Back to Multiple platform build/check report for BioC 3.10 |
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This page was generated on 2020-04-15 12:22:41 -0400 (Wed, 15 Apr 2020).
Package 1008/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
metaseqR 1.26.0 Panagiotis Moulos
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: metaseqR |
Version: 1.26.0 |
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metaseqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings metaseqR_1.26.0.tar.gz |
StartedAt: 2020-04-15 04:36:19 -0400 (Wed, 15 Apr 2020) |
EndedAt: 2020-04-15 04:45:02 -0400 (Wed, 15 Apr 2020) |
EllapsedTime: 522.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: metaseqR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metaseqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings metaseqR_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/metaseqR.Rcheck' * using R version 3.6.3 (2020-02-29) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'metaseqR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'metaseqR' version '1.26.0' * 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 'metaseqR' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. * 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 'library' or 'require' calls in package code: 'BSgenome' 'BiocManager' 'GenomicRanges' 'RMySQL' 'RSQLite' 'Rsamtools' 'TCC' 'VennDiagram' 'parallel' 'rtracklayer' 'survcomp' 'zoo' Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE biasPlotToJSON: no visible binding for global variable 'nams' cddat: no visible global function definition for 'assayData' cddat: no visible global function definition for 'ks.test' cddat: no visible global function definition for 'p.adjust' cdplot: no visible global function definition for 'plot' cdplot: no visible global function definition for 'lines' correct.transcripts: no visible global function definition for 'makeGRangesFromDataFrame' correct.transcripts: no visible global function definition for 'flank' correct.transcripts: no visible global function definition for 'resize' correct.transcripts: no visible global function definition for 'start' correct.transcripts: no visible global function definition for 'end' countsBioToJSON: no visible binding for global variable 'nams' diagplot.avg.ftd : <anonymous>: no visible binding for global variable 'sd' diagplot.avg.ftd: no visible global function definition for 'par' diagplot.avg.ftd: no visible global function definition for 'plot.new' diagplot.avg.ftd: no visible global function definition for 'plot.window' diagplot.avg.ftd: no visible global function definition for 'axis' diagplot.avg.ftd: no visible global function definition for 'lines' diagplot.avg.ftd: no visible global function definition for 'grid' diagplot.avg.ftd: no visible global function definition for 'title' diagplot.cor: no visible global function definition for 'cor' diagplot.cor: no visible global function definition for 'colorRampPalette' diagplot.edaseq: no visible global function definition for 'AnnotatedDataFrame' diagplot.edaseq: no visible global function definition for 'grid' diagplot.filtered: no visible global function definition for 'par' diagplot.filtered: no visible global function definition for 'plot.new' diagplot.filtered: no visible global function definition for 'plot.window' diagplot.filtered: no visible global function definition for 'axis' diagplot.filtered: no visible global function definition for 'text' diagplot.filtered: no visible global function definition for 'title' diagplot.filtered: no visible global function definition for 'mtext' diagplot.filtered: no visible global function definition for 'grid' diagplot.ftd: no visible global function definition for 'par' diagplot.ftd: no visible global function definition for 'plot.new' diagplot.ftd: no visible global function definition for 'plot.window' diagplot.ftd: no visible global function definition for 'axis' diagplot.ftd: no visible global function definition for 'lines' diagplot.ftd: no visible global function definition for 'grid' diagplot.ftd: no visible global function definition for 'title' diagplot.mds: no visible global function definition for 'as.dist' diagplot.mds: