Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-10-13 11:38 -0400 (Mon, 13 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 1503/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ORFik 1.28.3  (landing page)
Haakon Tjeldnes
Snapshot Date: 2025-10-09 13:40 -0400 (Thu, 09 Oct 2025)
git_url: https://git.bioconductor.org/packages/ORFik
git_branch: RELEASE_3_21
git_last_commit: 7cf3d1e
git_last_commit_date: 2025-09-22 04:08:21 -0400 (Mon, 22 Sep 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for ORFik on nebbiolo1

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: 1.28.3
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ORFik.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ORFik_1.28.3.tar.gz
StartedAt: 2025-10-13 01:58:00 -0400 (Mon, 13 Oct 2025)
EndedAt: 2025-10-13 02:16:09 -0400 (Mon, 13 Oct 2025)
EllapsedTime: 1088.2 seconds
RetCode: 0
Status:   OK  
CheckDir: ORFik.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ORFik.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ORFik_1.28.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ORFik.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ORFik/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ORFik’ version ‘1.28.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... NOTE
Found the following non-portable file path:
  ORFik/inst/extdata/test_processing/contaminants_depletion/LOGS/contaminants_output_template_Log.final.out

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ORFik’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    help   1.1Mb
    libs   1.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘GenomicFeatures:::.merge_seqinfo_and_infer_missing_seqlengths’
  ‘IRanges:::regroupBySupergroup’ ‘S4Vectors:::normarg_mcols’
  ‘biomartr:::getENSEMBL.Seq’ ‘biomartr:::getENSEMBL.gtf’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘go_analaysis_gorilla’ ‘pseudoIntronsPerGroup’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DEG.plot.static: no visible binding for global variable ‘Regulation’
DEG.plot.static: no visible binding for global variable ‘meanCounts’
DEG.plot.static: no visible binding for global variable ‘LFC’
DEG_gorilla: no visible binding for global variable ‘contrast’
DEG_gorilla: no visible binding for global variable ‘Regulation’
DEG_gorilla: no visible binding for global variable
  ‘external_gene_name’
DEG_model_simple: no visible binding for global variable ‘id’
DEG_model_simple: no visible binding for global variable ‘contrast’
DTEG.plot: no visible binding for global variable ‘Regulation’
DTEG.plot: no visible binding for global variable ‘rna.lfc’
DTEG.plot: no visible binding for global variable ‘rfp.lfc’
DTEG_add_regulation_categories: no visible binding for global variable
  ‘te.sign’
DTEG_add_regulation_categories: no visible binding for global variable
  ‘rfp.sign’
DTEG_add_regulation_categories: no visible binding for global variable
  ‘rna.sign’
DTEG_add_regulation_categories: no visible binding for global variable
  ‘Regulation’
DTEG_add_regulation_categories: no visible binding for global variable
  ‘all_models_sign’
DTEG_add_regulation_categories: no visible binding for global variable
  ‘te.lfc’
DTEG_add_regulation_categories: no visible binding for global variable
  ‘rna.lfc’
DTEG_pair_results: no visible binding for global variable ‘rna.sign’
DTEG_pair_results: no visible binding for global variable ‘rna.padj’
DTEG_pair_results: no visible binding for global variable ‘rfp.sign’
DTEG_pair_results: no visible binding for global variable ‘rfp.padj’
DTEG_pair_results: no visible binding for global variable ‘te.sign’
DTEG_pair_results: no visible binding for global variable ‘te.padj’
DTEG_pair_results: no visible binding for global variable
  ‘all_models_sign’
QCstats.plot: no visible binding for global variable ‘variable’
QCstats.plot: no visible binding for global variable ‘sample_total’
QCstats.plot: no visible binding for global variable ‘value’
QCstats.plot: no visible global function definition for ‘.’
QCstats.plot: no visible binding for global variable ‘sample_id’
QCstats.plot: no visible binding for global variable ‘percentage’
QCstats.plot: no visible binding for global variable
  ‘perc_of_counts_per_sample’
QCstats.plot: no visible binding for global variable ‘read length’
RiboQC.plot: no visible binding for global variable ‘variable’
