Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-05-04 11:40:53 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1487/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ORFik 1.24.0  (landing page)
Haakon Tjeldnes
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/ORFik
git_branch: RELEASE_3_19
git_last_commit: d2ff2c0
git_last_commit_date: 2024-04-30 11:06:37 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for ORFik on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: ORFik
Version: 1.24.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:ORFik.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings ORFik_1.24.0.tar.gz
StartedAt: 2024-05-04 10:19:53 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 10:32:15 -0000 (Sat, 04 May 2024)
EllapsedTime: 742.4 seconds
RetCode: 0
Status:   OK  
CheckDir: ORFik.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:ORFik.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings ORFik_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ORFik.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ORFik/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ORFik’ version ‘1.24.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ORFik’ can be installed ... OK
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
  installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    extdata   1.4Mb
    libs      3.7Mb
* 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
detect_ribo_orfs: warning in outputLibs(df, type = "pshifted", output =
  "envirlist"): partial argument match of 'output' to 'output.mode'
DEG.plot.static: no visible binding for global variable ‘Regulation’
DEG.plot.static: no visible binding for global variable ‘meanCounts’
DEG.plot.static: no visible binding for global variable ‘LFC’
DEG_model_simple: no visible binding for global variable ‘id’
DEG_model_simple: no visible binding for global variable ‘contrast’
DTEG.plot: no visible binding for global variable ‘Regulation’
DTEG.plot: no visible binding for global variable ‘rna’
DTEG.plot: no visible binding for global variable ‘rfp’
QCplots: no visible binding for global variable ‘leaders’
QCplots: no visible binding for global variable ‘trailers’
QCstats.plot: no visible binding for global variable ‘variable’
QCstats.plot: no visible binding for global variable ‘sample_total’
QCstats.plot: no visible binding for global variable ‘value’
QCstats.plot: no visible global function definition for ‘.’
QCstats.plot: no visible binding for global variable ‘sample_id’
QCstats.plot: no visible binding for global variable ‘percentage’
QCstats.plot: no visible binding for global variable
  ‘perc_of_counts_per_sample’
QCstats.plot: no visible binding for global variable ‘read length’
RiboQC.plot: no visible binding for global variable ‘variable’
RiboQC.plot: no visible binding for global variable ‘sample_total’
RiboQC.plot: no visible binding for global variable ‘value’
RiboQC.plot: no visible global function definition for ‘.’
RiboQC.plot: no visible binding for global variable ‘sample_id’
RiboQC.plot: no visible binding for global variable ‘percentage’
RiboQC.plot: no visible binding for global variable ‘percent’
RiboQC.plot: no visible binding for global variable ‘frame’
STAR.multiQC: no visible binding for global variable ‘sample_id’
STAR.multiQC: no visible binding for global variable ‘value’
TOP.Motif.ecdf: no visible binding for global variable ‘seq1’
TOP.Motif.ecdf: no visible binding for global variable ‘TOP’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘percentage_mrna_aligned’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘mRNA’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘percentage_tx_aligned’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘Transcript’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘ratio_cds_mrna’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘CDS’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘ratio_cds_leader’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘LEADERS’
allFeaturesHelper: no visible binding for global variable ‘te’
allFeaturesHelper: no visible binding for global variable ‘fpkmRFP’
allFeaturesHelper: no visible binding for global variable ‘fpkmRNA’
allFeaturesHelper: no visible binding for global variable ‘countRFP’
allFeaturesHelper: no visible binding for global variable ‘entropyRFP’
allFeaturesHelper: no visible binding for global variable
  ‘disengagementScores’
allFeaturesHelper: no visible binding for global variable ‘RRS’
allFeaturesHelper: no visible binding for global variable ‘RSS’
allFeaturesHelper: no visible binding for global variable ‘ORFScores’
allFeaturesHelper: no visible binding for global variable ‘ioScore’
allFeaturesHelper: no visible binding for global variable
  ‘startCodonCoverage’
allFeaturesHelper: no visible binding for global variable
  ‘startRegionRelative’
allFeaturesHelper: no visible binding for global variable ‘kozak’
allFeaturesHelper: no visible binding for global variable ‘StartCodons’
allFeaturesHelper: no visible binding for global variable ‘StopCodons’
allFeaturesHelper: no visible binding for global variable
  ‘fractionLengths’
allFeaturesHelper: no visible binding for global variable ‘distORFCDS’
allFeaturesHelper: no visible binding for global variable ‘inFrameCDS’
allFeaturesHelper: no visible binding for global variable
  ‘isOverlappingCds’
allFeaturesHelper: no visible binding for global variable ‘rankInTx’
appendZeroes: no visible binding for global variable ‘frame’
appendZeroes: no visible binding for global variable ‘position’
appendZeroes: no visible binding for global variable ‘count’
artificial.orfs: no visible binding for global variable ‘random’
artificial.orfs: no visible binding for global variable ‘pick’
artificial.orfs: no visible global function definition for ‘.’