no visible global function definition for 'cor' diagplot.mds: no visible global function definition for 'cmdscale' diagplot.mds: no visible global function definition for 'plot' diagplot.mds: no visible global function definition for 'text' diagplot.mds: no visible global function definition for 'grid' diagplot.noiseq: no visible global function definition for 'grid' diagplot.noiseq: no visible global function definition for 'new' diagplot.noiseq : <anonymous>: no visible global function definition for 'quantile' diagplot.noiseq.saturation: no visible global function definition for 'par' diagplot.noiseq.saturation: no visible global function definition for 'plot.new' diagplot.noiseq.saturation: no visible global function definition for 'plot.window' diagplot.noiseq.saturation: no visible global function definition for 'axis' diagplot.noiseq.saturation: no visible global function definition for 'title' diagplot.noiseq.saturation: no visible global function definition for 'lines' diagplot.noiseq.saturation: no visible global function definition for 'points' diagplot.noiseq.saturation: no visible global function definition for 'grid' diagplot.noiseq.saturation: no visible global function definition for 'mtext' diagplot.pairs: no visible global function definition for 'par' diagplot.pairs: no visible global function definition for 'plot' diagplot.pairs: no visible global function definition for 'text' diagplot.pairs: no visible global function definition for 'arrows' diagplot.pairs: no visible global function definition for 'lines' diagplot.pairs: no visible global function definition for 'cor' diagplot.roc: no visible global function definition for 'par' diagplot.roc: no visible global function definition for 'plot.new' diagplot.roc: no visible global function definition for 'plot.window' diagplot.roc: no visible global function definition for 'axis' diagplot.roc: no visible global function definition for 'lines' diagplot.roc: no visible global function definition for 'grid' diagplot.roc: no visible global function definition for 'title' diagplot.venn: no visible global function definition for 'runif' diagplot.venn: no visible global function definition for 'draw.pairwise.venn' diagplot.venn: no visible global function definition for 'draw.triple.venn' diagplot.venn: no visible global function definition for 'draw.quad.venn' diagplot.venn: no visible global function definition for 'draw.quintuple.venn' diagplot.volcano: no visible global function definition for 'runif' diagplot.volcano: no visible global function definition for 'par' diagplot.volcano: no visible global function definition for 'plot.new' diagplot.volcano: no visible global function definition for 'plot.window' diagplot.volcano: no visible global function definition for 'axis' diagplot.volcano: no visible global function definition for 'title' diagplot.volcano: no visible global function definition for 'points' diagplot.volcano: no visible global function definition for 'abline' diagplot.volcano: no visible global function definition for 'grid' estimate.aufc.weights: no visible global function definition for 'runif' estimate.aufc.weights : <anonymous>: no visible global function definition for 'rollmean' estimate.sim.params : <anonymous>: no visible global function definition for 'var' estimate.sim.params : <anonymous>: no visible global function definition for 'optimize' estimate.sim.params: no visible global function definition for 'dev.new' estimate.sim.params: no visible global function definition for 'plot' estimate.sim.params: no visible global function definition for 'title' estimate.sim.params: no visible global function definition for 'grid' filter.genes: no visible binding for global variable 'quantile' filter.genes: no visible global function definition for 'median' filter.genes: no visible global function definition for 'quantile' fisher.method: no visible global function definition for 'pchisq' fisher.method: no visible global function definition for 'p.adjust' fisher.method.perm : <anonymous> : <anonymous> : <anonymous>: no visible global function definition for 'na.exclude' fisher.method.perm: no visible global function definition for 'p.adjust' get.defaults: no visible binding for global variable 'median' get.gc.content: no visible global function definition for 'GRanges' get.gc.content: no visible global function definition for 'Rle' get.gc.content: no visible global function definition for 'IRanges' get.gc.content: no visible global function definition for 'makeGRangesFromDataFrame' get.gc.content: no visible global function definition for 'getSeq' get.gc.content: no visible global function definition for 'alphabetFrequency' get.ucsc.annotation: no visible global function definition for 'dbDriver' get.ucsc.annotation: no visible global function definition for 'dbConnect' get.ucsc.annotation: no visible global function definition for 'dbGetQuery' get.ucsc.annotation: no visible global function definition for 'dbDisconnect' get.ucsc.annotation : <anonymous>: no visible global function definition for 'makeGRangesFromDataFrame' get.ucsc.annotation: no visible global function definition for 'seqnames' get.ucsc.annotation: no visible global function definition for 'start' get.ucsc.annotation: no visible global function definition for 'end' get.ucsc.annotation: no visible global function definition for 'strand' get.ucsc.dbl: no visible global function definition for 'dbDriver' get.ucsc.dbl: no visible global function definition for 'dbConnect' get.ucsc.dbl: no visible global function definition for 'dbWriteTable' get.ucsc.dbl: no visible global function definition for 'dbDisconnect' graphics.close: no visible global function definition for 'dev.off' graphics.open: no visible global function definition for 'dev.new' graphics.open: no visible global function definition for 'pdf' graphics.open: no visible global function definition for 'postscript' graphics.open: no visible global function definition for 'png' graphics.open: no visible global function definition for 'jpeg' graphics.open: no visible global function definition for 'bmp' graphics.open: no visible global function definition for 'tiff' load.bs.genome: no visible global function definition for 'installed.genomes' load.bs.genome: no visible global function definition for 'getBSgenome' make.sim.data.sd: no visible global function definition for 'runif' make.sim.data.sd: no visible global function definition for 'rnbinom' make.sim.data.sd: no visible global function definition for 'rexp' make.sim.data.tcc: no visible global function definition for 'runif' make.stat : <anonymous>: no visible global function definition for 'median' make.stat : <anonymous>: no visible global function definition for 'sd' make.stat : <anonymous>: no visible global function definition for 'mad' meta.perm : <anonymous>: no visible global function definition for 'runif' meta.perm: no visible global function definition for 'mclapply' meta.test : <anonymous>: no visible binding for global variable 'combine.test' metaseqr: no visible binding for global variable 'p.adjust.methods' metaseqr : <anonymous>: no visible binding for global variable 'p.adjust' metaseqr : <anonymous>: no visible global function definition for 'p.adjust' normalize.edaseq: no visible global function definition for 'AnnotatedDataFrame' normalize.noiseq: no visible global function definition for 'assayData' read2count: no visible global function definition for 'GRanges' read2count: no visible global function definition for 'Rle' read2count: no visible global function definition for 'IRanges' read2count: no visible global function definition for 'makeGRangesFromDataFrame' read2count: no visible global function definition for 'seqnames' read2count: no visible global function definition for 'start' read2count: no visible global function definition for 'end' read2count: no visible global function definition for 'strand' read2count: no visible global function definition for 'promoters' read2count: no visible global function definition for 'resize' read2count : <anonymous>: no visible global function definition for 'import.bed' read2count : <anonymous>: no visible global function definition for 'as' read2count : <anonymous>: no visible global function definition for 'seqnames' read2count : <anonymous>: no visible global function definition for 'seqlevels' read2count : <anonymous>: no