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This page was generated on 2025-09-06 12:05 -0400 (Sat, 06 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4618
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4565
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4544
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 1496/2322HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ORFik 1.29.7  (landing page)
Haakon Tjeldnes
Snapshot Date: 2025-09-05 13:45 -0400 (Fri, 05 Sep 2025)
git_url: https://git.bioconductor.org/packages/ORFik
git_branch: devel
git_last_commit: 495edf9
git_last_commit_date: 2025-07-14 17:32:13 -0400 (Mon, 14 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 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 lconway

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: 1.29.7
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_1.29.7.tar.gz
StartedAt: 2025-09-05 22:39:13 -0400 (Fri, 05 Sep 2025)
EndedAt: 2025-09-05 22:53:23 -0400 (Fri, 05 Sep 2025)
EllapsedTime: 850.3 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_1.29.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ORFik.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ORFik/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ORFik’ version ‘1.29.7’
* 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 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... 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 ‘.’
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
  ‘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’
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: no visible binding for global variable
  ‘file_paths’
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’
readBam: no visible global function definition for ‘bamTag<-’
readBam: no visible global function definition for ‘bamWhat<-’
readLengthTable: no visible binding for global variable
  ‘counts_per_sample’
readLengthTable: no visible binding for global variable ‘sample_id’
readLengthTable: no visible binding for global variable
  ‘perc_of_counts_per_sample’
regionPerReadLength : <anonymous>: no visible binding for global
  variable ‘fraction’
remakeTxdbExonIds: no visible global function definition for ‘.’
remakeTxdbExonIds: no visible binding for global variable ‘chr’
removeTxdbExons: no visible binding for global variable ‘exon_rank’
removeTxdbExons: no visible binding for global variable ‘ranks’
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’
collapseDuplicatedReads,GAlignmentPairs: no visible global function
  definition for ‘.’
collapseDuplicatedReads,GAlignmentPairs: no visible binding for global
  variable ‘start1’
collapseDuplicatedReads,GAlignmentPairs: no visible binding for global
  variable ‘start2’
collapseDuplicatedReads,GAlignmentPairs: no visible binding for global
  variable ‘cigar1’
collapseDuplicatedReads,GAlignmentPairs: no visible binding for global
  variable ‘cigar2’
collapseDuplicatedReads,GAlignments: no visible global function
  definition for ‘.’
collapseDuplicatedReads,GRanges: no visible binding for global variable
  ‘size’
collapseDuplicatedReads,GRanges: no visible global function definition
  for ‘.’
collapseDuplicatedReads,data.table: no visible global function
  definition for ‘.’
design,experiment: no visible binding for global variable ‘..formula’
seqlevels,experiment: no visible binding for global variable ‘df’
show,covRleList: no visible global function definition for ‘head’
Undefined global functions or variables:
  . ..formula ..to_keep AA CDS CDSGrouping Cor 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_paths
  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 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
  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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DTEG.analysis.Rd: SummarizedExperiment
  ORFikQC.Rd: SummarizedExperiment
  QCreport.Rd: SummarizedExperiment
  allFeaturesHelper.Rd: GRangesList, GAlignments, GRanges, FaFile
  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
  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       62.978  9.154  25.572
orfScore                    25.054  3.687   4.253
makeTxdbFromGenome          22.013  0.427  22.554
codon_usage_exp             11.288  0.483  11.753
detect_ribo_orfs             7.896  0.603   8.468
STAR.allsteps.multiQC        7.860  0.083   8.002
shiftPlots                   4.895  1.644   0.769
findUORFs_exp                5.864  0.054   5.943
computeFeatures              5.186  0.066   5.291
shiftFootprintsByExperiment  1.250  0.053   6.985
download.SRA.metadata        0.145  0.015   6.760
* 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: 7 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-x86_64/Resources/library’
* installing *source* package ‘ORFik’ ...