browseSRA: no visible global function definition for ‘browseURL’
cellTypeNames: missing arguments not allowed in calls to ‘c’
codonSumsPerGroup: no visible binding for global variable ‘genes’
codon_usage: no visible binding for global variable ‘merged’
codon_usage: no visible binding for global variable ‘AA’
codon_usage: no visible binding for global variable ‘codon’
codon_usage_plot: no visible binding for global variable ‘seqs’
collapse.by.scores: no visible global function definition for ‘.’
collapse.fastq.internal: no visible binding for global variable ‘N’
cor_plot: no visible binding for global variable ‘Var2’
cor_plot: no visible binding for global variable ‘Var1’
cor_plot: no visible binding for global variable ‘Cor’
cor_table: no visible binding for global variable ‘Var1’
cor_table: no visible binding for global variable ‘Var2’
cor_table: no visible binding for global variable ‘Cor’
coverageHeatMap: no visible binding for global variable ‘position’
coverageHeatMap: no visible binding for global variable ‘fraction’
coveragePerORFStatistics: no visible global function definition for ‘.’
coveragePerORFStatistics: no visible binding for global variable
  ‘count’
coveragePerORFStatistics: no visible binding for global variable
  ‘genes’
coverageScorings: no visible binding for global variable ‘count’
coverageScorings: no visible binding for global variable ‘zscore’
coverageScorings: no visible binding for global variable ‘windowMean’
coverageScorings: no visible binding for global variable ‘windowSD’
coverageScorings: no visible global function definition for ‘.’
coverageScorings: no visible binding for global variable ‘gene_sum’
coverageScorings: no visible binding for global variable ‘fraction’
coverage_random_access_file: no visible binding for global variable
  ‘genes’
coverage_random_access_file: no visible binding for global variable
  ‘position’
coverage_random_access_file: no visible binding for global variable
  ‘frame’
coverage_to_dt: no visible binding for global variable ‘frame’
coverage_to_dt: no visible binding for global variable ‘genes’
coverage_to_dt: no visible binding for global variable ‘position’
detectRibosomeShifts: no visible global function definition for ‘.’
detectRibosomeShifts: no visible binding for global variable ‘size’
detectRibosomeShifts: no visible binding for global variable ‘fraction’
detectRibosomeShifts: no visible binding for global variable ‘pShifted’
detectRibosomeShifts: no visible binding for global variable
  ‘sum.count’
detectRibosomeShifts: no visible binding for global variable ‘count’
detectRibosomeShifts: no visible binding for global variable ‘genes’
detectRibosomeShifts: no visible binding for global variable
  ‘frac.score’
entropy: no visible binding for global variable ‘Hx’
entropy: no visible binding for global variable ‘codonSums’
entropy: no visible global function definition for ‘.’
entropy: no visible binding for global variable ‘genes’
fetch_xml_attributes: no visible binding for global variable
  ‘..to_keep’
filterExtremePeakGenes: no visible binding for global variable ‘count’
filterExtremePeakGenes: no visible binding for global variable
  ‘median_per_gene’
filterExtremePeakGenes: no visible binding for global variable ‘genes’
filterExtremePeakGenes: no visible global function definition for ‘.’
