value’
QCstats.plot: no visible global function definition for ‘.’
QCstats.plot: no visible binding for global variable ‘sample_id’
QCstats.plot: no visible binding for global variable ‘percentage’
QCstats.plot: no visible binding for global variable
  ‘perc_of_counts_per_sample’
QCstats.plot: no visible binding for global variable ‘read length’
RiboQC.plot: no visible binding for global variable ‘variable’
RiboQC.plot: no visible binding for global variable ‘sample_total’
RiboQC.plot: no visible binding for global variable ‘value’
RiboQC.plot: no visible global function definition for ‘.’
RiboQC.plot: no visible binding for global variable ‘sample_id’
RiboQC.plot: no visible binding for global variable ‘percentage’
RiboQC.plot: no visible binding for global variable ‘percent’
RiboQC.plot: no visible binding for global variable ‘frame’
STAR.multiQC_plot: no visible binding for global variable ‘value’
STAR.multiQC_plot: no visible binding for global variable ‘sample_id’
TOP.Motif.ecdf: no visible binding for global variable ‘seq1’
TOP.Motif.ecdf: no visible binding for global variable ‘TOP’
alignmentFeatureStatistics : <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’
append_gene_symbols: no visible binding for global variable
  ‘id_original’
append_gene_symbols: no visible binding for global variable ‘id’
append_gene_symbols: no visible binding for global variable
  ‘external_gene_name’
append_gene_symbols: no visible binding for global variable ‘label’
artificial.orfs: no visible binding for global variable ‘random’
artificial.orfs: no visible binding for global variable ‘pick’
artificial.orfs: no visible global function definition for ‘.’
bamLoadCollapsedScores: no visible global function definition for
  ‘bamTag<-’
bamLoadCollapsedScores: no visible global function definition for
  ‘bamWhat<-’
browseSRA: no visible global function definition for ‘browseURL’
cellTypeNames: missing arguments not allowed in calls to ‘c’
codonSumsPerGroup: no visible binding for global variable ‘genes’
codon_usage: no visible binding for global variable ‘merged’
codon_usage: no visible binding for global variable ‘AA’
codon_usage: no visible binding for global variable ‘codon’
codon_usage_plot: no visible binding for global variable ‘seqs’
collapse.by.scores: no visible global function definition for ‘.’
collapse.fastq.internal: no visible binding for global variable ‘N’
cor_plot: no visible binding for global variable ‘Var2’
cor_plot: no visible binding for global variable ‘Var1’
cor_plot: no visible binding for global variable ‘Cor’
cor_table: no visible binding for global variable ‘Var1’
cor_table: no visible binding for global variable ‘Var2’
cor_table: no visible binding for global variable ‘Cor’
coverageByTranscriptFST: no visible binding for global variable
  ‘file_forward’
coverageByTranscriptFST: no visible binding for global variable
  ‘file_reverse’
coverageByTranscriptFST : <anonymous>: no visible binding for global
  variable ‘chr’
coverageByTranscriptFST : <anonymous>: no visible binding for global
  variable ‘query_id’
coverageByTranscriptFST : <anonymous>: no visible global function
  definition for ‘foverlaps’
coverageByTranscriptFST : <anonymous>: no visible binding for global
  variable ‘start_segment’
coverageByTranscriptFST : <anonymous>: no visible binding for global
  variable ‘i.start’
coverageByTranscriptFST : <anonymous>: no visible binding for global
  variable ‘end_segment’
coverageByTranscriptFST : <anonymous>: no visible binding for global
  variable ‘i.end’
coverageByTranscriptFST : <anonymous>: no visible binding for global
  variable ‘file_forward’
coverageByTranscriptFST : <anonymous>: no visible binding for global
  variable ‘file_reverse’
coverageByTranscriptFST : <anonymous>: no visible global function
  definition for ‘.’
coverageHeatMap: no visible binding for global variable ‘position’
coverageHeatMap: no visible binding for global variable ‘fraction’
coveragePerORFStatistics: no visible global function definition for ‘.’
coveragePerORFStatistics: no visible binding for global variable
  ‘count’
coveragePerORFStatistics: no visible binding for global variable
  ‘genes’
coverageScorings: no visible binding for global variable ‘count’
coverageScorings: no visible binding for global variable ‘zscore’
coverageScorings: no visible binding for global variable ‘windowMean’
coverageScorings: no visible binding for global variable ‘windowSD’
coverageScorings: no visible global function definition for ‘.’