visible global function definition for 'countOverlaps' read2count: no visible global function definition for 'asBam' read2count : <anonymous>: no visible global function definition for 'readGAlignments' read2count : <anonymous>: no visible global function definition for 'BamFile' read2count : <anonymous>: no visible global function definition for 'countBam' read2count : <anonymous>: no visible global function definition for 'ScanBamParam' read2count : <anonymous>: no visible global function definition for 'scanBamFlag' read2count : <anonymous>: no visible global function definition for 'strand<-' read2count : <anonymous>: no visible global function definition for 'strand' read2count : <anonymous>: no visible global function definition for 'summarizeOverlaps' read2count : <anonymous>: no visible global function definition for 'assays' reduce.exons : <anonymous>: no visible global function definition for 'reduce' reduce.exons : <anonymous>: no visible global function definition for 'DataFrame' reduce.exons : <anonymous>: no visible global function definition for 'mcols<-' reduce.transcripts.utr : <anonymous>: no visible global function definition for 'reduce' reduce.transcripts.utr : <anonymous>: no visible global function definition for 'DataFrame' reduce.transcripts.utr : <anonymous>: no visible global function definition for 'mcols<-' reduce.transcripts.utr.transcript : <anonymous>: no visible global function definition for 'reduce' reduce.transcripts.utr.transcript : <anonymous>: no visible global function definition for 'DataFrame' reduce.transcripts.utr.transcript : <anonymous>: no visible global function definition for 'mcols<-' stat.bayseq: no visible global function definition for 'new' stat.deseq: no visible global function definition for 'sizeFactors<-' stat.edger: no visible global function definition for 'model.matrix' stat.limma: no visible global function definition for 'model.matrix' stat.nbpseq: no visible global function definition for 'sizeFactors<-' stat.noiseq: no visible global function definition for 'assayData' stat.noiseq: no visible global function definition for 'sizeFactors<-' wapply: no visible global function definition for 'mclapply' wp.adjust: no visible global function definition for 'p.adjust' Undefined global functions or variables: AnnotatedDataFrame BamFile DataFrame GRanges IRanges Rle ScanBamParam abline alphabetFrequency arrows as as.dist asBam assayData assays axis bmp cmdscale colorRampPalette combine.test cor countBam countOverlaps dbConnect dbDisconnect dbDriver dbGetQuery dbWriteTable dev.new dev.off draw.pairwise.venn draw.quad.venn draw.quintuple.venn draw.triple.venn end flank getBSgenome getSeq grid import.bed installed.genomes jpeg ks.test lines mad makeGRangesFromDataFrame mclapply mcols<- median model.matrix mtext na.exclude nams new optimize p.adjust p.adjust.methods par pchisq pdf plot plot.new plot.window png points postscript promoters quantile readGAlignments reduce resize rexp rnbinom rollmean runif scanBamFlag sd seqlevels seqnames sizeFactors<- start strand strand<- summarizeOverlaps text tiff title var Consider adding importFrom("grDevices", "bmp", "colorRampPalette", "dev.new", "dev.off", "jpeg", "pdf", "png", "postscript", "tiff") importFrom("graphics", "abline", "arrows", "axis", "grid", "lines", "mtext", "par", "plot", "plot.new", "plot.window", "points", "text", "title") importFrom("methods", "as", "new") importFrom("stats", "as.dist", "cmdscale", "cor", "end", "ks.test", "mad", "median", "model.matrix", "na.exclude", "optimize", "p.adjust", "p.adjust.methods", "pchisq", "quantile", "rexp", "rnbinom", "runif", "sd", "start", "var") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed diagplot.de.heatmap 9.75 0.44 10.19 diagplot.volcano 6.00 0.08 6.08 diagplot.filtered 2.45 0.11 5.61 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed diagplot.de.heatmap 9.37 0.14 9.52 diagplot.volcano 5.35 0.03 5.38 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' OK ** running tests for arch 'x64' ... Running 'runTests.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: 3 NOTEs See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/metaseqR.Rcheck/00check.log' for details.