filterTranscripts: no visible binding for global variable ‘utr5_len’
filterTranscripts: no visible binding for global variable ‘utr3_len’
filter_empty_runs: no visible binding for global variable ‘spots’
findNGSPairs: no visible global function definition for ‘.’
findNGSPairs: no visible binding for global variable ‘forward’
findPeaksPerGene: no visible binding for global variable ‘sum_per_gene’
findPeaksPerGene: no visible binding for global variable ‘count’
findPeaksPerGene: no visible binding for global variable ‘genes’
findPeaksPerGene: no visible binding for global variable
  ‘mean_per_gene’
findPeaksPerGene: no visible binding for global variable ‘sd_per_gene’
findPeaksPerGene: no visible binding for global variable ‘zscore’
findPeaksPerGene: no visible binding for global variable ‘gene_id’
find_url_ebi_safe: no visible binding for global variable
  ‘run_accession’
flankPerGroup: no visible global function definition for ‘.’
flankPerGroup: no visible binding for global variable ‘group_name’
floss: no visible binding for global variable ‘ORFGrouping’
floss: no visible binding for global variable ‘widths’
floss: no visible global function definition for ‘.’
floss: no visible binding for global variable ‘CDSGrouping’
floss: no visible binding for global variable ‘fraction.x’
floss: no visible binding for global variable ‘fraction.y’
gSort: no visible binding for global variable ‘grnames’
geneToSymbol: no visible binding for global variable ‘ensembl_gene_id’
geneToSymbol: no visible binding for global variable
  ‘external_gene_name’
geneToSymbol: no visible binding for global variable
  ‘ensembl_transcript_id’
geneToSymbol: no visible binding for global variable ‘uniprotswissprot’
getNGenesCoverage: no visible global function definition for ‘.’
getNGenesCoverage: no visible binding for global variable ‘genes’
getNGenesCoverage: no visible binding for global variable ‘fraction’
get_phix_genome: no visible binding for global variable ‘phix.url’
initiationScore: no visible global function definition for ‘.’
initiationScore: no visible binding for global variable ‘dif’
initiationScore: no visible binding for global variable ‘fraction’
initiationScore: no visible binding for global variable ‘genes’
initiationScore: no visible binding for global variable ‘difPer’
install.sratoolkit: no visible binding for global variable ‘osVersion’
isPeriodic: no visible binding for global variable ‘spec’
kozakHeatmap: no visible global function definition for ‘.’
kozakHeatmap: no visible binding for global variable ‘variable’
kozakHeatmap: no visible binding for global variable ‘value’
kozakHeatmap: no visible binding for global variable
  ‘count_seq_pos_with_count’
kozakHeatmap: no visible binding for global variable ‘median_score’
kozak_IR_ranking: no visible global function definition for ‘.’
kozak_IR_ranking: no visible binding for global variable ‘IR’
kozak_IR_ranking: no visible binding for global variable
  ‘upstream_kozak_strength’
kozak_IR_ranking: no visible binding for global variable ‘count’
kozak_IR_ranking: no visible binding for global variable ‘mean_IR’
list.genomes: no visible binding for global variable ‘STAR_index’
longestORFs: no visible global function definition for ‘.’
metaWindow: no visible binding for global variable ‘position’
metaWindow: no visible binding for global variable ‘frame’
metadata.autnaming: no visible binding for global variable
  ‘LIBRARYTYPE’
metadata.autnaming: no visible binding for global variable
  ‘LibraryStrategy’
orfFrameDistributions : <anonymous>: no visible binding for global
  variable ‘fraction’
orfFrameDistributions: no visible binding for global variable ‘percent’
orfFrameDistributions: no visible binding for global variable
  ‘fraction’
orfFrameDistributions: no visible binding for global variable
  ‘percent_length’
orfFrameDistributions: no visible global function definition for ‘.’