RiboQC.plot: no visible binding for global variable ‘sample_total’
RiboQC.plot: no visible binding for global variable ‘value’
RiboQC.plot: no visible global function definition for ‘.’
RiboQC.plot: no visible binding for global variable ‘sample_id’
RiboQC.plot: no visible binding for global variable ‘percentage’
RiboQC.plot: no visible binding for global variable ‘percent’
RiboQC.plot: no visible binding for global variable ‘frame’
STAR.multiQC_plot: no visible binding for global variable ‘value’
STAR.multiQC_plot: no visible binding for global variable ‘sample_id’
TOP.Motif.ecdf: no visible binding for global variable ‘seq1’
TOP.Motif.ecdf: no visible binding for global variable ‘TOP’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘percentage_mrna_aligned’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘mRNA’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘percentage_tx_aligned’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘Transcript’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘ratio_cds_mrna’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘CDS’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘ratio_cds_leader’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘LEADERS’
allFeaturesHelper: no visible binding for global variable ‘te’
allFeaturesHelper: no visible binding for global variable ‘fpkmRFP’
allFeaturesHelper: no visible binding for global variable ‘fpkmRNA’
allFeaturesHelper: no visible binding for global variable ‘countRFP’
allFeaturesHelper: no visible binding for global variable ‘entropyRFP’
allFeaturesHelper: no visible binding for global variable
  ‘disengagementScores’
allFeaturesHelper: no visible binding for global variable ‘RRS’
allFeaturesHelper: no visible binding for global variable ‘RSS’
allFeaturesHelper: no visible binding for global variable ‘ORFScores’
allFeaturesHelper: no visible binding for global variable ‘ioScore’
allFeaturesHelper: no visible binding for global variable
  ‘startCodonCoverage’
allFeaturesHelper: no visible binding for global variable
  ‘startRegionRelative’
allFeaturesHelper: no visible binding for global variable ‘kozak’
allFeaturesHelper: no visible binding for global variable ‘StartCodons’
allFeaturesHelper: no visible binding for global variable ‘StopCodons’
allFeaturesHelper: no visible binding for global variable
  ‘fractionLengths’
allFeaturesHelper: no visible binding for global variable ‘distORFCDS’
allFeaturesHelper: no visible binding for global variable ‘inFrameCDS’
allFeaturesHelper: no visible binding for global variable
  ‘isOverlappingCds’
allFeaturesHelper: no visible binding for global variable ‘rankInTx’
appendZeroes: no visible binding for global variable ‘frame’
appendZeroes: no visible binding for global variable ‘position’
appendZeroes: no visible binding for global variable ‘count’
append_gene_symbols: no visible binding for global variable
  ‘id_original’
append_gene_symbols: no visible binding for global variable ‘id’
append_gene_symbols: no visible binding for global variable
  ‘external_gene_name’
append_gene_symbols: no visible binding for global variable ‘label’
artificial.orfs: no visible binding for global variable ‘random’
artificial.orfs: no visible binding for global variable ‘pick’
artificial.orfs: no visible global function definition for ‘.’
bamLoadCollapsedScores: no visible global function definition for
  ‘bamTag<-’
bamLoadCollapsedScores: no visible global function definition for
  ‘bamWhat<-’
browseSRA: no visible global function definition for ‘browseURL’
cellTypeNames: missing arguments not allowed in calls to ‘c’
codonSumsPerGroup: no visible binding for global variable ‘genes’
codon_usage: no visible binding for global variable ‘merged’
codon_usage: no visible binding for global variable ‘AA’
codon_usage: no visible binding for global variable ‘codon’
codon_usage_plot: no visible binding for global variable ‘seqs’
collapse.by.scores: no visible global function definition for ‘.’
collapse.fastq.internal: no visible binding for global variable ‘N’
cor_plot: no visible binding for global variable ‘Var2’
cor_plot: no visible binding for global variable ‘Var1’
cor_plot: no visible binding for global variable ‘Cor’
cor_table: no visible binding for global variable ‘Var1’
cor_table: no visible binding for global variable ‘Var2’
cor_table: no visible binding for global variable ‘Cor’