coverageScorings: no visible binding for global variable ‘modzscore’
coverageScorings: no visible binding for global variable ‘windowMedian’
coverageScorings: no visible binding for global variable ‘windowMAD’
coverageScorings: no visible binding for global variable ‘gene_sum’
coverageScorings: no visible binding for global variable ‘fraction’
coverage_random_access_file: no visible binding for global variable
  ‘count’
coverage_random_access_file: no visible binding for global variable
  ‘genes’
coverage_random_access_file: no visible binding for global variable
  ‘position’
coverage_random_access_file: no visible binding for global variable
  ‘frame’
coverage_to_dt: no visible binding for global variable ‘frame’
coverage_to_dt: no visible binding for global variable ‘genes’
coverage_to_dt: no visible binding for global variable ‘position’
detectRibosomeShifts: no visible global function definition for ‘.’
detectRibosomeShifts: no visible binding for global variable ‘size’
detectRibosomeShifts: no visible binding for global variable ‘fraction’
detectRibosomeShifts: no visible binding for global variable ‘pShifted’
detectRibosomeShifts: no visible binding for global variable
  ‘sum.count’
detectRibosomeShifts: no visible binding for global variable ‘count’
detectRibosomeShifts: no visible binding for global variable ‘genes’
detectRibosomeShifts: no visible binding for global variable
  ‘frac.score’
detect_ribo_orfs: no visible global function definition for ‘organism’
download_gene_homologues: no visible binding for global variable
  ‘species’
entropy: no visible binding for global variable ‘Hx’
entropy: no visible binding for global variable ‘codonSums’
entropy: no visible global function definition for ‘.’
entropy: no visible binding for global variable ‘genes’
experiment_parse_list_info: no visible binding for global variable
  ‘index’
fetch_xml_attributes: no visible binding for global variable
  ‘..to_keep’
filterExtremePeakGenes: no visible binding for global variable ‘count’
filterExtremePeakGenes: no visible binding for global variable
  ‘median_per_gene’
filterExtremePeakGenes: no visible binding for global variable ‘genes’
filterExtremePeakGenes: no visible global function definition for ‘.’
filterTranscripts: no visible binding for global variable ‘utr5_len’
filterTranscripts: no visible binding for global variable ‘utr3_len’
filter_empty_runs: no visible binding for global variable ‘spots’
findNGSPairs: no visible global function definition for ‘.’
findNGSPairs: no visible binding for global variable ‘forward’
findPeaksPerGene: no visible binding for global variable ‘sum_per_gene’
findPeaksPerGene: no visible binding for global variable ‘count’
findPeaksPerGene: no visible binding for global variable ‘genes’
findPeaksPerGene: no visible binding for global variable
  ‘mean_per_gene’
findPeaksPerGene: no visible binding for global variable
  ‘median_per_gene’
findPeaksPerGene: no visible binding for global variable ‘sd_per_gene’
findPeaksPerGene: no visible binding for global variable ‘mad_per_gene’
findPeaksPerGene: no visible binding for global variable ‘zscore’
findPeaksPerGene: no visible binding for global variable ‘modzscore’
findPeaksPerGene: no visible binding for global variable ‘gene_id’
find_url_ebi_safe: no visible binding for global variable
  ‘run_accession’
floss: no visible binding for global variable ‘ORFGrouping’
floss: no visible binding for global variable ‘widths’
floss: no visible global function definition for ‘.’
floss: no visible binding for global variable ‘CDSGrouping’
floss: no visible binding for global variable ‘fraction.x’
floss: no visible binding for global variable ‘fraction.y’
gSort: no visible binding for global variable ‘grnames’
geneToSymbol: no visible global function definition for ‘organism’
geneToSymbol: no visible binding for global variable ‘ensembl_gene_id’
geneToSymbol: no visible binding for global variable
  ‘external_gene_name’
geneToSymbol: no visible binding for global variable
  ‘ensembl_transcript_id’
geneToSymbol: no visible binding for global variable ‘uniprotswissprot’
getNGenesCoverage: no visible global function definition for ‘.’
getNGenesCoverage: no visible binding for global variable ‘genes’
getNGenesCoverage: no visible binding for global variable ‘fraction’
get_phix_genome: no visible binding for global variable ‘phix.url’
go_analaysis_gorilla: no visible global function definition for
  ‘browseURL’
grl_has_any_valid_lengths: no visible binding for global variable ‘grl’
initiationScore: no visible global function definition for ‘.’