orfFrameDistributions: no visible binding for global variable
  ‘best_frame’
orfScore: no visible binding for global variable ‘genes’
orfScore: no visible binding for global variable ‘frame’
orfScore: no visible binding for global variable ‘frame_one_RP’
orfScore: no visible binding for global variable ‘frame_two_RP’
pSitePlot: no visible binding for global variable ‘count’
pSitePlot: no visible binding for global variable ‘frame’
pSitePlot: no visible binding for global variable ‘position’
pcaExperiment: no visible binding for global variable ‘PC1’
pcaExperiment: no visible binding for global variable ‘PC2’
readBam: no visible global function definition for ‘bamWhat<-’
readLengthTable: no visible binding for global variable
  ‘counts_per_sample’
readLengthTable: no visible binding for global variable
  ‘perc_of_counts_per_sample’
regionPerReadLength : <anonymous>: no visible binding for global
  variable ‘fraction’
remakeTxdbExonIds: no visible global function definition for ‘.’
remakeTxdbExonIds: no visible binding for global variable ‘chr’
removeTxdbExons: no visible binding for global variable ‘exon_rank’
removeTxdbExons: no visible binding for global variable ‘ranks’
ribo_fft: no visible binding for global variable ‘fraction’
ribo_fft_plot: no visible binding for global variable ‘periods’
ribo_fft_plot: no visible binding for global variable ‘amplitude’
rnaNormalize: no visible binding for global variable ‘genes’
rnaNormalize: no visible binding for global variable ‘feature’
scaledWindowPositions: no visible binding for global variable
  ‘scalingFactor’
scaledWindowPositions: no visible binding for global variable ‘genes’
scaledWindowPositions: no visible binding for global variable
  ‘position’
scaledWindowPositions: no visible global function definition for ‘.’
scoreSummarizedExperiment: no visible global function definition for
  ‘rowSums2’
seq_usage: no visible binding for global variable ‘variable’
seq_usage: no visible binding for global variable ‘codon_sum’
seq_usage: no visible global function definition for ‘.’
seq_usage: no visible binding for global variable ‘gene_sum’
seq_usage: no visible binding for global variable
  ‘N_AA_of_type_per_gene’
seq_usage: no visible binding for global variable ‘as_prob_normalized’
seq_usage: no visible binding for global variable ‘N_total’
seq_usage: no visible binding for global variable ‘N’
seq_usage: no visible binding for global variable ‘mean_txNorm’
seq_usage: no visible binding for global variable ‘sum_txNorm’
seq_usage: no visible binding for global variable ‘dispersion’
seq_usage: no visible binding for global variable ‘dispersion_txNorm’
seq_usage: no visible binding for global variable ‘var_txNorm’
seq_usage: no visible binding for global variable ‘mean_percentage’
seq_usage: no visible binding for global variable ‘mean_txNorm_prob’
seq_usage: no visible binding for global variable
  ‘mean_txNorm_percentage’
seq_usage: no visible binding for global variable
  ‘relative_to_max_score’
shiftPlots : <anonymous>: no visible binding for global variable
  ‘frame’
shiftPlots : <anonymous>: no visible binding for global variable
  ‘position’
te.plot: no visible global function definition for ‘rowMin’
te.plot: no visible binding for global variable ‘variable’
te.plot: no visible binding for global variable ‘LFC_TE’
te.plot: no visible binding for global variable ‘rfp_log2’
te.plot: no visible binding for global variable ‘rna_log2’
te.plot: no visible binding for global variable ‘rna_log10’
te.table: no visible global function definition for ‘rowMin’
te.table: no visible binding for global variable ‘variable’
te.table: no visible binding for global variable ‘TE_log2’
te.table: no visible binding for global variable ‘rfp_log2’
te.table: no visible binding for global variable ‘rna_log2’
te_rna.plot: no visible binding for global variable ‘subtitle’
te_rna.plot: no visible binding for global variable ‘rna_log10’
te_rna.plot: no visible binding for global variable ‘TE_log2’
topMotif: no visible binding for global variable ‘seq1’
topMotif: no visible binding for global variable ‘seq2’
topMotif: no visible binding for global variable ‘seq3’
topMotif: no visible binding for global variable ‘seq4’
topMotif: no visible binding for global variable ‘seq5’
transcriptWindow: no visible binding for global variable ‘fractions’
transcriptWindow: no visible binding for global variable ‘feature’
windowCoveragePlot: no visible binding for global variable ‘feature’
windowCoveragePlot: no visible binding for global variable ‘fraction’
windowCoveragePlot: no visible binding for global variable
  ‘fraction_min’
windowCoveragePlot: no visible binding for global variable ‘position’
collapseDuplicatedReads,GAlignmentPairs: no visible global function
  definition for ‘.’
