Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 1445/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ORFik 1.25.0 (landing page) Haakon Tjeldnes
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
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. |
Package: ORFik |
Version: 1.25.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ORFik.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ORFik_1.25.0.tar.gz |
StartedAt: 2024-06-10 06:44:22 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 07:08:37 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 1455.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ORFik.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ORFik.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ORFik_1.25.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/ORFik.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'ORFik/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ORFik' version '1.25.0' * 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 whether package 'ORFik' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: R 1.0Mb extdata 1.3Mb libs 1.0Mb * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: 'GenomicFeatures:::.merge_seqinfo_and_infer_missing_seqlengths' 'IRanges:::regroupBySupergroup' 'S4Vectors:::normarg_mcols' 'biomartr:::getENSEMBL.Seq' 'biomartr:::getENSEMBL.gtf' See the note in ?`:::` about the use of this operator. * 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 'bamTag<-' readBam: no visible global function definition for 'bamWhat<-' readLengthTable: no visible binding for global variable 'counts_per_sample' readLengthTable: no visible binding for global variable '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 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 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: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: Lost braces in \itemize; meant \describe ? checkRd: (-1) STAR.align.single.Rd:68-69: 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:94: Lost braces in \itemize; meant \describe ? checkRd: (-1) STAR.align.single.Rd:104: Lost braces in \itemize; meant \describe ? checkRd: (-1) STAR.align.single.Rd:105: 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 for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/ORFik/libs/x64/ORFik.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed codon_usage_exp 10.08 0.60 46.39 detect_ribo_orfs 6.75 0.50 42.11 findUORFs_exp 4.76 0.59 5.47 codon_usage 4.60 0.52 6.27 codon_usage_plot 4.56 0.53 41.09 orfFrameDistributions 2.74 0.55 70.50 regionPerReadLength 2.16 0.15 70.97 shiftFootprintsByExperiment 2.06 0.16 43.42 outputLibs 1.88 0.11 41.41 * 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 'F:/biocbuild/bbs-3.20-bioc/meat/ORFik.Rcheck/00check.log' for details.