coverageByTranscriptFST: no visible binding for global variable
  ‘file_forward’
coverageByTranscriptFST: no visible binding for global variable
  ‘file_reverse’
coverageByTranscriptFST : <anonymous>: no visible binding for global
  variable ‘chr’
coverageByTranscriptFST : <anonymous>: no visible binding for global
  variable ‘query_id’
coverageByTranscriptFST : <anonymous>: no visible global function
  definition for ‘foverlaps’
coverageByTranscriptFST : <anonymous>: no visible binding for global
  variable ‘start_segment’
coverageByTranscriptFST : <anonymous>: no visible binding for global
  variable ‘i.start’
coverageByTranscriptFST : <anonymous>: no visible binding for global
  variable ‘end_segment’
coverageByTranscriptFST : <anonymous>: no visible binding for global
  variable ‘i.end’
coverageByTranscriptFST : <anonymous>: no visible binding for global
  variable ‘file_forward’
coverageByTranscriptFST : <anonymous>: no visible binding for global
  variable ‘file_reverse’
coverageByTranscriptFST : <anonymous>: no visible global function
  definition for ‘.’
coverageHeatMap: no visible binding for global variable ‘position’
coverageHeatMap: no visible binding for global variable ‘fraction’
coveragePerORFStatistics: no visible global function definition for ‘.’
coveragePerORFStatistics: no visible binding for global variable
  ‘count’
coveragePerORFStatistics: no visible binding for global variable
  ‘genes’
coverageScorings: no visible binding for global variable ‘count’
coverageScorings: no visible binding for global variable ‘zscore’
coverageScorings: no visible binding for global variable ‘windowMean’
coverageScorings: no visible binding for global variable ‘windowSD’
coverageScorings: no visible global function definition for ‘.’
coverageScorings: no visible binding for global variable ‘modzscore’
coverageScorings: no visible binding for global variable ‘windowMedian’
coverageScorings: no visible binding for global variable ‘windowMAD’
coverageScorings: no visible binding for global variable ‘gene_sum’
coverageScorings: no visible binding for global variable ‘fraction’
coverage_random_access_file: no visible binding for global variable
  ‘count’
coverage_random_access_file: no visible binding for global variable
  ‘genes’
coverage_random_access_file: no visible binding for global variable
  ‘position’
coverage_random_access_file: no visible binding for global variable
  ‘frame’
coverage_to_dt: no visible binding for global variable ‘frame’
coverage_to_dt: no visible binding for global variable ‘genes’
coverage_to_dt: no visible binding for global variable ‘position’
detectRibosomeShifts: no visible global function definition for ‘.’
detectRibosomeShifts: no visible binding for global variable ‘size’
detectRibosomeShifts: no visible binding for global variable ‘fraction’
detectRibosomeShifts: no visible binding for global variable ‘pShifted’
detectRibosomeShifts: no visible binding for global variable
  ‘sum.count’
detectRibosomeShifts: no visible binding for global variable ‘count’
detectRibosomeShifts: no visible binding for global variable ‘genes’
detectRibosomeShifts: no visible binding for global variable
  ‘frac.score’
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 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’
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’
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
  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 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       43.347  3.373  18.946
STAR.allsteps.multiQC       22.413  0.408  23.581
makeTxdbFromGenome          19.990  1.170  21.220
codon_usage_exp             16.785  0.636  20.287
orfScore                    15.492  1.106   0.754
detect_ribo_orfs            11.771  1.069  13.575
DEG.analysis                10.032  0.380  10.656
computeFeatures              9.640  0.161  13.136
countTable_regions           7.195  2.056   5.706
codon_usage_plot             7.461  0.572  11.917
findUORFs_exp                7.218  0.212   7.660
STAR.multiQC                 6.574  0.110   7.144
codon_usage                  5.112  0.054   5.139
shiftFootprintsByExperiment  1.141  0.201   5.395
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 7 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/ORFik.Rcheck/00check.log’
for details.