collapseDuplicatedReads,GAlignmentPairs: no visible binding for global
  variable ‘start1’
collapseDuplicatedReads,GAlignmentPairs: no visible binding for global
  variable ‘start2’
collapseDuplicatedReads,GAlignmentPairs: no visible binding for global
  variable ‘cigar1’
collapseDuplicatedReads,GAlignmentPairs: no visible binding for global
  variable ‘cigar2’
collapseDuplicatedReads,GAlignments: no visible global function
  definition for ‘.’
collapseDuplicatedReads,GRanges: no visible binding for global variable
  ‘size’
collapseDuplicatedReads,GRanges: no visible global function definition
  for ‘.’
collapseDuplicatedReads,data.table: no visible global function
  definition for ‘.’
design,experiment: no visible binding for global variable ‘..formula’
seqlevels,experiment: no visible binding for global variable ‘df’
show,covRleList: no visible global function definition for ‘head’
Undefined global functions or variables:
  . ..formula ..to_keep AA CDS CDSGrouping Cor Hx IR LEADERS LFC LFC_TE
  LIBRARYTYPE LibraryStrategy N N_AA_of_type_per_gene N_total
  ORFGrouping ORFScores PC1 PC2 RRS RSS Regulation STAR_index
  StartCodons StopCodons TE_log2 TOP Transcript Var1 Var2 amplitude
  as_prob_normalized bamWhat<- best_frame browseURL chr cigar1 cigar2
  codon codonSums codon_sum contrast count countRFP
  count_seq_pos_with_count counts_per_sample df dif difPer
  disengagementScores dispersion dispersion_txNorm distORFCDS
  ensembl_gene_id ensembl_transcript_id entropyRFP exon_rank
  external_gene_name feature forward fpkmRFP fpkmRNA frac.score
  fraction fraction.x fraction.y fractionLengths fraction_min fractions
  frame frame_one_RP frame_two_RP gene_id gene_sum genes grnames
  group_name head id inFrameCDS ioScore isOverlappingCds kozak leaders
  mRNA meanCounts mean_IR mean_per_gene mean_percentage mean_txNorm
  mean_txNorm_percentage mean_txNorm_prob median_per_gene median_score
  merged osVersion pShifted perc_of_counts_per_sample percent
  percent_length percentage percentage_mrna_aligned
  percentage_tx_aligned periods phix.url pick position random rankInTx
  ranks ratio_cds_leader ratio_cds_mrna read length
  relative_to_max_score rfp rfp_log2 rna rna_log10 rna_log2 rowMin
  rowSums2 run_accession sample_id sample_total scalingFactor
  sd_per_gene seq1 seq2 seq3 seq4 seq5 seqs size spec spots start1
  start2 startCodonCoverage startRegionRelative subtitle sum.count
  sum_per_gene sum_txNorm te trailers uniprotswissprot
  upstream_kozak_strength utr3_len utr5_len value var_txNorm variable
  widths windowMean windowSD zscore
Consider adding
  importFrom("base", "length")
  importFrom("graphics", "frame")
  importFrom("stats", "df")
  importFrom("utils", "browseURL", "head", "osVersion")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) STAR.align.folder.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) STAR.align.folder.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) STAR.align.folder.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) STAR.align.folder.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) STAR.align.folder.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) STAR.align.folder.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) STAR.align.folder.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) STAR.align.folder.Rd:77-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) STAR.align.folder.Rd:101: Lost braces in \itemize; meant \describe ?
