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This page was generated on 2025-10-18 12:06 -0400 (Sat, 18 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1516/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ORFik 1.29.9  (landing page)
Haakon Tjeldnes
Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 Oct 2025)
git_url: https://git.bioconductor.org/packages/ORFik
git_branch: devel
git_last_commit: 91fe5a2
git_last_commit_date: 2025-09-19 07:15:59 -0400 (Fri, 19 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for ORFik on kjohnson3

To the developers/maintainers of the ORFik package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ORFik.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: ORFik
Version: 1.29.9
Command: /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_1.29.9.tar.gz
StartedAt: 2025-10-17 21:15:06 -0400 (Fri, 17 Oct 2025)
EndedAt: 2025-10-17 21:19:12 -0400 (Fri, 17 Oct 2025)
EllapsedTime: 245.7 seconds
RetCode: 0
Status:   OK  
CheckDir: ORFik.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /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_1.29.9.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ORFik.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ORFik/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ORFik’ version ‘1.29.9’
* 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: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.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 ... 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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
orfFrameDistributions 18.473  1.828   6.382
makeTxdbFromGenome     8.930  0.081   9.032
* 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: 8 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/ORFik.Rcheck/00check.log’
for details.


Installation output

ORFik.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘ORFik’ ...
** this is package ‘ORFik’ version ‘1.29.9’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-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/4.5-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/4.5-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/4.5-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/4.5-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
installing to /Library/Frameworks/R.framework/Versions/4.5-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)

Tests output

ORFik.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 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
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 
 33.571   1.416  41.025 