Installation output

ORFik.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL ORFik
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘ORFik’ ...
** this is package ‘ORFik’ version ‘1.28.3’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c findORFsHelpers.cpp -o findORFsHelpers.o
findORFsHelpers.cpp: In function ‘Rcpp::IntegerMatrix orfs_as_matrix(std::string&, std::string, std::string, int)’:
findORFsHelpers.cpp:214:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  214 |   for (int i = 0; i < uorfSize/2; i++) {
      |                   ~~^~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c findOrfs.cpp -o findOrfs.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c findOrfsFasta.cpp -o findOrfsFasta.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pmapFromTranscripts.cpp -o pmapFromTranscripts.o
pmapFromTranscripts.cpp: In function ‘Rcpp::List pmapFromTranscriptsCPP(const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const char&, bool)’:
pmapFromTranscripts.cpp:151:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  151 |   for(auto i = 0;i < xSize; i++){
      |                  ~~^~~~~~~
pmapFromTranscripts.cpp:155:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  155 |   for(auto i = 0; i < indexSize; i++){
      |                   ~~^~~~~~~~~~~
pmapFromTranscripts.cpp:161:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  161 |   for(auto i = 1; i < indexSize; i++){
      |                   ~~^~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pmapToTranscripts.cpp -o pmapToTranscripts.o
pmapToTranscripts.cpp: In function ‘void pmapToPositive(vi&, const int&, int&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&)’:
pmapToTranscripts.cpp:22:7: warning: variable ‘currentWidth’ set but not used [-Wunused-but-set-variable]
   22 |   int currentWidth = 0;
      |       ^~~~~~~~~~~~
pmapToTranscripts.cpp: In function ‘void pmapToNegative(vi&, const int&, int&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&)’:
pmapToTranscripts.cpp:68:7: warning: variable ‘currentWidth’ set but not used [-Wunused-but-set-variable]
   68 |   int currentWidth = 0;
      |       ^~~~~~~~~~~~
pmapToTranscripts.cpp: In function ‘Rcpp::List pmapToTranscriptsCPP(const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const char&, const std::vector<int>&)’:
pmapToTranscripts.cpp:126:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  126 |   for(auto i = 0;i < xSize; i++){ // Width per exon in x
      |                  ~~^~~~~~~
pmapToTranscripts.cpp:130:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  130 |   for(auto i = 0; i < indexSize; i++){ // Width per exon in tx
      |                   ~~^~~~~~~~~~~
pmapToTranscripts.cpp:136:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  136 |   for(auto i = 1; i < indexSize; i++){
      |                   ~~^~~~~~~~~~~
pmapToTranscripts.cpp:147:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  147 |   for (auto i = 1; i < 2 * xSize; i = i + 2) {
      |                    ~~^~~~~~~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o ORFik.so RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o pmapFromTranscripts.o pmapToTranscripts.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-ORFik/00new/ORFik/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘symbols’ in package ‘ORFik’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ORFik)

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-pc-linux-gnu

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

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

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

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

Attaching package: 'generics'

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

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


Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

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

Attaching package: 'MatrixGenerics'

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

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

Loading required package: Biobase
Welcome to Bioconductor

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


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: Rsamtools

Attaching package: 'ORFik'

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

    symbols

> 
> test_check("ORFik")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 444 ]
> 
> proc.time()
   user  system elapsed 
120.290   3.735 127.822 