checkRd: (-1) STAR.align.folder.Rd:102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) STAR.align.folder.Rd:103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) STAR.align.folder.Rd:113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) STAR.align.folder.Rd:114: Lost braces in \itemize; meant \describe ?
checkRd: (-1) STAR.align.single.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) STAR.align.single.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) STAR.align.single.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) STAR.align.single.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) STAR.align.single.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) STAR.align.single.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) STAR.align.single.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) STAR.align.single.Rd:67-68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) STAR.align.single.Rd:91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) STAR.align.single.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) STAR.align.single.Rd:93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) STAR.align.single.Rd:103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) STAR.align.single.Rd:104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) codon_usage.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) codon_usage.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) codon_usage.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) codon_usage.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) codon_usage.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) codon_usage.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) codon_usage.Rd:62-63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) codon_usage.Rd:65-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) codon_usage.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) codon_usage.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) codon_usage.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) codon_usage_exp.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) codon_usage_exp.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) codon_usage_exp.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) codon_usage_exp.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) codon_usage_exp.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) codon_usage_exp.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) codon_usage_exp.Rd:74-75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) codon_usage_exp.Rd:77-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) codon_usage_exp.Rd:81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) codon_usage_exp.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) codon_usage_exp.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeFeatures.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeFeatures.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeFeatures.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeFeatures.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeFeatures.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeFeatures.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeFeatures.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeFeatures.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeFeatures.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeFeatures.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeFeatures.Rd:86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeFeatures.Rd:87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeFeatures.Rd:88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeFeatures.Rd:89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeFeatures.Rd:93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeFeatures.Rd:94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeFeatures.Rd:95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeFeatures.Rd:96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeFeatures.Rd:97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeFeatures.Rd:101: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeFeatures.Rd:102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeFeatures.Rd:103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeFeatures.Rd:104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coverageHeatMap.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coverageHeatMap.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coverageHeatMap.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coverageHeatMap.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coverageHeatMap.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coverageHeatMap.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coverageHeatMap.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) detect_ribo_orfs.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) detect_ribo_orfs.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) detect_ribo_orfs.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) detect_ribo_orfs.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) detect_ribo_orfs.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) detect_ribo_orfs.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) detect_ribo_orfs.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) detect_ribo_orfs.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) detect_ribo_orfs.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) experiment-class.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) experiment-class.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) experiment-class.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) experiment-class.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) experiment-class.Rd:23-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) experiment-class.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readBam.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readBam.Rd:14-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readBam.Rd:17-20: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
codon_usage_exp             12.344  0.491  12.688
detect_ribo_orfs             8.899  0.798   9.553
findUORFs_exp                7.162  0.192   7.370
computeFeatures              5.955  0.036   6.003
shifts.load                  4.657  0.739   0.696
codon_usage_plot             4.709  0.525   5.097
shiftFootprintsByExperiment  1.454  0.044   6.106
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/ORFik.Rcheck/00check.log’
for details.


