Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-06-24 12:07:55 -0400 (Fri, 24 Jun 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.2.0 (2022-04-22) -- "Vigorous Calisthenics" | 4380 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" | 4156 |
merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.0 (2022-04-22) -- "Vigorous Calisthenics" | 4221 |
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 |
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1386/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ORFik 1.16.0 (landing page) Haakon Tjeldnes
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | NA | |||||||||
Package: ORFik |
Version: 1.16.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ORFik.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ORFik_1.16.0.tar.gz |
StartedAt: 2022-06-24 06:21:01 -0400 (Fri, 24 Jun 2022) |
EndedAt: 2022-06-24 06:35:26 -0400 (Fri, 24 Jun 2022) |
EllapsedTime: 864.9 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: ORFik.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ORFik.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ORFik_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/ORFik.Rcheck’ * using R version 4.2.0 (2022-04-22) * 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 ‘1.16.0’ * 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 * 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: ‘find_url_ebi’ ‘trimming.table’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE DEG.plot.static: no visible binding for global variable ‘Regulation’ DEG.plot.static: no visible binding for global variable ‘meanCounts’ DEG.plot.static: no visible binding for global variable ‘LFC’ 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 ‘.’ 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’ 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’ getNGenesCoverage: no visible global function definition for ‘.’ 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 ‘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 ‘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 ‘.’ design,experiment: no visible binding for global variable ‘..formula’ Undefined global functions or variables: . ..formula CDS CDSGrouping Hx IR LEADERS LFC 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 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 group_name inFrameCDS ioScore isOverlappingCds kozak leaders mRNA meanCounts 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 phix.url 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 ... ERROR Running examples in ‘ORFik-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: download.SRA.metadata > ### Title: Downloads metadata from SRA > ### Aliases: download.SRA.metadata > > ### ** Examples > > ## Originally on SRA > download.SRA.metadata("SRP226389") trying URL 'https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?save=efetch&db=sra&rettype=runinfo&term=SRP226389' Warning in download.file(url, destfile) : cannot open URL 'https://www.ncbi.nlm.nih.gov/sviewer/?db=sra&1%3Fdb=sra&rettype=runinfo&save=efetch&term=SRP226389': HTTP status was '400 Bad Request' Error in download.file(url, destfile) : cannot open URL 'https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?save=efetch&db=sra&rettype=runinfo&term=SRP226389' Calls: download.SRA.metadata -> download.file Execution halted * 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: 1 ERROR, 3 NOTEs See ‘/Users/biocbuild/bbs-3.15-bioc/meat/ORFik.Rcheck/00check.log’ for details.
ORFik.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ORFik ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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/4.2/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/4.2/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/4.2/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/4.2/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/4.2/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/4.2/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/4.2/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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics" Copyright (C) 2022 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 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, 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.:1.500 Median :12 Median :2.000 Mean :12 Mean :1.667 3rd Qu.:15 3rd Qu.:2.000 Max. :18 Max. :2.000 [1] "CAGE_Mutant_r1" [1] "CAGE_Mutant_r2" [1] "CAGE_WT_r1" [1] "CAGE_WT_r2" [1] "PAS_Mutant_r1" [1] "PAS_Mutant_r2" [1] "PAS_WT_r1" [1] "PAS_WT_r2" [1] "RFP_Mutant_r1" [1] "RFP_Mutant_r2" [1] "RFP_WT_r1" [1] "RFP_WT_r2" [1] "RNA_Mutant_r1" [1] "RNA_Mutant_r2" [1] "RNA_WT_r1" [1] "RNA_WT_r2" [1] "RFP" [1] "RFP" [1] "RFP" [1] "RFP" [ FAIL 0 | WARN 0 | SKIP 0 | PASS 361 ] > > proc.time() user system elapsed 148.647 5.229 158.497
ORFik.Rcheck/ORFik-Ex.timings
name | user | system | elapsed | |
DEG.analysis | 1.132 | 0.112 | 1.252 | |
DEG.plot.static | 0.855 | 0.084 | 0.946 | |
DTEG.analysis | 0.872 | 0.037 | 0.920 | |
DTEG.plot | 0.791 | 0.004 | 0.800 | |
ORFik.template.experiment | 0.850 | 0.005 | 0.860 | |
ORFik.template.experiment.zf | 0.114 | 0.002 | 0.117 | |
ORFikQC | 0.785 | 0.006 | 0.796 | |
QCreport | 0.834 | 0.053 | 0.893 | |
QCstats | 0.807 | 0.003 | 0.820 | |
QCstats.plot | 0.798 | 0.004 | 0.810 | |
RiboQC.plot | 0.794 | 0.005 | 0.807 | |
STAR.align.folder | 0.000 | 0.000 | 0.001 | |
STAR.align.single | 0 | 0 | 0 | |
STAR.index | 0.001 | 0.000 | 0.000 | |
STAR.install | 0.001 | 0.000 | 0.000 | |
STAR.remove.crashed.genome | 0.001 | 0.000 | 0.000 | |
TOP.Motif.ecdf | 0.001 | 0.001 | 0.001 | |
artificial.orfs | 0.787 | 0.005 | 0.800 | |
asTX | 1.498 | 0.006 | 1.526 | |
assignTSSByCage | 0.003 | 0.002 | 0.004 | |
bamVarName | 1.641 | 0.005 | 1.670 | |
collapse.by.scores | 0.217 | 0.001 | 0.219 | |
collapse.fastq | 0.000 | 0.001 | 0.001 | |
collapseDuplicatedReads-GAlignmentPairs-method | 0.139 | 0.001 | 0.141 | |
collapseDuplicatedReads-GAlignments-method | 0.056 | 0.001 | 0.056 | |
collapseDuplicatedReads-GRanges-method | 0.052 | 0.001 | 0.053 | |
collapseDuplicatedReads | 0.054 | 0.001 | 0.056 | |
combn.pairs | 1.828 | 0.028 | 1.876 | |
computeFeatures | 9.428 | 0.076 | 9.836 | |
computeFeaturesCage | 0 | 0 | 0 | |
config | 0 | 0 | 0 | |
config.exper | 0.000 | 0.001 | 0.000 | |
config.save | 0 | 0 | 0 | |
convertLibs | 0.781 | 0.003 | 0.924 | |
convertToOneBasedRanges | 0.268 | 0.002 | 0.330 | |
countOverlapsW | 0.155 | 0.001 | 0.188 | |
countTable | 0.816 | 0.003 | 0.946 | |
countTable_regions | 0.794 | 0.003 | 0.951 | |
coverageHeatMap | 2.457 | 0.011 | 2.708 | |
coveragePerTiling | 1.599 | 0.007 | 1.716 | |
coverageScorings | 0.014 | 0.001 | 0.015 | |
create.experiment | 0.773 | 0.004 | 0.836 | |
defineTrailer | 0.263 | 0.001 | 0.285 | |
design-experiment-method | 0.825 | 0.004 | 0.899 | |
detectRibosomeShifts | 0.002 | 0.001 | 0.004 | |
disengagementScore | 1.077 | 0.003 | 1.174 | |
distToCds | 0.471 | 0.001 | 0.509 | |
distToTSS | 0.432 | 0.001 | 0.460 | |
download.SRA | 0.000 | 0.001 | 0.001 | |