Example timings

ORFik.Rcheck/ORFik-Ex.timings

nameusersystemelapsed
DEG.analysis10.032 0.38010.656
DEG.plot.static0.4260.0040.434
DEG_model0.5020.0010.503
DEG_model_results0.5280.0250.553
DEG_model_simple0.4860.0070.493
DTEG.analysis0.5120.0160.528
DTEG.plot0.2970.0210.318
ORFik.template.experiment0.3100.0020.311
ORFik.template.experiment.zf0.0550.0010.057
ORFikQC0.2860.0020.288
QCreport0.3070.0030.311
QCstats0.3000.0030.303
QCstats.plot0.3610.0020.363
RiboQC.plot0.2740.0000.273
STAR.align.folder0.0000.0010.001
STAR.align.single0.0000.0000.001
STAR.allsteps.multiQC22.413 0.40823.581
STAR.index000
STAR.install000
STAR.multiQC6.5740.1107.144
STAR.remove.crashed.genome000
TOP.Motif.ecdf0.0000.0010.001
append_gene_symbols1.2330.0381.281
artificial.orfs0.4650.0070.473
asTX0.8930.0210.914
assignTSSByCage0.0030.0010.004
bamVarName0.4910.0020.493
browseSRA000
canonical_isoforms-experiment-method1.3320.0671.400
canonical_isoforms1.5210.0391.589
codon_usage5.1120.0545.139
codon_usage_exp16.785 0.63620.287
codon_usage_plot 7.461 0.57211.917
collapse.by.scores0.2850.0090.294
collapse.fastq0.0000.0010.001
collapseDuplicatedReads-GAlignmentPairs-method0.1590.0050.164
collapseDuplicatedReads-GAlignments-method0.0600.0020.061
collapseDuplicatedReads-GRanges-method0.0530.0010.058
collapseDuplicatedReads-data.table-method0.0650.0010.159
collapseDuplicatedReads0.0660.0020.137
combn.pairs0.6300.0060.958
computeFeatures 9.640 0.16113.136
computeFeaturesCage000
config0.0000.0000.001
config.exper0.1840.0090.193
config.save0.0000.0000.001
config_file0.2110.0050.216
convertLibs0.4730.0050.478
convertToOneBasedRanges0.2210.0050.269
convert_bam_to_ofst0.4680.0280.482
convert_to_bigWig1.3040.0081.304
convert_to_covRle0.6680.0210.681
convert_to_covRleList1.0440.0191.063
countOverlapsW0.0980.0020.101
countTable0.5240.0020.526
countTable_regions7.1952.0565.706
covRle1.7560.6820.214
covRleFromGR0.1320.0080.256
covRleList0.0300.0010.035
coverageByTranscriptFST0.2180.0260.262
coverageHeatMap1.9650.1092.066
coveragePerTiling1.1130.0021.118
coverageScorings0.0170.0030.012
create.experiment0.7320.0070.738
defineTrailer0.1680.0010.170
design-experiment-method0.4640.0030.467
detectRibosomeShifts0.0030.0020.005
detect_drive0.0020.0050.008
detect_ribo_orfs11.771 1.06913.575
disengagementScore0.9040.0981.001
distToCds0.4320.0330.465
distToTSS0.3160.0300.345
download.SRA000
download.SRA.metadata0.3480.0291.190
download_gene_info0.2800.0180.407
entropy1.5680.1561.687
exonsWithPseudoIntronsPerGroup2.2800.1932.448
experiment-class0.3870.0590.446
export.bed120.0170.0040.021
export.bigWig0.0290.0070.036
export.fstwig0.0500.0060.056
export.ofst-GAlignmentPairs-method0.0520.0050.057
export.ofst-GAlignments-method0.0520.0040.056
export.ofst-GRanges-method0.0550.0020.057
export.ofst0.0550.0020.057
export.wiggle0.0320.0010.033
extendLeaders1.1200.0891.318
extendLeadersUntil1.5730.0931.788
extendTrailers0.8630.0600.917
extendTrailersUntil3.2900.1974.417
extract_run_id0.0000.0010.001
file_ext_without_compression0.0010.0000.001
filepath0.7280.0440.772
filterTranscripts2.7850.1153.523
fimport0.4910.0260.518
findFa0.0060.0000.006
findMapORFs0.8370.0320.895
findORFs0.2470.0100.258
findORFsFasta0.1130.0030.111
findPeaksPerGene1.3850.0121.394
findUORFs0.0010.0000.002
findUORFs_exp7.2180.2127.660
find_url_ebi0.2000.0181.311
firstEndPerGroup0.1390.0050.246
firstExonPerGroup0.1550.0150.237
firstStartPerGroup0.1300.0150.221
fix_malformed_gff0.0010.0000.000
flankPerGroup0.3110.0140.410
floss0.7020.0511.071
