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This page was generated on 2021-10-15 15:06:45 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the ORFik package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1323/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ORFik 1.12.13 (landing page) Haakon Tjeldnes
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: ORFik |
Version: 1.12.13 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ORFik.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ORFik_1.12.13.tar.gz |
StartedAt: 2021-10-14 21:59:56 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 22:11:10 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 674.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ORFik.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ORFik.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ORFik_1.12.13.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/ORFik.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ORFik/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ORFik’ version ‘1.12.13’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ORFik’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R 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. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘coverageByTranscriptW’ ‘find_url_ebi’ ‘groupings’ ‘trimming.table’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE 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.align.folder: no visible global function definition for ‘detectCores’ STAR.align.single: no visible global function definition for ‘detectCores’ STAR.index: no visible global function definition for ‘detectCores’ 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 ‘.’ collapse.by.scores: no visible global function definition for ‘.’ collapse.fastq: no visible binding for global variable ‘N’ coverageHeatMap: no visible binding for global variable ‘position’ coverageHeatMap: no visible binding for global variable ‘fraction’ coveragePerTiling: no visible binding for global variable ‘frame’ coveragePerTiling: no visible binding for global variable ‘position’ 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’ 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 ‘frac.score’ download.SRA.metadata: no visible binding for global variable ‘spots’ download.SRA.metadata: no visible binding for global variable ‘MONTH’ download.SRA.metadata: no visible binding for global variable ‘ReleaseDate’ download.SRA.metadata: no visible binding for global variable ‘YEAR’ download.SRA.metadata: no visible binding for global variable ‘Run’ download.SRA.metadata: no visible binding for global variable ‘LIBRARYTYPE’ download.SRA.metadata: no visible binding for global variable ‘LibraryStrategy’ entropy: no visible binding for global variable ‘Hx’ entropy: no visible binding for global variable ‘codonSums’ entropy: no visible global function definition for ‘.’ filterExtremePeakGenes: no visible binding for global variable ‘count’ filterExtremePeakGenes: no visible binding for global variable ‘median_per_gene’ 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’ 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 ‘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’ 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’ getNGenesCoverage: no visible global function definition for ‘.’ getNGenesCoverage: no visible binding for global variable ‘fraction’ 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 ‘difPer’ 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’ 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 ‘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’ 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’ rnaNormalize: no visible binding for global variable ‘feature’ scaledWindowPositions: no visible binding for global variable ‘scalingFactor’ scaledWindowPositions: no visible binding for global variable ‘position’ scaledWindowPositions: no visible global function definition for ‘.’ scoreSummarizedExperiment: no visible global function definition for ‘rowSums2’ 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 ‘df.rfp’ te_rna.plot: no visible binding for global variable ‘df.rna’ 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’ 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 ‘.’ Undefined global functions or variables: . CDS CDSGrouping Hx IR LEADERS LFC_TE LIBRARYTYPE LibraryStrategy MONTH N ORFGrouping ORFScores PC1 PC2 RRS RSS Regulation ReleaseDate Run STAR_index StartCodons StopCodons TE_log2 TOP Transcript YEAR best_frame chr cigar1 cigar2 codonSums count countRFP count_seq_pos_with_count counts_per_sample detectCores df.rfp df.rna dif difPer disengagementScores distORFCDS entropyRFP exon_rank 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 grnames inFrameCDS ioScore isOverlappingCds kozak leaders mRNA mean_IR mean_per_gene median_per_gene median_score pShifted perc_of_counts_per_sample percent percent_length percentage percentage_mrna_aligned percentage_tx_aligned pick position random rankInTx ranks ratio_cds_leader ratio_cds_mrna read length 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 size spec spots start1 start2 startCodonCoverage startRegionRelative subtitle sum.count sum_per_gene te trailers upstream_kozak_strength utr3_len utr5_len value variable widths windowMean windowSD zscore Consider adding importFrom("base", "length") importFrom("graphics", "frame") to your NAMESPACE file. * checking Rd files ... OK * 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 line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... 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 computeFeatures 10.190 0.041 14.918 shiftFootprintsByExperiment 6.656 0.069 6.735 orfFrameDistributions 4.657 0.926 3.988 findPeaksPerGene 3.849 0.023 6.080 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/ORFik.Rcheck/00check.log’ for details.