** this is package ‘ORFik’ version ‘1.29.7’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c findORFsHelpers.cpp -o findORFsHelpers.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c findOrfs.cpp -o findOrfs.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c findOrfsFasta.cpp -o findOrfsFasta.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c pmapFromTranscripts.cpp -o pmapFromTranscripts.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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-x86_64/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 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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 441 ]
> 
> proc.time()
   user  system elapsed 
114.363   3.812 118.330 

Example timings

ORFik.Rcheck/ORFik-Ex.timings

nameusersystemelapsed
DEG.analysis0.7040.0090.715
DEG.plot.static1.3330.0341.392
DEG_model0.4740.0050.480
DEG_model_results0.4900.0430.537
DEG_model_simple0.4740.0450.521
DTEG.analysis0.4960.0400.538
DTEG.plot0.4480.0050.456
ORFik.template.experiment0.5240.0070.533
ORFik.template.experiment.zf0.0720.0030.074
ORFikQC0.4610.0040.468
QCreport0.4820.0050.488
QCstats0.5080.0060.518
QCstats.plot0.4870.0050.496
RiboQC.plot0.4890.0060.500
STAR.align.folder0.0000.0010.001
STAR.align.single0.0000.0010.000
STAR.allsteps.multiQC7.8600.0838.002
STAR.index0.0000.0000.001
STAR.install0.0000.0000.001
STAR.multiQC2.4620.0162.490
STAR.remove.crashed.genome000
TOP.Motif.ecdf0.0000.0010.000
append_gene_symbols1.2370.0271.298
artificial.orfs0.4450.0030.450
asTX0.8370.0090.853
assignTSSByCage0.0030.0020.007
bamVarName0.8980.0090.916
browseSRA0.0000.0000.001
canonical_isoforms-experiment-method1.2330.0221.266
canonical_isoforms1.1400.0211.172
codon_usage3.7480.0483.823
codon_usage_exp11.288 0.48311.753
codon_usage_plot4.0980.4634.515
collapse.by.scores0.1280.0090.137
collapse.fastq0.0000.0000.001
collapseDuplicatedReads-GAlignmentPairs-method0.1000.0080.109
collapseDuplicatedReads-GAlignments-method0.0380.0030.041
collapseDuplicatedReads-GRanges-method0.0400.0030.043
collapseDuplicatedReads-data.table-method0.0390.0020.042
collapseDuplicatedReads0.0350.0020.037
combn.pairs0.5330.0170.555
computeFeatures5.1860.0665.291
computeFeaturesCage000
config0.0000.0010.001
config.exper0.1430.0120.160
config.save000
config_file0.1730.0060.179
convertLibs0.4420.0050.448
convertToOneBasedRanges0.1540.0020.157
convert_bam_to_ofst0.1790.0130.196
convert_to_bigWig1.0970.0171.121
convert_to_covRle0.6280.0160.648
convert_to_covRleList0.8840.0220.912
countOverlapsW0.0810.0010.082
countTable0.4880.0050.497
countTable_regions0.4860.0060.495
covRle0.0560.0010.057
covRleFromGR0.1190.0020.121
covRleList0.0190.0010.019
coverageByTranscriptFST0.1580.0060.165
coverageHeatMap1.3160.0141.342
coveragePerTiling0.8320.0060.842
coverageScorings0.0110.0010.013
create.experiment0.9190.0090.931
defineTrailer0.1890.0020.191
design-experiment-method0.5180.0050.526
detectRibosomeShifts0.0020.0020.004
detect_ribo_orfs7.8960.6038.468
disengagementScore0.5670.0030.573
distToCds0.2950.0010.297
distToTSS0.2590.0010.261
download.SRA000
download.SRA.metadata0.1450.0156.760
download_gene_info0.0330.0050.212
entropy1.8430.0431.894
exonsWithPseudoIntronsPerGroup2.3770.0222.406
experiment-class0.5200.0070.530
export.bed120.0270.0000.028
export.bigWig0.0430.0000.044
export.fstwig0.0730.0010.074
export.ofst-GAlignmentPairs-method0.0750.0010.075
export.ofst-GAlignments-method0.0670.0010.069
export.ofst-GRanges-method0.0660.0010.066
export.ofst0.0650.0010.066
export.wiggle0.0310.0000.031
extendLeaders1.2190.0251.252
extendLeadersUntil1.9590.0121.978
extendTrailers0.7700.0170.791
extendTrailersUntil1.9430.0101.959
extract_run_id0.0000.0000.001
file_ext_without_compression0.0000.0000.001
filepath0.5390.0050.547