metaseqR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/metaseqR_1.26.0.tar.gz && rm -rf metaseqR.buildbin-libdir && mkdir metaseqR.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=metaseqR.buildbin-libdir metaseqR_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL metaseqR_1.26.0.zip && rm metaseqR_1.26.0.tar.gz metaseqR_1.26.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 1412k 100 1412k 0 0 9691k 0 --:--:-- --:--:-- --:--:-- 9948k install for i386 * installing *source* package 'metaseqR' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'metaseqR' finding HTML links ... done as.class.vector html build.export html calc.f1score html calc.otr html cddat html cdplot html check.contrast.format html check.file.args html check.graphics.file html check.graphics.type html check.libsize html check.main.args html check.num.args html check.packages html check.parallel html check.text.args html combine.bonferroni html combine.maxp html combine.minp html combine.simes html combine.weight html construct.gene.model html construct.utr.model html diagplot.avg.ftd html diagplot.boxplot html diagplot.cor html diagplot.de.heatmap html diagplot.edaseq html diagplot.filtered html diagplot.ftd html diagplot.mds html diagplot.metaseqr html diagplot.noiseq html diagplot.noiseq.saturation html diagplot.pairs html diagplot.roc html diagplot.venn html diagplot.volcano html disp html downsample.counts html estimate.aufc.weights html estimate.sim.params html filter.exons html filter.genes html filter.high html filter.low html fisher.method html fisher.method.perm html fisher.sum html get.annotation html get.arg html get.biotypes html get.bs.organism html get.dataset html get.defaults html get.ensembl.annotation html get.exon.attributes html get.gc.content html get.gene.attributes html get.host html get.preset.opts html get.strict.biofilter html get.transcript.utr.attributes html get.ucsc.annotation html get.ucsc.credentials html get.ucsc.dbl html get.ucsc.organism html get.ucsc.query html get.ucsc.tabledef html get.ucsc.tbl.tpl html get.valid.chrs html get.weights html graphics.close html graphics.open html hg19.exon.counts html libsize.list.hg19 html libsize.list.mm9 html load.bs.genome html log2disp html make.avg.expression html make.contrast.list html make.export.list html make.fold.change html make.grid html make.highcharts.points html make.html.body html make.html.cells html make.html.header html make.html.rows html make.html.table html make.matrix html make.path.struct html make.permutation html make.project.path html make.report.messages html make.sample.list html make.sim.data.sd html make.sim.data.tcc html make.stat html make.transformation html make.venn.areas html make.venn.colorscheme html make.venn.counts html make.venn.pairs html meta.perm html meta.test html meta.worker html metaseqR-package html metaseqr html mlfo html mm9.gene.counts html nat2log html normalize.deseq html normalize.edaseq html normalize.edger html normalize.nbpseq html normalize.noiseq html read.targets html read2count html reduce.exons html reduce.gene.data html sample.list.hg19 html sample.list.mm9 html set.arg html stat.bayseq html stat.deseq html stat.edger html stat.limma html stat.nbpseq html stat.noiseq html validate.alg.args html validate.list.args html wapply html wp.adjust html ** 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 install for x64 * installing *source* package 'metaseqR' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'metaseqR' as metaseqR_1.26.0.zip * DONE (metaseqR) * installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library' package 'metaseqR' successfully unpacked and MD5 sums checked
metaseqR.Rcheck/tests_i386/runTests.Rout R version 3.6.3 (2020-02-29) -- "Holding the Windsock" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-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. > BiocGenerics:::testPackage("metaseqR") 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, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians Attaching package: 'DelayedArray' The following objects are masked from 'package:matrixStats': colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following objects are masked from 'package:base': aperm, apply, rowsum locfit 1.5-9.4 2020-03-24 Attaching package: 'locfit' The following objects are masked from 'package:ShortRead': left, right Welcome to 'DESeq'. For improved performance, usability and functionality, please consider migrating to 