ORFik.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ORFik ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘ORFik’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c findORFsHelpers.cpp -o findORFsHelpers.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c findOrfs.cpp -o findOrfs.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c findOrfsFasta.cpp -o findOrfsFasta.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c pmapFromTranscripts.cpp -o pmapFromTranscripts.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c pmapToTranscripts.cpp -o pmapToTranscripts.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o ORFik.so RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o pmapFromTranscripts.o pmapToTranscripts.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-ORFik/00new/ORFik/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** 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)
ORFik.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(ORFik) Loading required package: IRanges Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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, 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, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' 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 > > test_check("ORFik") widths group.size Min. : 6 Min. :1.000 1st Qu.: 9 1st Qu.:1.000 Median :12 Median :1.000 Mean :12 Mean :1.667 3rd Qu.:15 3rd Qu.:2.000 Max. :18 Max. :3.000 [1] "CAGE_heart" [1] "RFP_heart" [1] "RFP" [1] "RNA_heart" [ FAIL 0 | WARN 0 | SKIP 0 | PASS 359 ] > > proc.time() user system elapsed 122.177 7.128 119.966
ORFik.Rcheck/ORFik-Ex.timings
name | user | system | elapsed | |
DTEG.analysis | 0.000 | 0.001 | 0.001 | |
DTEG.plot | 0.000 | 0.000 | 0.001 | |
ORFik.template.experiment | 0.327 | 0.004 | 0.527 | |
ORFikQC | 0.188 | 0.003 | 0.275 | |
QCreport | 0.137 | 0.005 | 0.143 | |
QCstats | 0.156 | 0.015 | 0.173 | |
QCstats.plot | 0.162 | 0.016 | 0.180 | |
RiboQC.plot | 0.158 | 0.015 | 0.174 | |
STAR.align.folder | 0.001 | 0.001 | 0.001 | |
STAR.align.single | 0.000 | 0.000 | 0.001 | |
STAR.index | 0 | 0 | 0 | |
STAR.install | 0 | 0 | 0 | |
STAR.remove.crashed.genome | 0 | 0 | 0 | |
TOP.Motif.ecdf | 0.001 | 0.000 | 0.001 | |
artificial.orfs | 0.158 | 0.014 | 0.173 | |
asTX | 1.751 | 0.070 | 2.275 | |
assignTSSByCage | 0.002 | 0.000 | 0.003 | |
bamVarName | 0.237 | 0.002 | 0.384 | |
collapse.by.scores | 0.303 | 0.002 | 0.522 | |
collapse.fastq | 0 | 0 | 0 | |
collapseDuplicatedReads-GAlignmentPairs-method | 0.163 | 0.001 | 0.286 | |
collapseDuplicatedReads-GAlignments-method | 0.087 | 0.000 | 0.137 | |
collapseDuplicatedReads-GRanges-method | 0.103 | 0.001 | 0.177 | |
collapseDuplicatedReads | 0.085 | 0.000 | 0.147 | |
combn.pairs | 0.181 | 0.002 | 0.317 | |
computeFeatures | 10.190 | 0.041 | 14.918 | |
computeFeaturesCage | 0.000 | 0.000 | 0.001 | |
config | 0.001 | 0.000 | 0.000 | |