filterTranscripts1.5560.0171.580
fimport0.3990.0290.430
findFa0.0030.0000.004
findMapORFs0.6330.0040.639
findORFs0.1880.0040.192
findORFsFasta0.0830.0040.089
findPeaksPerGene1.2860.0151.305
findUORFs0.0010.0010.001
findUORFs_exp5.8640.0545.943
find_url_ebi0.0350.0061.849
firstEndPerGroup0.0680.0000.069
firstExonPerGroup0.0840.0010.085
firstStartPerGroup0.0730.0010.074
fix_malformed_gff000
flankPerGroup0.1480.0010.150
floss0.3310.0020.335
fpkm0.1290.0010.132
fractionLength0.0750.0000.075
fread.bed0.0360.0080.061
gcContent0.4860.0040.493
geneToSymbol0.0000.0010.000
getGenomeAndAnnotation0.0000.0000.001
get_bioproject_candidates000
get_genome_fasta0.0000.0010.001
get_genome_gtf0.0000.0000.001
get_noncoding_rna000
get_phix_genome0.0000.0010.000
get_silva_rRNA000
get_system_usage0.1680.4910.738
go_analaysis_gorilla0.0030.0010.004
groupGRangesBy0.0670.0010.071
groupings0.0460.0010.047
heatMapRegion0.4930.0050.500
import.ofst0.0670.0010.068
initiationScore1.1730.0061.183
insideOutsideORF0.9970.0061.009
install.fastp000
install.sratoolkit000
isInFrame0.3050.0020.310
isOverlapping0.3040.0020.308
kozakHeatmap0.0000.0000.001
kozakSequenceScore0.6550.0070.666
lastExonEndPerGroup0.0570.0010.059
lastExonPerGroup0.0730.0020.075
lastExonStartPerGroup0.0580.0010.059
libraryTypes0.4500.0040.456
list.experiments0.3180.0030.323
list.genomes0.0000.0000.001
loadRegion1.6740.0331.717
loadRegions0.7370.0180.759
loadTranscriptType0.0000.0010.000
loadTxdb0.1480.0080.156
longestORFs0.1570.0020.159
makeORFNames0.1440.0020.147
makeSummarizedExperimentFromBam0.4730.0030.479
makeTxdbFromGenome22.013 0.42722.554
mergeFastq0.0000.0010.001
mergeLibs0.4300.0130.445
metaWindow0.2280.0180.246
model.matrix-experiment-method0.4710.0430.515
numExonsPerGroup0.0450.0030.050
optimizedTranscriptLengths1.5830.0601.653
orfFrameDistributions62.978 9.15425.572
orfScore25.054 3.687 4.253
organism-experiment-method0.4460.0040.451
outputLibs1.4310.7171.618
pSitePlot0.3990.0530.458
pcaExperiment1.4450.1231.583
pcaPlot1.1450.0831.238
pmapFromTranscriptF0.1160.0080.125
pmapToTranscriptF1.0130.0241.042
pseudoIntronsPerGroup2.0500.0182.077
rankOrder0.0970.0010.098
read.experiment0.4770.0050.484
readBam0.1120.0200.134
readWidths0.0190.0010.019
read_RDSQS0.5010.0070.509
reassignTSSbyCage0.9600.0230.987
reassignTxDbByCage0.0000.0000.001
reduceKeepAttr0.1380.0010.140
regionPerReadLength0.4070.2861.077
remove.experiments0.7530.3240.671
riboORFs0.5270.0390.570
riboORFsFolder0.5000.0330.537
ribo_fft3.4080.1593.582
ribo_fft_plot3.2210.0423.277
ribosomeReleaseScore0.2630.0020.266
ribosomeStallingScore0.3740.0030.379
save.experiment0.6780.0070.688
save_RDSQS0.0090.0100.019
scaledWindowPositions0.3520.0040.358
seqnamesPerGroup0.0770.0010.079
shiftFootprints0.0030.0010.004
shiftFootprintsByExperiment1.2500.0536.985
shiftPlots4.8951.6440.769
shifts_load0.5010.0400.544
shifts_save0.0600.0080.067
simpleLibs0.7750.0450.824
sortPerGroup0.3140.0260.341
startCodons0.6140.0450.660
startDefinition0.0000.0000.001
startRegion0.7020.0430.748
startRegionCoverage0.4560.0040.461
startSites0.3390.0040.344
stopCodons0.8400.0080.852
stopDefinition000
stopRegion0.6670.0030.672
stopSites0.3890.0030.393
strandBool0.0130.0010.015
strandPerGroup0.0890.0020.092
subsetToFrame0.0250.0010.028
symbols0.5190.0060.527
te.plot0.0000.0000.001
te.table0.5180.0060.527
te_rna.plot0.4780.0050.485
tile10.2340.0030.238
topMotif0.0000.0000.001
transcriptWindow1.4180.0241.447
translationalEff0.1840.0010.186
trimming.table0.0310.0040.035
txNames0.0510.0010.051
txNamesToGeneNames1.0710.0211.098
uORFSearchSpace0.6710.0150.690
uniqueGroups0.4290.0050.438
uniqueOrder0.2520.0030.257
unlistGrl0.0460.0000.047
widthPerGroup0.0480.0010.048
windowCoveragePlot0.7670.0180.793
windowPerGroup1.1550.0121.177
windowPerReadLength1.3400.0111.360