ORFik.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL ORFik ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'ORFik' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 long unsigned int'} [-Wsign-compare] 214 | for (int i = 0; i < uorfSize/2; i++) { | ~~^~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c findOrfs.cpp -o findOrfs.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c findOrfsFasta.cpp -o findOrfsFasta.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 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 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 long unsigned int'} [-Wsign-compare] 161 | for(auto i = 1; i < indexSize; i++){ | ~~^~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 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 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 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 long unsigned int'} [-Wsign-compare] 147 | for (auto i = 1; i < 2 * xSize; i = i + 2) { | ~~^~~~~~~~~~~ g++ -std=gnu++17 -shared -s -static-libgcc -o ORFik.dll tmp.def RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o pmapFromTranscripts.o pmapToTranscripts.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-ORFik/00new/ORFik/libs/x64 ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ORFik)
ORFik.Rcheck/tests/testthat.Rout
R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows 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 427 ] > > proc.time() user system elapsed 102.06 18.20 336.31
ORFik.Rcheck/ORFik-Ex.timings
name | user | system | elapsed | |
DEG.analysis | 0.63 | 0.03 | 0.65 | |
DEG.plot.static | 0.61 | 0.10 | 0.70 | |
DEG_model | 0.36 | 0.03 | 0.39 | |
DEG_model_results | 1.41 | 0.00 | 1.41 | |
DEG_model_simple | 0.37 | 0.00 | 0.37 | |
DTEG.analysis | 0.46 | 0.03 | 0.57 | |
DTEG.plot | 0.50 | 0.06 | 0.56 | |
ORFik.template.experiment | 0.60 | 0.06 | 0.66 | |
ORFik.template.experiment.zf | 0.07 | 0.00 | 0.09 | |
ORFikQC | 0.54 | 0.00 | 0.54 | |
QCreport | 0.50 | 0.03 | 0.53 | |
QCstats | 0.53 | 0.00 | 0.56 | |
QCstats.plot | 0.54 | 0.02 | 0.60 | |
RiboQC.plot | 0.57 | 0.02 | 0.67 | |
STAR.align.folder | 0.00 | 0.00 | 0.02 | |
STAR.align.single | 0 | 0 | 0 | |
STAR.index | 0 | 0 | 0 | |
STAR.install | 0 | 0 | 0 | |
STAR.remove.crashed.genome | 0 | 0 | 0 | |
TOP.Motif.ecdf | 0 | 0 | 0 | |
artificial.orfs | 0.54 | 0.01 | 0.67 | |
asTX | 0.99 | 0.00 | 1.05 | |
assignTSSByCage | 0.00 | 0.02 | 0.05 | |
bamVarName | 1.11 | 0.01 | 1.20 | |
browseSRA | 0 | 0 | 0 | |
codon_usage | 4.60 | 0.52 | 6.27 | |
codon_usage_exp | 10.08 | 0.60 | 46.39 | |
codon_usage_plot | 4.56 | 0.53 | 41.09 | |
collapse.by.scores | 0.11 | 0.00 | 0.11 | |
collapse.fastq | 0 | 0 | 0 | |
collapseDuplicatedReads-GAlignmentPairs-method | 0.06 | 0.00 | 0.06 | |
collapseDuplicatedReads-GAlignments-method | 0.05 | 0.00 | 0.08 | |
collapseDuplicatedReads-GRanges-method | 0.04 | 0.00 | 0.05 | |
collapseDuplicatedReads-data.table-method | 0.02 | 0.00 | 0.01 | |
collapseDuplicatedReads | 0.03 | 0.00 | 0.03 | |
combn.pairs | 0.36 | 0.00 | 0.36 | |
computeFeatures | 4.22 | 0.06 | 4.35 | |
computeFeaturesCage | 0 | 0 | 0 | |
config | 0 | 0 | 0 | |
config.exper | 0.06 | 0.10 | 0.28 | |
config.save | 0 | 0 | 0 | |
config_file | 0.13 | 0.00 | 0.12 | |
convertLibs | 0.34 | 0.00 | 0.35 | |
convertToOneBasedRanges | 0.07 | 0.01 | 0.10 | |