'DESeq2'. Attaching package: 'limma' The following object is masked from 'package:DESeq': plotMA The following object is masked from 'package:BiocGenerics': plotMA Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:Rsamtools': index, index<- The following objects are masked from 'package:base': as.Date, as.Date.numeric Cache found 2020-04-15 04:44:16: Data processing started... Read counts file: imported custom data frame Conditions: G1, G2 Samples to include: G1_rep1, G1_rep2, G1_rep3, G2_rep1, G2_rep2, G2_rep3 Samples to exclude: none Requested contrasts: G1_vs_G2 Annotation: embedded Organism: mm9 Reference source: ensembl Count type: gene Analysis preset: all.basic Transcriptional level: gene Exon filters: none applied Gene filters: none applied Filter application: postnorm Normalization algorithm: edaseq Normalization arguments: within.which: loess between.which: full Statistical algorithm: edger, limma Statistical arguments: edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1) limma: none Meta-analysis method: simes Multiple testing correction: BH Logarithmic transformation offset: 1 Analysis preset: all.basic Quality control plots: Figure format: png Output directory: C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\RtmpI7J7AO Output data: annotation, p.value, adj.p.value, meta.p.value, adj.meta.p.value, fold.change Output scale(s): natural, log2 Output values: normalized Saving gene model to C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\RtmpI7J7AO/data/gene_model.RData Removing genes with zero counts in all samples... Normalizing with: edaseq Running statistical tests with: edger Contrast: G1_vs_G2 Running statistical tests with: limma Contrast: G1_vs_G2 Performing meta-analysis with simes Building output files... Contrast: G1_vs_G2 Adding non-filtered data... binding annotation... binding p-values... binding FDRs... binding meta p-values... binding adjusted meta p-values... binding natural normalized fold changes... binding log2 normalized fold changes... Writing output... 2020-04-15 04:44:16: Data processing finished! Total processing time: 00 seconds Estimating AUFC weights... Please wait... Processing edger Processing limma Retrieving edger Retrieving limma 2020-04-15 04:44:17: Data processing started... Read counts file: imported custom data frame Conditions: e14.5, adult_8_weeks Samples to include: e14.5_1, e14.5_2, a8w_1, a8w_2 Samples to exclude: none Requested contrasts: e14.5_vs_adult_8_weeks Library sizes: e14.5_1: 3102907 e14.5_2: 2067905 a8w_1: 3742059 a8w_2: 4403954 Annotation: download Organism: mm9 Reference source: ensembl Count type: gene Analysis preset: medium.basic Transcriptional level: gene Exon filters: min.active.exons min.active.exons: exons.per.gene: 5 min.exons: 2 frac: 0.2 Gene filters: length, avg.reads, expression, biotype length: length: 500 avg.reads: average.per.bp: 100 quantile: 0.25 expression: median: TRUE mean: FALSE quantile: NA known: NA custom: NA biotype: pseudogene: FALSE snRNA: FALSE protein_coding: FALSE antisense: FALSE miRNA: FALSE lincRNA: FALSE snoRNA: FALSE processed_transcript: FALSE misc_RNA: FALSE rRNA: TRUE sense_overlapping: FALSE sense_intronic: FALSE polymorphic_pseudogene: FALSE non_coding: FALSE three_prime_overlapping_ncrna: FALSE IG_C_gene: FALSE IG_J_gene: FALSE IG_D_gene: FALSE IG_V_gene: FALSE ncrna_host: FALSE Filter application: postnorm Normalization algorithm: edger Normalization arguments: method: TMM logratioTrim: 0.3 sumTrim: 0.05 doWeighting: TRUE Acutoff: -1e+10 p: 0.75 Statistical algorithm: edger, limma Statistical arguments: edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1) limma: none Meta-analysis method: simes Multiple testing correction: BH p-value threshold: 0.05 Logarithmic transformation offset: 1 Analysis preset: medium.basic Quality control plots: mds Figure format: png Output directory: C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\RtmpI7J7AO Output data: annotation, p.value, adj.p.value, meta.p.value, adj.meta.p.value, fold.change Output scale(s): natural, log2 Output values: normalized Downloading gene annotation for mm9...Cache found Saving gene model to C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\RtmpI7J7AO/data/gene_model.RData Removing genes with zero counts in all samples... Normalizing with: edger Applying gene filter length... Threshold below which ignored: 500 Applying gene filter avg.reads... Threshold below which ignored: 0.0659670745106788 Applying