Installation output

ORFik.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL ORFik
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘ORFik’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -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/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c findOrfs.cpp -o findOrfs.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c findOrfsFasta.cpp -o findOrfsFasta.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -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/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -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/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o ORFik.so RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o pmapFromTranscripts.o pmapToTranscripts.o -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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 418 ]
> 
> proc.time()
   user  system elapsed 
128.125   5.782 133.213 

Example timings

ORFik.Rcheck/ORFik-Ex.timings

nameusersystemelapsed
DEG.analysis0.7020.0040.707
DEG.plot.static0.7170.0040.721
DEG_model1.6200.0761.698
DEG_model_results0.5730.0000.574
DEG_model_simple0.5420.0270.571
DTEG.analysis0.5660.0360.603
DTEG.plot0.5260.0560.583
ORFik.template.experiment0.6150.0040.620
ORFik.template.experiment.zf0.0830.0000.084
ORFikQC0.5480.0000.549
QCreport0.5490.0000.550
QCstats0.5530.0080.561
QCstats.plot0.5770.0000.579
RiboQC.plot0.5660.0000.567
STAR.align.folder000
STAR.align.single0.0010.0000.000
STAR.index000
STAR.install000
STAR.remove.crashed.genome000
TOP.Motif.ecdf000
artificial.orfs0.5650.0000.566
asTX0.9840.0040.990
assignTSSByCage0.0020.0000.003
bamVarName1.1070.0041.113
browseSRA000
codon_usage4.6130.0724.698
codon_usage_exp12.344 0.49112.688
codon_usage_plot4.7090.5255.097
collapse.by.scores0.1300.0120.142
collapse.fastq0.0010.0000.001
collapseDuplicatedReads-GAlignmentPairs-method0.0960.0070.104
collapseDuplicatedReads-GAlignments-method0.0410.0010.041
collapseDuplicatedReads-GRanges-method0.0330.0070.041
collapseDuplicatedReads-data.table-method0.0420.0010.042
collapseDuplicatedReads0.0390.0000.039
combn.pairs0.5440.0310.576
computeFeatures5.9550.0366.003
computeFeaturesCage000
config000
config.exper000
config.save000
config_file0.1580.0040.167
convertLibs0.5250.0080.535
convertToOneBasedRanges0.1650.0000.165
convert_bam_to_ofst0.2370.0080.245
convert_to_bigWig1.2560.0001.258
convert_to_covRle0.6960.0000.698
convert_to_covRleList1.0300.0041.037
countOverlapsW0.0920.0040.097
countTable0.5340.0000.536
countTable_regions0.5360.0000.536
covRle0.0660.0000.066
covRleFromGR0.1160.0000.117
covRleList0.0230.0000.023
coverageHeatMap1.6930.0121.708
coveragePerTiling0.9330.0080.942
coverageScorings0.0090.0040.012
create.experiment0.5410.0200.562
defineTrailer0.2080.0040.212
design-experiment-method0.5710.0000.573
detectRibosomeShifts0.0020.0000.003
detect_ribo_orfs8.8990.7989.553
disengagementScore0.7350.0390.777
distToCds0.3500.0520.403
distToTSS0.2950.0120.308
download.SRA000
download.SRA.metadata0.2180.0204.199
entropy2.2240.1322.359
experiment-class0.6890.0160.707
export.bed120.0320.0000.032
export.bigWig0.0460.0080.054
export.fstwig0.0880.0000.088
export.ofst-GAlignmentPairs-method0.0920.0040.096
export.ofst-GAlignments-method0.0970.0000.097
export.ofst-GRanges-method0.0850.0030.089
export.ofst0.0850.0040.089
export.wiggle0.0490.0000.049
extendLeaders1.5260.0961.625
extendTrailers0.9410.0731.017
extract_run_id0.0010.0000.000