convert_bam_to_ofst | 0.14 | 0.00 | 0.22 | |
convert_to_bigWig | 0.86 | 0.00 | 0.86 | |
convert_to_covRle | 0.72 | 0.01 | 0.77 | |
convert_to_covRleList | 0.71 | 0.00 | 0.70 | |
countOverlapsW | 0.06 | 0.00 | 0.06 | |
countTable | 0.39 | 0.02 | 0.41 | |
countTable_regions | 0.34 | 0.01 | 0.36 | |
covRle | 0.05 | 0.00 | 0.04 | |
covRleFromGR | 0.09 | 0.00 | 0.10 | |
covRleList | 0.02 | 0.00 | 0.01 | |
coverageHeatMap | 1.58 | 0.02 | 1.61 | |
coveragePerTiling | 0.78 | 0.01 | 0.80 | |
coverageScorings | 0.01 | 0.00 | 0.01 | |
create.experiment | 0.36 | 0.00 | 0.36 | |
defineTrailer | 0.13 | 0.00 | 0.13 | |
design-experiment-method | 0.40 | 0.02 | 0.42 | |
detectRibosomeShifts | 0.02 | 0.00 | 0.02 | |
detect_ribo_orfs | 6.75 | 0.50 | 42.11 | |
disengagementScore | 0.41 | 0.02 | 0.42 | |
distToCds | 0.2 | 0.0 | 0.2 | |
distToTSS | 0.22 | 0.00 | 0.22 | |
download.SRA | 0 | 0 | 0 | |
download.SRA.metadata | 0.14 | 0.00 | 1.69 | |
entropy | 1.37 | 0.00 | 1.37 | |
experiment-class | 0.46 | 0.00 | 0.46 | |
export.bed12 | 0.01 | 0.00 | 0.01 | |
export.bigWig | 0.03 | 0.00 | 0.03 | |
export.fstwig | 0.05 | 0.00 | 0.05 | |
export.ofst-GAlignmentPairs-method | 0.07 | 0.01 | 0.10 | |
export.ofst-GAlignments-method | 0.07 | 0.00 | 0.06 | |
export.ofst-GRanges-method | 0.04 | 0.00 | 0.05 | |
export.ofst | 0.05 | 0.00 | 0.04 | |
export.wiggle | 0.02 | 0.00 | 0.02 | |
extendLeaders | 0.95 | 0.40 | 1.36 | |
extendTrailers | 0.62 | 0.44 | 1.07 | |
extract_run_id | 0 | 0 | 0 | |
filepath | 0.46 | 0.02 | 0.47 | |
filterTranscripts | 1.25 | 0.00 | 1.25 | |
fimport | 0.26 | 0.11 | 0.55 | |
findFa | 0 | 0 | 0 | |
findMapORFs | 0.58 | 0.00 | 0.58 | |
findORFs | 0.14 | 0.01 | 0.15 | |
findORFsFasta | 0.06 | 0.00 | 0.10 | |
findPeaksPerGene | 1.27 | 0.38 | 1.65 | |
findUORFs | 0 | 0 | 0 | |
findUORFs_exp | 4.76 | 0.59 | 5.47 | |
find_url_ebi | 0.02 | 0.00 | 1.54 | |
firstEndPerGroup | 0.08 | 0.00 | 0.08 | |
firstExonPerGroup | 0.06 | 0.00 | 0.07 | |
firstStartPerGroup | 0.04 | 0.00 | 0.04 | |
fix_malformed_gff | 0 | 0 | 0 | |
flankPerGroup | 0.08 | 0.00 | 0.08 | |
floss | 0.24 | 0.02 | 0.25 | |
fpkm | 0.15 | 0.00 | 0.16 | |
fractionLength | 0.10 | 0.00 | 0.09 | |
fread.bed | 0.08 | 0.00 | 0.09 | |
gcContent | 0.42 | 0.00 | 0.43 | |
geneToSymbol | 0 | 0 | 0 | |
getGenomeAndAnnotation | 0 | 0 | 0 | |
get_bioproject_candidates | 0 | 0 | 0 | |
get_genome_fasta | 0 | 0 | 0 | |
get_genome_gtf | 0 | 0 | 0 | |
get_noncoding_rna | 0 | 0 | 0 | |
get_phix_genome | 0 | 0 | 0 | |
get_silva_rRNA | 0 | 0 | 0 | |
groupGRangesBy | 0.05 | 0.00 | 0.05 | |
groupings | 0.05 | 0.00 | 0.05 | |
heatMapRegion | 0.39 | 0.00 | 0.39 | |
import.ofst | 0.04 | 0.00 | 0.05 | |
initiationScore | 0.83 | 0.00 | 0.83 | |
insideOutsideORF | 0.74 | 0.00 | 0.73 | |
install.fastp | 0 | 0 | 0 | |
install.sratoolkit | 0 | 0 | 0 | |
isInFrame | 0.20 | 0.01 | 0.22 | |
isOverlapping | 0.22 | 0.00 | 0.22 | |
kozakHeatmap | 0.00 | 0.00 | 0.01 | |
kozakSequenceScore | 0.44 | 0.02 | 0.46 | |
lastExonEndPerGroup | 0.05 | 0.00 | 0.04 | |
lastExonPerGroup | 0.06 | 0.00 | 0.07 | |