gene filter expression... Threshold below which ignored: 68 Applying gene filter biotype... Biotypes ignored: rRNA 2106 genes filtered out 1681 genes remain after filtering Running statistical tests with: edger Contrast: e14.5_vs_adult_8_weeks Contrast e14.5_vs_adult_8_weeks: found 906 genes Running statistical tests with: limma Contrast: e14.5_vs_adult_8_weeks Contrast e14.5_vs_adult_8_weeks: found 911 genes Performing meta-analysis with simes Building output files... Contrast: e14.5_vs_adult_8_weeks Adding non-filtered data... binding annotation... binding p-values... binding FDRs... binding meta p-values... binding adjusted meta p-values... binding natural normalized fold changes... binding log2 normalized fold changes... Writing output... Adding filtered data... binding annotation... binding p-values... binding FDRs... binding meta p-values... binding adjusted meta p-values... binding natural normalized fold changes... binding log2 normalized fold changes... Writing output... Creating quality control graphs... Plotting in png format... Plotting mds... Creating HTML report... Compressing figures... adding: Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpI7J7AO/plots/qc/mds.png (deflated 62%) 2020-04-15 04:44:23: Data processing finished! Total processing time: 05 seconds RUNIT TEST PROTOCOL -- Wed Apr 15 04:44:23 2020 *********************************************** Number of test functions: 2 Number of errors: 0 Number of failures: 0 1 Test Suite : metaseqR RUnit Tests - 2 test functions, 0 errors, 0 failures Number of test functions: 2 Number of errors: 0 Number of failures: 0 There were 50 or more warnings (use warnings() to see the first 50) > > proc.time() user system elapsed 22.70 1.76 27.35 |
metaseqR.Rcheck/tests_x64/runTests.Rout R version 3.6.3 (2020-02-29) -- "Holding the Windsock" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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. > BiocGenerics:::testPackage("metaseqR") 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, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians Attaching package: 'DelayedArray' The following objects are masked from 'package:matrixStats': colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following objects are masked from 'package:base': aperm, apply, rowsum locfit 1.5-9.4 2020-03-24 Attaching package: 'locfit' The following objects are masked from 'package:ShortRead': left, right Welcome to 'DESeq'. For improved performance, usability and functionality, please consider migrating to 'DESeq2'. Attaching package: 'limma' The following object is masked from 'package:DESeq': plotMA The following object is masked from 'package:BiocGenerics': plotMA Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:Rsamtools': index, index<- The following objects are masked from 'package:base': as.Date, as.Date.numeric Cache found 2020-04-15 04:44:45: Data processing started... Read counts file: imported custom data frame Conditions: G1, G2 Samples to include: G1_rep1, G1_rep2, G1_rep3, G2_rep1, G2_rep2, G2_rep3 Samples to exclude: none Requested contrasts: G1_vs_G2 Annotation: embedded Organism: mm9 Reference source: ensembl Count type: gene Analysis preset: all.basic Transcriptional level: gene Exon filters: none applied Gene filters: none applied Filter application: postnorm Normalization algorithm: edaseq Normalization arguments: within.which: loess between.which: full Statistical algorithm: edger, limma Statistical arguments: edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1) limma: none Meta-analysis method: simes Multiple testing correction: BH Logarithmic transformation offset: 1 Analysis preset: all.basic Quality control plots: Figure format: png Output directory: C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\RtmpsNrz4n Output data: annotation, p.value, adj.p.value, meta.p.value, adj.meta.p.value, fold.change Output scale(s): natural, log2 Output values: normalized Saving gene model to C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\RtmpsNrz4n/data/gene_model.RData Removing genes with zero counts in all samples... Normalizing with: edaseq Running statistical tests with: edger Contrast: G1_vs_G2 Running statistical tests with: limma Contrast: G1_vs_G2 Performing meta-analysis with simes Building output files... Contrast: G1_vs_G2 Adding non-filtered data... binding annotation... binding p-values... binding FDRs... binding meta p-values... binding adjusted meta p-values... binding natural normalized fold changes... binding log2 normalized fold changes... Writing output... 