config.exper | 0.000 | 0.001 | 0.000 | |
config.save | 0 | 0 | 0 | |
convertLibs | 0.127 | 0.001 | 0.128 | |
convertToOneBasedRanges | 0.297 | 0.002 | 0.299 | |
countOverlapsW | 0.131 | 0.000 | 0.132 | |
countTable | 0.134 | 0.001 | 0.136 | |
countTable_regions | 0.136 | 0.001 | 0.137 | |
coverageHeatMap | 1.802 | 0.009 | 1.813 | |
coveragePerTiling | 1.122 | 0.003 | 1.125 | |
coverageScorings | 0.008 | 0.000 | 0.009 | |
create.experiment | 0.087 | 0.001 | 0.088 | |
defineTrailer | 0.188 | 0.001 | 0.189 | |
detectRibosomeShifts | 0.002 | 0.001 | 0.002 | |
disengagementScore | 0.911 | 0.003 | 1.059 | |
distToCds | 0.536 | 0.003 | 0.691 | |
distToTSS | 0.531 | 0.012 | 0.547 | |
download.SRA | 0.001 | 0.000 | 0.000 | |
download.SRA.metadata | 0.406 | 0.016 | 1.708 | |
entropy | 1.763 | 0.007 | 2.816 | |
experiment-class | 0.181 | 0.003 | 0.304 | |
export.bed12 | 0.066 | 0.001 | 0.106 | |
export.bigWig | 0.103 | 0.001 | 0.173 | |
export.ofst-GAlignmentPairs-method | 0.157 | 0.001 | 0.258 | |
export.ofst-GAlignments-method | 0.153 | 0.001 | 0.249 | |
export.ofst-GRanges-method | 0.153 | 0.001 | 0.261 | |
export.ofst | 0.156 | 0.000 | 0.252 | |
export.wiggle | 0.097 | 0.000 | 0.159 | |
extendLeaders | 2.767 | 0.027 | 4.653 | |
extendTrailers | 1.622 | 0.019 | 2.404 | |
filepath | 0.154 | 0.002 | 0.186 | |
filterTranscripts | 3.237 | 0.016 | 4.519 | |
fimport | 0.687 | 0.023 | 1.069 | |
findFa | 0.008 | 0.000 | 0.010 | |
findMapORFs | 1.163 | 0.024 | 1.224 | |
findORFs | 0.347 | 0.005 | 0.441 | |
findORFsFasta | 0.181 | 0.009 | 0.327 | |
findPeaksPerGene | 3.849 | 0.023 | 6.080 | |
findUORFs | 0.001 | 0.001 | 0.002 | |
find_url_ebi | 0.051 | 0.008 | 4.212 | |
firstEndPerGroup | 0.153 | 0.001 | 0.155 | |
firstExonPerGroup | 0.195 | 0.002 | 0.296 | |
firstStartPerGroup | 0.153 | 0.002 | 0.252 | |
floss | 0.682 | 0.003 | 1.144 | |
fpkm | 0.304 | 0.002 | 0.516 | |
fractionLength | 0.177 | 0.002 | 0.309 | |
fread.bed | 0.095 | 0.010 | 0.177 | |
gcContent | 0.887 | 0.003 | 1.133 | |
getGenomeAndAnnotation | 0.000 | 0.001 | 0.027 | |
get_genome_fasta | 0.000 | 0.001 | 0.001 | |
get_genome_gtf | 0.001 | 0.001 | 0.003 | |
get_noncoding_rna | 0.000 | 0.001 | 0.033 | |
get_phix_genome | 0.000 | 0.001 | 0.006 | |
get_silva_rRNA | 0.000 | 0.000 | 0.004 | |
groupGRangesBy | 0.163 | 0.002 | 0.303 | |
groupings | 0.094 | 0.000 | 0.098 | |
heatMapRegion | 0.156 | 0.004 | 0.217 | |
import.ofst | 0.150 | 0.004 | 0.158 | |
initiationScore | 2.309 | 0.009 | 3.828 | |
insideOutsideORF | 1.971 | 0.007 | 3.331 | |
install.fastp | 0.000 | 0.000 | 0.001 | |
install.sratoolkit | 0 | 0 | 0 | |
isInFrame | 0.556 | 0.001 | 0.876 | |
isOverlapping | 0.652 | 0.002 | 1.054 | |
kozakHeatmap | 0.000 | 0.000 | 0.001 | |
kozakSequenceScore | 1.289 | 0.004 | 2.065 | |
lastExonEndPerGroup | 0.172 | 0.001 | 0.271 | |
lastExonPerGroup | 0.199 | 0.002 | 0.309 | |
lastExonStartPerGroup | 0.150 | 0.001 | 0.242 | |