filepath0.6670.0310.701
filterTranscripts1.8610.0401.904
fimport0.4380.0430.483
findFa0.0000.0040.004
findMapORFs0.7590.0400.800
findORFs0.2530.0000.253
findORFsFasta0.0930.0040.100
findPeaksPerGene1.5800.0761.660
findUORFs0.0020.0000.001
findUORFs_exp7.1620.1927.370
find_url_ebi0.0460.0044.514
firstEndPerGroup0.0850.0080.094
firstExonPerGroup0.0960.0040.101
firstStartPerGroup0.0820.0040.086
fix_malformed_gff000
flankPerGroup0.1290.0240.153
floss0.3860.0080.394
fpkm0.1580.0040.163
fractionLength0.0950.0000.095
fread.bed0.0450.0040.051
gcContent0.5070.0360.545
geneToSymbol0.0000.0000.001
getGenomeAndAnnotation0.0010.0000.000
get_bioproject_candidates000
get_genome_fasta0.0000.0000.001
get_genome_gtf0.0010.0000.000
get_noncoding_rna000
get_phix_genome000
get_silva_rRNA000
groupGRangesBy0.1110.0000.111
groupings0.0510.0040.056
heatMapRegion0.5750.0200.596
import.ofst0.0810.0000.081
initiationScore1.3980.0191.420
insideOutsideORF1.1550.0161.173
install.fastp000
install.sratoolkit000
isInFrame0.3330.0000.334
isOverlapping0.3320.0000.333
kozakHeatmap000
kozakSequenceScore0.8060.0350.843
lastExonEndPerGroup0.0850.0000.086
lastExonPerGroup0.0910.0000.092
lastExonStartPerGroup0.0800.0000.081
libraryTypes0.5680.0200.588
list.experiments0.3690.0160.386
list.genomes0.0010.0000.001
loadRegion2.0240.0642.092
loadRegions0.8710.0160.889
loadTranscriptType000
loadTxdb0.1540.0120.167
longestORFs0.1730.0040.177
makeORFNames0.1120.0000.112
makeSummarizedExperimentFromBam0.5860.0040.591
makeTxdbFromGenome000
mergeFastq0.0010.0000.000
mergeLibs0.5340.0000.534
metaWindow0.2560.0040.261
model.matrix-experiment-method0.5590.0000.561
numExonsPerGroup0.0500.0000.051
optimizedTranscriptLengths1.2840.0161.302
orfFrameDistributions1.0530.1791.504
orfScore1.3230.2951.237
organism-experiment-method0.5580.0360.594
outputLibs1.3670.5691.579
pSitePlot0.4350.0480.484
pcaExperiment1.4710.1031.579
pmapFromTranscriptF0.1690.0040.173
pmapToTranscriptF1.1500.0041.157
rankOrder0.1010.0000.101
read.experiment0.5420.0030.547
readBam0.2120.0090.221
readWidths0.0210.0000.021
reassignTSSbyCage0.8180.0110.832
reassignTxDbByCage0.0010.0000.000
reduceKeepAttr0.1800.0000.181
regionPerReadLength0.4360.2430.935
remove.experiments0.8240.3070.725
riboORFs0.5830.2320.817
riboORFsFolder0.6090.0910.702
ribo_fft3.7650.3244.097
ribo_fft_plot3.7550.2394.002
ribosomeReleaseScore0.2980.0040.303
ribosomeStallingScore0.4060.0080.415
save.experiment0.5480.0080.557
scaledWindowPositions0.4670.0080.476
seqnamesPerGroup0.0890.0000.091
shiftFootprints0.0030.0000.003
shiftFootprintsByExperiment1.4540.0446.106
shiftPlots0.0640.0200.085
shifts.load4.6570.7390.696
simpleLibs0.5410.0590.603
sortPerGroup0.3400.0440.385
startCodons0.6670.0600.729
startDefinition0.0000.0000.001
startRegion0.7990.0080.809
startRegionCoverage0.5030.0310.536
startSites0.3950.0080.404
stopCodons0.6620.0040.667
stopDefinition000
stopRegion0.7760.0080.786
stopSites0.3760.0000.376
strandBool0.0110.0000.012
strandPerGroup0.0790.0000.079
subsetToFrame0.0210.0000.020
te.plot000
te.table0.5290.0000.529
te_rna.plot0.5330.0000.534
tile10.2950.0000.296
topMotif000
transcriptWindow1.4000.0041.407
translationalEff0.2020.0000.202
trimming.table000
txNames0.0550.0000.055
txNamesToGeneNames1.1940.0081.204
uORFSearchSpace0.7720.0040.777
uniqueGroups0.1880.0000.188
uniqueOrder0.2730.0000.273
unlistGrl0.0590.0000.059
widthPerGroup0.0900.0040.094
windowCoveragePlot0.8600.0040.865
windowPerGroup0.5290.0000.529
windowPerReadLength1.1860.0041.192