2020-04-15 04:44:45: Data processing finished! Total processing time: 00 seconds Estimating AUFC weights... Please wait... Processing edger Processing limma Retrieving edger Retrieving limma 2020-04-15 04:44:46: Data processing started... Read counts file: imported custom data frame Conditions: e14.5, adult_8_weeks Samples to include: e14.5_1, e14.5_2, a8w_1, a8w_2 Samples to exclude: none Requested contrasts: e14.5_vs_adult_8_weeks Library sizes: e14.5_1: 3102907 e14.5_2: 2067905 a8w_1: 3742059 a8w_2: 4403954 Annotation: download Organism: mm9 Reference source: ensembl Count type: gene Analysis preset: medium.basic Transcriptional level: gene Exon filters: min.active.exons min.active.exons: exons.per.gene: 5 min.exons: 2 frac: 0.2 Gene filters: length, avg.reads, expression, biotype length: length: 500 avg.reads: average.per.bp: 100 quantile: 0.25 expression: median: TRUE mean: FALSE quantile: NA known: NA custom: NA biotype: pseudogene: FALSE snRNA: FALSE protein_coding: FALSE antisense: FALSE miRNA: FALSE lincRNA: FALSE snoRNA: FALSE processed_transcript: FALSE misc_RNA: FALSE rRNA: TRUE sense_overlapping: FALSE sense_intronic: FALSE polymorphic_pseudogene: FALSE non_coding: FALSE three_prime_overlapping_ncrna: FALSE IG_C_gene: FALSE IG_J_gene: FALSE IG_D_gene: FALSE IG_V_gene: FALSE ncrna_host: FALSE Filter application: postnorm Normalization algorithm: edger Normalization arguments: method: TMM logratioTrim: 0.3 sumTrim: 0.05 doWeighting: TRUE Acutoff: -1e+10 p: 0.75 Statistical algorithm: edger, limma Statistical arguments: edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1) limma: none Meta-analysis method: simes Multiple testing correction: BH p-value threshold: 0.05 Logarithmic transformation offset: 1 Analysis preset: medium.basic Quality control plots: mds Figure format: png Output directory: C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\RtmpsNrz4n Output data: annotation, p.value, adj.p.value, meta.p.value, adj.meta.p.value, fold.change Output scale(s): natural, log2 Output values: normalized Downloading gene annotation for mm9...Cache found Saving gene model to C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\RtmpsNrz4n/data/gene_model.RData Removing genes with zero counts in all samples... Normalizing with: edger Applying gene filter length... Threshold below which ignored: 500 Applying gene filter avg.reads... Threshold below which ignored: 0.0659670745106788 Applying gene filter expression... Threshold below which ignored: 68 Applying gene filter biotype... Biotypes ignored: rRNA 2106 genes filtered out 1681 genes remain after filtering Running statistical tests with: edger Contrast: e14.5_vs_adult_8_weeks Contrast e14.5_vs_adult_8_weeks: found 906 genes Running statistical tests with: limma Contrast: e14.5_vs_adult_8_weeks Contrast e14.5_vs_adult_8_weeks: found 911 genes Performing meta-analysis with simes Building output files... Contrast: e14.5_vs_adult_8_weeks Adding non-filtered data... binding annotation... binding p-values... binding FDRs... binding meta p-values... binding adjusted meta p-values... binding natural normalized fold changes... binding log2 normalized fold changes... Writing output... Adding filtered data... binding annotation... binding p-values... binding FDRs... binding meta p-values... binding adjusted meta p-values... binding natural normalized fold changes... binding log2 normalized fold changes... Writing output... Creating quality control graphs... Plotting in png format... Plotting mds... Creating HTML report... Compressing figures... adding: Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpsNrz4n/plots/qc/mds.png (deflated 62%) 2020-04-15 04:44:53: Data processing finished! Total processing time: 06 seconds RUNIT TEST PROTOCOL -- Wed Apr 15 04:44:53 2020 *********************************************** Number of test functions: 2 Number of errors: 0 Number of failures: 0 1 Test Suite : metaseqR RUnit Tests - 2 test functions, 0 errors, 0 failures Number of test functions: 2 Number of errors: 0 Number of failures: 0 There were 50 or more warnings (use warnings() to see the first 50) > > proc.time() user system elapsed 25.53 0.73 28.76 |
metaseqR.Rcheck/examples_i386/metaseqR-Ex.timings
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metaseqR.Rcheck/examples_x64/metaseqR-Ex.timings
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