initiationScore: no visible binding for global variable ‘dif’
initiationScore: no visible binding for global variable ‘fraction’
initiationScore: no visible binding for global variable ‘genes’
initiationScore: no visible binding for global variable ‘difPer’
install.sratoolkit: no visible binding for global variable ‘osVersion’
isPeriodic: no visible binding for global variable ‘spec’
kozakHeatmap: no visible global function definition for ‘.’
kozakHeatmap: no visible binding for global variable ‘variable’
kozakHeatmap: no visible binding for global variable ‘value’
kozakHeatmap: no visible binding for global variable
  ‘count_seq_pos_with_count’
kozakHeatmap: no visible binding for global variable ‘median_score’
kozak_IR_ranking: no visible global function definition for ‘.’
kozak_IR_ranking: no visible binding for global variable ‘IR’
kozak_IR_ranking: no visible binding for global variable
  ‘upstream_kozak_strength’
kozak_IR_ranking: no visible binding for global variable ‘count’
kozak_IR_ranking: no visible binding for global variable ‘mean_IR’
list.genomes: no visible binding for global variable ‘STAR_index’
longestORFs: no visible global function definition for ‘.’
metaWindow: no visible binding for global variable ‘position’
metaWindow: no visible binding for global variable ‘frame’
metadata.autnaming: no visible binding for global variable
  ‘LIBRARYTYPE’
metadata.autnaming: no visible binding for global variable
  ‘LibraryStrategy’
ofst_merge_internal : <anonymous>: no visible global function
  definition for ‘.’
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’
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’
riboORFsFolder: no visible global function definition for ‘organism’
ribo_fft: no visible binding for global variable ‘fraction’
ribo_fft_plot: no visible binding for global variable ‘periods’
ribo_fft_plot: no visible binding for global variable ‘amplitude’
rnaNormalize: no visible binding for global variable ‘genes’
rnaNormalize: no visible binding for global variable ‘feature’
sample_info_append_SRA: no visible binding for global variable ‘GEO’
scaledWindowPositions: no visible binding for global variable
  ‘scalingFactor’
scaledWindowPositions: no visible binding for global variable ‘genes’
scaledWindowPositions: no visible binding for global variable
  ‘position’
scaledWindowPositions: no visible global function definition for ‘.’
scoreSummarizedExperiment: no visible global function definition for
  ‘rowSums2’
seq_usage: no visible binding for global variable ‘variable’
seq_usage: no visible binding for global variable ‘codon_sum’
seq_usage: no visible global function definition for ‘.’
seq_usage: no visible binding for global variable ‘gene_sum’
seq_usage: no visible binding for global variable
  ‘N_AA_of_type_per_gene’
seq_usage: no visible binding for global variable ‘as_prob_normalized’
seq_usage: no visible binding for global variable ‘N_total’
seq_usage: no visible binding for global variable ‘N’
seq_usage: no visible binding for global variable ‘mean_txNorm’
seq_usage: no visible binding for global variable ‘sum_txNorm’
seq_usage: no visible binding for global variable ‘dispersion’
seq_usage: no visible binding for global variable ‘dispersion_txNorm’
seq_usage: no visible binding for global variable ‘var_txNorm’
seq_usage: no visible binding for global variable ‘mean_percentage’
seq_usage: no visible binding for global variable ‘mean_txNorm_prob’
seq_usage: no visible binding for global variable
  ‘mean_txNorm_percentage’
seq_usage: no visible binding for global variable
  ‘relative_to_max_score’
shiftPlots : <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’
unlistToExtremities: no visible binding for global variable
  ‘group_name’
unlistToExtremities: no visible global function definition for ‘.’