fpkm0.2320.0220.401
fractionLength0.1410.0070.295
fread.bed0.0600.0180.142
gcContent0.7290.0451.009
geneToSymbol000
getGenomeAndAnnotation0.0010.0000.001
get_bioproject_candidates000
get_genome_fasta0.0010.0000.001
get_genome_gtf0.0000.0010.001
get_noncoding_rna0.0000.0000.001
get_phix_genome0.0000.0010.001
get_silva_rRNA0.0000.0000.001
get_system_usage0.1660.1120.479
go_analaysis_gorilla0.0010.0010.003
groupGRangesBy0.0610.0050.066
groupings0.0380.0030.041
heatMapRegion0.5010.0640.566
import.ofst0.0960.0070.103
initiationScore1.3080.1151.412
insideOutsideORF0.7970.0690.863
install.fastp0.0000.0000.001
install.sratoolkit0.0000.0000.001
isInFrame0.2140.0100.224
isOverlapping0.2310.0160.247
kozakHeatmap000
kozakSequenceScore0.4930.0230.515
lastExonEndPerGroup0.0590.0030.062
lastExonPerGroup0.0650.0050.071
lastExonStartPerGroup0.0520.0040.056
libraryTypes0.2870.0490.336
list.experiments0.2540.0160.269
list.genomes0.0010.0010.001
loadRegion1.2410.0751.316
loadRegions0.6180.0230.641
loadTranscriptType000
loadTxdb0.1080.0090.117
longestORFs0.1140.0100.125
makeGRangesListFromCharacter0.0720.0080.080
makeORFNames0.0780.0120.090
makeSummarizedExperimentFromBam0.3160.0110.327
makeTxdbFromGenome19.99 1.1721.22
mergeFastq000
mergeLibs1.0330.3531.302
metaWindow0.1770.0010.176
model.matrix-experiment-method0.3100.0010.309
numExonsPerGroup0.0370.0010.039
optimizedTranscriptLengths0.7700.0800.849
orfFrameDistributions43.347 3.37318.946
orfScore15.492 1.106 0.754
organism-experiment-method0.2800.0450.325
outputLibs0.9071.2201.281
pSitePlot1.0210.2421.264
pcaExperiment0.9440.1681.113
pcaPlot0.9140.1031.017
pmapFromTranscriptF0.2740.0620.337
pmapToTranscriptF0.7330.0720.805
pseudoIntronsPerGroup1.7490.1961.929
rankOrder0.0670.0140.081
read.experiment0.2740.0230.297
readBam0.100.020.12
readBamIsUniqueMapper0.0890.0150.104
readBamSeqs0.0760.0070.083
readWidths0.0150.0020.017
read_RDSQS0.3050.0340.339
reassignTSSbyCage0.5520.0650.617
reassignTxDbByCage0.0000.0000.001
reduceKeepAttr0.1080.0160.124
regionPerReadLength0.3370.4160.930
remove.experiments0.4850.2510.377
riboORFs0.3210.0420.363
riboORFsFolder0.5320.1210.653
ribo_fft2.8200.5183.309
ribo_fft_plot2.6440.2892.910
ribosomeReleaseScore0.1980.0160.214
ribosomeStallingScore0.2530.0060.259
save.experiment0.2830.0320.316
save_RDSQS0.0050.0030.009
scaledWindowPositions0.2770.0440.317
seqnamesPerGroup0.0560.0110.067
shiftFootprints0.0020.0010.003
shiftFootprintsByExperiment1.1410.2015.395
shiftPlots3.7571.1040.574
shifts_load0.5080.0610.569
shifts_save0.0730.0170.090
simpleLibs0.5400.0720.612
sortPerGroup0.4690.0380.513
startCodons0.9070.0911.143
startDefinition0.0010.0000.001
startRegion0.9040.0991.002
startRegionCoverage1.1620.1761.346
startSites0.5660.0270.594
stopCodons0.8630.0740.937
stopDefinition0.0000.0010.001
stopRegion0.8820.0380.920
stopSites0.5150.0490.564
strandBool0.0170.0030.021
strandPerGroup0.0770.0050.084
subsetToFrame0.0250.0040.029
symbols0.5760.0370.613
te.plot0.0010.0000.001
te.table0.9430.1371.080
te_rna.plot0.5030.0370.540
template_shift_table0.3520.0340.386
tile10.1740.0150.190
topMotif0.0000.0000.001
transcriptWindow0.8690.0870.957
translationalEff0.1430.0120.155
trimming.table0.0230.0040.026
txNames0.0370.0080.044
txNamesToGeneNames1.1330.1131.247
uORFSearchSpace1.3400.0821.522
uniqueGroups0.3000.0120.311
uniqueOrder0.4830.0250.509
unlistGrl0.1380.0120.151
widthPerGroup0.1150.0100.125
windowCoveragePlot1.5460.1171.646
windowPerGroup1.0580.1191.192
windowPerReadLength0.7290.0210.732