libraryTypes | 0.153 | 0.001 | 0.237 | |
list.experiments | 0.120 | 0.001 | 0.192 | |
list.genomes | 0.001 | 0.001 | 0.001 | |
loadRegion | 2.589 | 0.011 | 3.328 | |
loadRegions | 1.611 | 0.007 | 1.622 | |
loadTranscriptType | 0.001 | 0.000 | 0.000 | |
loadTxdb | 0.198 | 0.005 | 0.202 | |
longestORFs | 0.255 | 0.001 | 0.255 | |
makeORFNames | 0.159 | 0.001 | 0.160 | |
makeSummarizedExperimentFromBam | 0.164 | 0.001 | 0.165 | |
makeTxdbFromGenome | 0.000 | 0.001 | 0.000 | |
mergeFastq | 0.000 | 0.000 | 0.001 | |
metaWindow | 0.335 | 0.000 | 0.335 | |
numExonsPerGroup | 0.058 | 0.000 | 0.059 | |
orfFrameDistributions | 4.657 | 0.926 | 3.988 | |
orfScore | 1.359 | 0.111 | 1.470 | |
organism-experiment-method | 0.130 | 0.002 | 0.132 | |
outputLibs | 0.724 | 0.568 | 0.632 | |
pSitePlot | 0.561 | 0.057 | 0.618 | |
pmapFromTranscriptF | 0.195 | 0.017 | 0.212 | |
pmapToTranscriptF | 1.626 | 0.055 | 1.682 | |
rankOrder | 0.180 | 0.002 | 0.182 | |
read.experiment | 0.146 | 0.003 | 0.147 | |
readBam | 0.246 | 0.012 | 0.259 | |
readWidths | 0.029 | 0.002 | 0.030 | |
reassignTSSbyCage | 1.040 | 0.015 | 1.059 | |
reassignTxDbByCage | 0 | 0 | 0 | |
reduceKeepAttr | 0.286 | 0.003 | 0.289 | |
regionPerReadLength | 0.714 | 0.009 | 0.724 | |
remove.experiments | 0.087 | 0.001 | 0.088 | |
ribosomeReleaseScore | 0.325 | 0.001 | 0.326 | |
ribosomeStallingScore | 0.554 | 0.001 | 0.556 | |
save.experiment | 0.135 | 0.002 | 0.138 | |
scaledWindowPositions | 0.633 | 0.009 | 0.643 | |
seqnamesPerGroup | 0.121 | 0.001 | 0.121 | |
shiftFootprints | 0.002 | 0.000 | 0.003 | |
shiftFootprintsByExperiment | 6.656 | 0.069 | 6.735 | |
shiftPlots | 0.145 | 0.002 | 0.147 | |
shifts.load | 0.118 | 0.001 | 0.120 | |
simpleLibs | 0.133 | 0.002 | 0.135 | |
sortPerGroup | 0.463 | 0.003 | 0.465 | |
startCodons | 0.802 | 0.003 | 0.806 | |
startDefinition | 0 | 0 | 0 | |
startRegion | 1.033 | 0.003 | 1.038 | |
startSites | 0.451 | 0.001 | 0.453 | |
stopCodons | 0.758 | 0.003 | 0.762 | |
stopDefinition | 0.001 | 0.001 | 0.002 | |
stopRegion | 0.954 | 0.003 | 0.957 | |
stopSites | 0.511 | 0.001 | 0.513 | |
strandBool | 0.023 | 0.000 | 0.023 | |
strandPerGroup | 0.102 | 0.001 | 0.103 | |
subsetToFrame | 0.037 | 0.001 | 0.037 | |
te.plot | 0.000 | 0.001 | 0.000 | |
te.table | 0 | 0 | 0 | |
te_rna.plot | 0 | 0 | 0 | |
tile1 | 0.427 | 0.004 | 0.431 | |
topMotif | 0.001 | 0.001 | 0.001 | |
transcriptWindow | 1.898 | 0.008 | 1.910 | |
translationalEff | 0.235 | 0.002 | 0.236 | |
trimming.table | 0 | 0 | 0 | |
txNames | 0.089 | 0.000 | 0.090 | |
txNamesToGeneNames | 1.354 | 0.011 | 1.371 | |
uORFSearchSpace | 1.083 | 0.007 | 1.092 | |
uniqueGroups | 0.253 | 0.002 | 0.256 | |
uniqueOrder | 0.453 | 0.002 | 0.456 | |
unlistGrl | 0.102 | 0.002 | 0.104 | |
widthPerGroup | 0.094 | 0.001 | 0.095 | |
windowCoveragePlot | 0.887 | 0.007 | 0.895 | |
windowPerGroup | 0.670 | 0.004 | 0.674 | |
windowPerReadLength | 1.522 | 0.005 | 1.527 | |