unlistToExtremities: no visible binding for global variable ‘group’
windowCoveragePlot: no visible binding for global variable ‘feature’
windowCoveragePlot: no visible binding for global variable ‘fraction’
windowCoveragePlot: no visible binding for global variable
  ‘fraction_min’
windowCoveragePlot: no visible binding for global variable ‘position’
as.character,GRangesList: no visible global function definition for
  ‘unstrsplit’
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’
show,experiment: no visible global function definition for ‘organism’
Undefined global functions or variables:
  . ..formula ..to_keep AA CDS CDSGrouping Cor GEO Hx IR LEADERS LFC
  LFC_TE LIBRARYTYPE LibraryStrategy N N_AA_of_type_per_gene N_total
  ORFGrouping ORFScores RRS RSS Regulation STAR_index StartCodons
  StopCodons TE_log2 TOP Transcript Var1 Var2 all_models_sign amplitude
  as_prob_normalized bamTag<- bamWhat<- best_frame browseURL chr cigar1
  cigar2 codon codonSums codon_sum contrast count countRFP
  count_seq_pos_with_count counts_per_sample df dif difPer
  disengagementScores dispersion dispersion_txNorm distORFCDS
  end_segment ensembl_gene_id ensembl_transcript_id entropyRFP
  exon_rank external_gene_name feature file_forward file_reverse
  forward foverlaps fpkmRFP fpkmRNA frac.score fraction fraction.x
  fraction.y fractionLengths fraction_min fractions frame frame_one_RP
  frame_two_RP gene_id gene_sum genes grl grnames group group_name head
  i.end i.start id id_original inFrameCDS index ioScore
  isOverlappingCds kozak label mRNA mad_per_gene meanCounts mean_IR
  mean_per_gene mean_percentage mean_txNorm mean_txNorm_percentage
  mean_txNorm_prob median_per_gene median_score merged modzscore
  organism osVersion pShifted perc_of_counts_per_sample percent
  percent_length percentage percentage_mrna_aligned
  percentage_tx_aligned periods phix.url pick position query_id random
  rankInTx ranks ratio_cds_leader ratio_cds_mrna read length
  relative_to_max_score rfp.lfc rfp.padj rfp.sign rfp_log2 rna.lfc
  rna.padj rna.sign rna_log10 rna_log2 rowMin rowSums2 run_accession
  sample_id sample_total scalingFactor sd_per_gene seq1 seq2 seq3 seq4
  seq5 seqs size spec species spots start1 start2 startCodonCoverage
  startRegionRelative start_segment subtitle sum.count sum_per_gene
  sum_txNorm te te.lfc te.padj te.sign uniprotswissprot unstrsplit
  upstream_kozak_strength utr3_len utr5_len value var_txNorm variable
  widths windowMAD windowMean windowMedian windowSD zscore
Consider adding
  importFrom("base", "length")
  importFrom("graphics", "frame")
  importFrom("stats", "df")
  importFrom("utils", "browseURL", "head", "osVersion")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) countTable_regions.Rd:78: Lost braces; missing escapes or markup?
    78 | if (!is.null(out.dir) {pasteDir(file.path(out.dir, rel.dir, "countTable_"))} else NULL,
       |                       ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DEG.analysis.Rd: estimateDispersions
  DEG_model.Rd: estimateDispersions
  DTEG.analysis.Rd: SummarizedExperiment, estimateDispersions
  ORFikQC.Rd: SummarizedExperiment
  QCreport.Rd: SummarizedExperiment
  allFeaturesHelper.Rd: GRangesList, GAlignments, GRanges, FaFile
  as.character-GRangesList-method.Rd: GRangesList
  asTX.Rd: GRangesList
  assignFirstExonsStartSite.Rd: GRangesList
  assignLastExonsStopSite.Rd: GRangesList
  bedToGR.Rd: GRanges
  codonSumsPerGroup.Rd: GRangesList, GAlignments, GRanges
  codon_usage_exp.Rd: FaFile
  computeFeatures.Rd: GRangesList, GAlignments, GRanges, FaFile
  computeFeaturesCage.Rd: GRangesList, GAlignments, GRanges, FaFile
  coverageByTranscriptC.Rd: coverageByTranscript, GRangesList
  coverageByTranscriptW.Rd: coverageByTranscript, GRanges, GAlignments,
    GRangesList
  coveragePerTiling.Rd: GRangesList, GAlignments, GRanges
  detectRibosomeShifts.Rd: GAlignments
  disengagementScore.Rd: GRangesList, TxDb
  distToCds.Rd: GRangesList
  distToTSS.Rd: GRangesList
  downstreamFromPerGroup.Rd: GRangesList
  downstreamOfPerGroup.Rd: GRangesList
  entropy.Rd: GRangesList, GRanges, GAlignments
  experiment-class.Rd: SummarizedExperiment
  export.ofst-GAlignmentPairs-method.Rd: fst-package