Example timings

ORFik.Rcheck/ORFik-Ex.timings

nameusersystemelapsed
DEG.analysis1.9960.0642.070
DEG.plot.static0.1050.0010.108
DEG_model0.1000.0010.100
DEG_model_results0.1000.0010.102
DEG_model_simple0.0960.0010.097
DTEG.analysis0.1010.0010.103
DTEG.plot0.0970.0010.098
ORFik.template.experiment0.1100.0020.113
ORFik.template.experiment.zf0.0180.0010.018
ORFikQC0.0940.0010.095
QCreport0.0940.0010.095
QCstats0.0950.0010.095
QCstats.plot0.0970.0010.097
RiboQC.plot0.1170.0020.118
STAR.align.folder0.0010.0000.000
STAR.align.single000
STAR.allsteps.multiQC3.2840.0523.373
STAR.index000
STAR.install000
STAR.multiQC0.8760.0020.884
STAR.remove.crashed.genome000
TOP.Motif.ecdf000
append_gene_symbols0.2560.0050.263
artificial.orfs0.0940.0010.094
asTX0.1550.0010.156
assignTSSByCage0.0010.0010.000
bamVarName0.0990.0010.100
browseSRA000
canonical_isoforms-experiment-method0.2580.0050.263
canonical_isoforms0.2360.0040.239
codon_usage0.8270.0120.841
codon_usage_exp3.3900.1923.561
codon_usage_plot0.9340.2221.131
collapse.by.scores0.0290.0080.037
collapse.fastq000
collapseDuplicatedReads-GAlignmentPairs-method0.0200.0060.025
collapseDuplicatedReads-GAlignments-method0.0070.0010.007
collapseDuplicatedReads-GRanges-method0.0070.0010.008
collapseDuplicatedReads-data.table-method0.0070.0000.007
collapseDuplicatedReads0.0070.0000.007
combn.pairs0.0940.0020.095
computeFeatures1.1490.0211.177
computeFeaturesCage000
config000
config.exper0.0420.0050.049
config.save000
config_file0.0450.0020.047
convertLibs0.0950.0010.097
convertToOneBasedRanges0.0370.0010.037
convert_bam_to_ofst0.0930.0100.110
convert_to_bigWig0.2640.0110.280
convert_to_covRle0.1280.0050.135
convert_to_covRleList0.1980.0090.223
countOverlapsW0.0190.0010.026
countTable0.0950.0010.100
countTable_regions1.4930.7871.184
covRle0.0150.0100.025
covRleFromGR0.0270.0170.044
covRleList0.0050.0030.007
coverageByTranscriptFST0.0550.0490.104
coverageHeatMap0.4390.1540.595
coveragePerTiling0.5000.2400.199
coverageScorings0.0030.0010.005
create.experiment0.2130.0130.228
defineTrailer0.0460.0030.049
design-experiment-method0.1100.0020.114
detectRibosomeShifts0.0000.0000.002
detect_drive0.0010.0040.006
detect_ribo_orfs2.1920.3432.520
disengagementScore0.1220.0010.122
distToCds0.0650.0000.065
distToTSS0.0470.0010.047
download.SRA000
download.SRA.metadata0.0440.0052.164
download_gene_info0.0170.0030.517
entropy0.3910.0020.399
exonsWithPseudoIntronsPerGroup0.5760.0050.601
experiment-class0.1200.0010.121
export.bed120.0060.0000.005
export.bigWig0.0090.0000.009
export.fstwig0.0160.0010.015
export.ofst-GAlignmentPairs-method0.0160.0000.016
export.ofst-GAlignments-method0.0160.0000.016
export.ofst-GRanges-method0.0150.0010.016
export.ofst0.0160.0000.016
export.wiggle0.0090.0000.008
extendLeaders0.2690.0050.276
extendLeadersUntil0.3770.0020.386
extendTrailers0.1620.0030.166
extendTrailersUntil0.4060.0130.466
extract_run_id000
file_ext_without_compression0.0000.0000.001
filepath0.1160.0020.128
filterTranscripts0.3490.0020.351
fimport0.0920.0060.099
findFa0.0010.0000.002
findMapORFs0.1340.0010.135
findORFs0.0540.0010.056
findORFsFasta0.0230.0030.026
findPeaksPerGene0.2890.0040.316
findUORFs0.0000.0000.001
findUORFs_exp1.3050.0121.344
find_url_ebi0.0130.0021.384
firstEndPerGroup0.0180.0010.018
firstExonPerGroup0.0170.0000.018
firstStartPerGroup0.0150.0010.016
fix_malformed_gff000
flankPerGroup0.0340.0000.033
floss0.0750.0000.076
fpkm0.0300.0010.031
fractionLength0.0170.0000.017
fread.bed0.0090.0040.014
gcContent0.1040.0010.104
geneToSymbol0.0000.0010.000
getGenomeAndAnnotation000
get_bioproject_candidates000
get_genome_fasta0.0000.0010.000
get_genome_gtf000
get_noncoding_rna000
get_phix_genome0.0000.0010.000
get_silva_rRNA000
get_system_usage0.0470.1140.163
go_analaysis_gorilla0.0010.0010.001
groupGRangesBy0.0170.0000.017
groupings0.010.000.01
heatMapRegion0.0960.0010.097
import.ofst0.0160.0010.016
initiationScore0.2390.0000.239
insideOutsideORF0.2020.0010.202
install.fastp000
install.sratoolkit000
isInFrame0.0590.0000.060
isOverlapping0.0590.0000.059
kozakHeatmap000
kozakSequenceScore0.1390.0010.140
lastExonEndPerGroup0.0180.0000.018
lastExonPerGroup0.0190.0000.020
lastExonStartPerGroup0.0170.0000.017
libraryTypes0.0970.0010.098
list.experiments0.0900.0020.092
list.genomes0.0000.0010.001
loadRegion0.3770.0080.386
loadRegions0.1660.0030.169
loadTranscriptType000
loadTxdb0.0330.0020.035
longestORFs0.0330.0000.033
makeGRangesListFromCharacter0.020.000.02
makeORFNames0.0220.0000.021
makeSummarizedExperimentFromBam0.0980.0010.100
makeTxdbFromGenome8.9300.0819.032
mergeFastq000
mergeLibs0.4070.0730.483
metaWindow0.0530.0000.053
model.matrix-experiment-method0.1080.0010.109
numExonsPerGroup0.0110.0000.011
optimizedTranscriptLengths0.2410.0160.258
orfFrameDistributions18.473 1.828 6.382
orfScore0.2090.0590.269
organism-experiment-method0.0940.0260.119
outputLibs0.3020.2970.404
pSitePlot0.3430.0570.402
pcaExperiment0.2940.0700.372
pcaPlot0.2870.0200.307
pmapFromTranscriptF0.1160.0020.118
pmapToTranscriptF0.2280.0080.237
pseudoIntronsPerGroup0.5210.0050.533
rankOrder0.0200.0000.019
read.experiment0.0910.0020.092
readBam0.0300.0060.036
readBamIsUniqueMapper0.0270.0040.031
readBamSeqs0.0210.0010.022
readWidths0.0050.0000.005
read_RDSQS0.1000.0020.103
reassignTSSbyCage0.1540.0100.163
reassignTxDbByCage000
reduceKeepAttr0.0320.0000.031
regionPerReadLength0.1050.1510.383
remove.experiments0.1630.1140.144
riboORFs0.0990.0210.128
riboORFsFolder0.1860.0370.223
ribo_fft0.8380.1420.992
ribo_fft_plot0.8050.0100.847
ribosomeReleaseScore0.0550.0010.056
ribosomeStallingScore0.0760.0010.076
save.experiment0.0940.0010.098
save_RDSQS0.0020.0050.006
scaledWindowPositions0.0820.0020.084
seqnamesPerGroup0.0170.0000.017
shiftFootprints0.0010.0000.001
shiftFootprintsByExperiment0.3650.0241.750
shiftPlots1.0620.4480.136
shifts_load0.0960.0200.116
shifts_save0.0140.0070.021
simpleLibs0.0950.0290.125
sortPerGroup0.0670.0250.094
startCodons0.1340.0340.167
startDefinition000
startRegion0.2210.0240.254
startRegionCoverage0.0930.0220.116
startSites0.0750.0070.082
stopCodons0.1240.0010.125
stopDefinition0.0000.0000.001
stopRegion0.1240.0010.124
stopSites0.0750.0010.077
strandBool0.0030.0010.002
strandPerGroup0.0130.0000.013
subsetToFrame0.0050.0010.005
symbols0.0970.0040.101
te.plot000
te.table0.1870.0010.189
te_rna.plot0.0970.0010.098
template_shift_table0.1150.0030.118
tile10.0510.0010.052
topMotif000
transcriptWindow0.2610.0080.279
translationalEff0.0480.0000.047
trimming.table0.0070.0020.008
txNames0.0110.0000.011
txNamesToGeneNames0.3360.0050.341
uORFSearchSpace0.1400.0030.146
uniqueGroups0.0340.0020.035
uniqueOrder0.0520.0000.052
unlistGrl0.0120.0000.012
widthPerGroup0.0130.0000.013
windowCoveragePlot0.2860.0090.321
windowPerGroup0.3140.0020.315
windowPerReadLength0.2050.0010.208