lastExonStartPerGroup | 0.05 | 0.00 | 0.04 | |
libraryTypes | 0.34 | 0.00 | 0.35 | |
list.experiments | 0.27 | 0.01 | 0.28 | |
list.genomes | 0 | 0 | 0 | |
loadRegion | 1.45 | 0.41 | 1.86 | |
loadRegions | 0.73 | 0.41 | 1.14 | |
loadTranscriptType | 0 | 0 | 0 | |
loadTxdb | 0.15 | 0.35 | 0.53 | |
longestORFs | 0.10 | 0.00 | 0.11 | |
makeORFNames | 0.08 | 0.00 | 0.08 | |
makeSummarizedExperimentFromBam | 0.44 | 0.02 | 0.45 | |
makeTxdbFromGenome | 0 | 0 | 0 | |
mergeFastq | 0 | 0 | 0 | |
mergeLibs | 0.34 | 0.00 | 0.36 | |
metaWindow | 0.16 | 0.00 | 0.16 | |
model.matrix-experiment-method | 0.39 | 0.00 | 0.39 | |
numExonsPerGroup | 0.03 | 0.00 | 0.03 | |
optimizedTranscriptLengths | 0.94 | 0.39 | 1.33 | |
orfFrameDistributions | 2.74 | 0.55 | 70.50 | |
orfScore | 0.67 | 0.00 | 0.67 | |
organism-experiment-method | 0.37 | 0.00 | 0.37 | |
outputLibs | 1.88 | 0.11 | 41.41 | |
pSitePlot | 0.29 | 0.00 | 0.30 | |
pcaExperiment | 1.32 | 0.00 | 1.31 | |
pmapFromTranscriptF | 0.09 | 0.00 | 0.11 | |
pmapToTranscriptF | 0.84 | 0.34 | 1.23 | |
rankOrder | 0.09 | 0.00 | 0.10 | |
read.experiment | 0.38 | 0.00 | 0.37 | |
readBam | 0.15 | 0.08 | 0.28 | |
readWidths | 0.02 | 0.00 | 0.02 | |
reassignTSSbyCage | 0.56 | 0.08 | 0.70 | |
reassignTxDbByCage | 0 | 0 | 0 | |
reduceKeepAttr | 0.14 | 0.00 | 0.14 | |
regionPerReadLength | 2.16 | 0.15 | 70.97 | |
remove.experiments | 0.36 | 0.00 | 0.36 | |
riboORFs | 0.47 | 0.00 | 0.47 | |
riboORFsFolder | 0.36 | 0.00 | 0.36 | |
ribo_fft | 2.81 | 0.39 | 3.26 | |
ribo_fft_plot | 2.73 | 0.39 | 3.19 | |
ribosomeReleaseScore | 0.18 | 0.00 | 0.17 | |
ribosomeStallingScore | 0.25 | 0.02 | 0.27 | |
save.experiment | 0.48 | 0.00 | 0.48 | |
scaledWindowPositions | 0.41 | 0.00 | 0.41 | |
seqnamesPerGroup | 0.04 | 0.00 | 0.05 | |
shiftFootprints | 0.02 | 0.00 | 0.01 | |
shiftFootprintsByExperiment | 2.06 | 0.16 | 43.42 | |
shiftPlots | 0.06 | 0.01 | 0.08 | |
shifts.load | 0.41 | 0.00 | 0.41 | |
simpleLibs | 0.53 | 0.03 | 0.56 | |
sortPerGroup | 0.35 | 0.00 | 0.35 | |
startCodons | 0.54 | 0.00 | 0.54 | |
startDefinition | 0 | 0 | 0 | |
startRegion | 0.47 | 0.00 | 0.47 | |
startRegionCoverage | 0.31 | 0.00 | 0.31 | |
startSites | 0.28 | 0.00 | 0.28 | |
stopCodons | 0.41 | 0.02 | 0.43 | |
stopDefinition | 0 | 0 | 0 | |
stopRegion | 0.49 | 0.00 | 0.48 | |
stopSites | 0.25 | 0.00 | 0.25 | |
strandBool | 0.01 | 0.00 | 0.02 | |
strandPerGroup | 0.05 | 0.00 | 0.04 | |
subsetToFrame | 0.01 | 0.00 | 0.02 | |
te.plot | 0 | 0 | 0 | |
te.table | 0.36 | 0.01 | 0.37 | |
te_rna.plot | 0.36 | 0.02 | 0.38 | |
tile1 | 0.22 | 0.00 | 0.22 | |
topMotif | 0 | 0 | 0 | |
transcriptWindow | 1.03 | 0.42 | 1.47 | |
translationalEff | 0.13 | 0.00 | 0.12 | |
trimming.table | 0 | 0 | 0 | |
txNames | 0.03 | 0.00 | 0.03 | |
txNamesToGeneNames | 0.89 | 0.39 | 1.30 | |
uORFSearchSpace | 0.57 | 0.11 | 0.73 | |
uniqueGroups | 0.11 | 0.00 | 0.11 | |
uniqueOrder | 0.15 | 0.00 | 0.16 | |
unlistGrl | 0.05 | 0.00 | 0.04 | |
widthPerGroup | 0.06 | 0.00 | 0.06 | |
windowCoveragePlot | 0.60 | 0.05 | 0.65 | |
windowPerGroup | 0.34 | 0.00 | 0.34 | |
windowPerReadLength | 0.69 | 0.03 | 0.72 | |