  export.ofst-GAlignments-method.Rd: fst-package
  export.ofst-GRanges-method.Rd: fst-package
  export.ofst.Rd: fst-package
  extendLeaders.Rd: GRangesList
  extendTrailers.Rd: GRangesList
  fimport.Rd: seqlevelsStyle, Seqinfo, GAlignments, GRanges
  findFa.Rd: FaFile
  findMapORFs.Rd: GRangesList, FaFile
  findORFs.Rd: IRanges, IRangesList, FaFile
  findUORFs.Rd: FaFile
  firstEndPerGroup.Rd: GRangesList
  firstExonPerGroup.Rd: GRangesList
  firstStartPerGroup.Rd: GRangesList
  flankPerGroup.Rd: GRangesList
  floss.Rd: GRangesList, GRanges, GAlignments
  fpkm.Rd: GRangesList, GRanges, GAlignments
  fractionLength.Rd: GRangesList
  fread.bed.Rd: import.bed, seqlevelsStyle, Seqinfo, GRanges
  gSort.Rd: GRangesList
  hasHits.Rd: GRangesList
  heatMapL.Rd: GRangesList
  heatMapRegion.Rd: GRanges, GAlignments
  heatMap_single.Rd: GRangesList, GAlignments, GRanges
  import.ofst.Rd: fst-package, GAlignmentPairs
  initiationScore.Rd: GRangesList, GAlignments
  insideOutsideORF.Rd: GRangesList, TxDb
  kozakSequenceScore.Rd: GRangesList, FaFile
  kozak_IR_ranking.Rd: FaFile
  lastExonEndPerGroup.Rd: GRangesList
  lastExonPerGroup.Rd: GRangesList
  lastExonStartPerGroup.Rd: GRangesList
  loadTxdb.Rd: seqlevelsStyle, Seqinfo
  longestORFs.Rd: GRangesList
  makeExonRanks.Rd: GRangesList
  makeORFNames.Rd: GRangesList
  makeSummarizedExperimentFromBam.Rd: GRangesList, SummarizedExperiment
  mapToGRanges.Rd: GRangesList
  matchNaming.Rd: GRangesList
  matchSeqStyle.Rd: seqlevelsStyle, Seqinfo
  numCodons.Rd: GRangesList
  numExonsPerGroup.Rd: GRangesList
  optimizeReads.Rd: GRangesList
  optimizedTranscriptLengths.Rd: transcriptLengths
  orfID.Rd: GRangesList
  orfScore.Rd: GRangesList, GAlignments, GRanges
  outputLibs.Rd: seqlevelsStyle, Seqinfo
  rankOrder.Rd: GRangesList
  readBam.Rd: readGAlignments, seqlevelsStyle, Seqinfo, GAlignments,
    GAlignmentPairs
  readBigWig.Rd: seqlevelsStyle, Seqinfo, GRanges
  readWig.Rd: seqlevelsStyle, Seqinfo, GRanges
  reduceKeepAttr.Rd: GRangesList, reduce
  regionPerReadLength.Rd: GRangesList, GAlignments, GRanges
  removeMetaCols.Rd: GRangesList
  reverseMinusStrandPerGroup.Rd: GRangesList
  ribo_fft.Rd: GAlignments, GRanges, GRangesList
  ribosomeReleaseScore.Rd: GRangesList, GAlignments, GRanges
  ribosomeStallingScore.Rd: GRangesList
  rnaNormalize.Rd: GRangesList
  scaledWindowPositions.Rd: GRangesList, GAlignments, GRanges
  seqnamesPerGroup.Rd: GRangesList
  shiftFootprints.Rd: GAlignments, GRanges
  sortPerGroup.Rd: sort.GenomicRanges, GRangesList
  splitIn3Tx.Rd: GRangesList
  startCodons.Rd: GRangesList
  startRegion.Rd: GRangesList
  startRegionCoverage.Rd: GRangesList
  startRegionString.Rd: GRangesList, FaFile
  startSites.Rd: GRangesList
  stopCodons.Rd: GRangesList
  stopRegion.Rd: GRangesList
  stopSites.Rd: GRangesList
  strandBool.Rd: GRangesList
  strandPerGroup.Rd: GRangesList
  tile1.Rd: GRangesList
  transcriptWindow.Rd: GRangesList
  transcriptWindowPer.Rd: GRangesList
  translationalEff.Rd: GRangesList, GRanges, GAlignments
  txNames.Rd: GRangesList
  txSeqsFromFa.Rd: GRangesList, FaFile, extractTranscriptSeqs,
    DNAStringSet
  uniqueGroups.Rd: GRangesList
  uniqueOrder.Rd: GRangesList, GRanges
  unlistToExtremities.Rd: GRangesList
  upstreamFromPerGroup.Rd: GRangesList
  upstreamOfPerGroup.Rd: GRangesList
  validSeqlevels.Rd: GRangesList
  widthPerGroup.Rd: GRangesList
  windowPerGroup.Rd: GRangesList
  windowPerReadLength.Rd: GRangesList, GAlignments, GRanges
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ORFik-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: download.SRA.metadata
> ### Title: Downloads metadata from SRA
> ### Aliases: download.SRA.metadata
> 
> ### ** Examples
> 
> ## Originally on SRA
> download.SRA.metadata("SRP226389")
Downloading metadata from:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=sra&id=9232220,9232221,9232222,9232223,9232224,9232225&rettype=fasta&retmode=xml&tool=ORFik
Warning: Failed to open 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=sra&id=9232220,9232221,9232222,9232223,9232224,9232225&rettype=fasta&retmode=xml&tool=ORFik': gnutls_handshake() failed: The TLS connection was non-properly terminated.
Error in open.connection(x, "rb") : cannot open the connection
Calls: download.SRA.metadata ... read_xml.character -> read_xml.connection -> open -> open.connection
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
codon_usage_exp       22.422  1.537  18.366
detect_ribo_orfs      18.795  1.391  17.786
countTable_regions     8.701  3.824   4.413
STAR.allsteps.multiQC 11.766  0.100  11.946
DEG.analysis          11.129  0.284  12.404
computeFeatures        8.918  0.578   9.378
codon_usage_plot       6.582  0.468   3.701
codon_usage            6.754  0.171   3.549
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 8 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/ORFik.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ORFik
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘ORFik’ ...
** this is package ‘ORFik’ version ‘1.29.9’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c findORFsHelpers.cpp -o findORFsHelpers.o
findORFsHelpers.cpp: In function ‘Rcpp::IntegerMatrix orfs_as_matrix(std::string&, std::string, std::string, int)’:
findORFsHelpers.cpp:214:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  214 |   for (int i = 0; i < uorfSize/2; i++) {
      |                   ~~^~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c findOrfs.cpp -o findOrfs.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c findOrfsFasta.cpp -o findOrfsFasta.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pmapFromTranscripts.cpp -o pmapFromTranscripts.o
pmapFromTranscripts.cpp: In function ‘Rcpp::List pmapFromTranscriptsCPP(const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const char&, bool)’:
pmapFromTranscripts.cpp:151:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  151 |   for(auto i = 0;i < xSize; i++){
      |                  ~~^~~~~~~
pmapFromTranscripts.cpp:155:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  155 |   for(auto i = 0; i < indexSize; i++){
      |                   ~~^~~~~~~~~~~
pmapFromTranscripts.cpp:161:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  161 |   for(auto i = 1; i < indexSize; i++){
      |                   ~~^~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pmapToTranscripts.cpp -o pmapToTranscripts.o
pmapToTranscripts.cpp: In function ‘void pmapToPositive(vi&, const int&, int&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&)’:
pmapToTranscripts.cpp:22:7: warning: variable ‘currentWidth’ set but not used [-Wunused-but-set-variable]
   22 |   int currentWidth = 0;
      |       ^~~~~~~~~~~~
pmapToTranscripts.cpp: In function ‘void pmapToNegative(vi&, const int&, int&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&)’:
pmapToTranscripts.cpp:68:7: warning: variable ‘currentWidth’ set but not used [-Wunused-but-set-variable]
   68 |   int currentWidth = 0;
      |       ^~~~~~~~~~~~
pmapToTranscripts.cpp: In function ‘Rcpp::List pmapToTranscriptsCPP(const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const char&, const std::vector<int>&)’:
pmapToTranscripts.cpp:126:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  126 |   for(auto i = 0;i < xSize; i++){ // Width per exon in x
      |                  ~~^~~~~~~
pmapToTranscripts.cpp:130:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  130 |   for(auto i = 0; i < indexSize; i++){ // Width per exon in tx
      |                   ~~^~~~~~~~~~~
pmapToTranscripts.cpp:136:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  136 |   for(auto i = 1; i < indexSize; i++){
      |                   ~~^~~~~~~~~~~
pmapToTranscripts.cpp:147:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  147 |   for (auto i = 1; i < 2 * xSize; i = i + 2) {
      |                    ~~^~~~~~~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o ORFik.so RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o pmapFromTranscripts.o pmapToTranscripts.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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':

    I, expand.grid, unname

Loading required package: GenomicRanges
Loading required package: Seqinfo
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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 444 ]
> 
> proc.time()
   user  system elapsed 
126.198   6.715 121.950