Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:44 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1805/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Rvisdiff 1.3.0 (landing page) David Barrios
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the Rvisdiff package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rvisdiff.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: Rvisdiff |
Version: 1.3.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rvisdiff.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rvisdiff_1.3.0.tar.gz |
StartedAt: 2024-08-26 23:04:42 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 23:07:42 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 180.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Rvisdiff.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rvisdiff.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rvisdiff_1.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Rvisdiff.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Rvisdiff/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Rvisdiff’ version ‘1.3.0’ * 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 ‘Rvisdiff’ 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed DEreport 37.162 1.011 38.398 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘Rvisdiff-Tests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
Rvisdiff.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rvisdiff ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘Rvisdiff’ ... ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Rvisdiff)
Rvisdiff.Rcheck/tests/Rvisdiff-Tests.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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(Rvisdiff) > > ### Prapare input data > > library("airway") 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: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb 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 > data("airway") > se <- airway > se$dex <- relevel(se$dex, ref="untrt") > countdata <- assay(se) > coldata <- colData(se) > > ### Produce interactive DE reports from DESeq2 results > > library("DESeq2") > dds <- DESeqDataSet(se, design = ~ cell + dex) > dds <- DESeq(dds) estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing > DEreport(dds, countdata) The report has been generated in the "/Users/biocbuild/bbs-3.20-bioc/meat/Rvisdiff.Rcheck/tests/DEreport/cell_N052611_N061011" path. The report has been generated in the "/Users/biocbuild/bbs-3.20-bioc/meat/Rvisdiff.Rcheck/tests/DEreport/cell_N052611_N080611" path. The report has been generated in the "/Users/biocbuild/bbs-3.20-bioc/meat/Rvisdiff.Rcheck/tests/DEreport/cell_N052611_N61311" path. The report has been generated in the "/Users/biocbuild/bbs-3.20-bioc/meat/Rvisdiff.Rcheck/tests/DEreport/cell_N061011_N080611" path. The report has been generated in the "/Users/biocbuild/bbs-3.20-bioc/meat/Rvisdiff.Rcheck/tests/DEreport/cell_N061011_N61311" path. The report has been generated in the "/Users/biocbuild/bbs-3.20-bioc/meat/Rvisdiff.Rcheck/tests/DEreport/cell_N080611_N61311" path. The report has been generated in the "/Users/biocbuild/bbs-3.20-bioc/meat/Rvisdiff.Rcheck/tests/DEreport/dex_untrt_trt" path. The index has been generated in the "/Users/biocbuild/bbs-3.20-bioc/meat/Rvisdiff.Rcheck/tests/DEreport" path. > > ### Produce interactive DE reports from edgeR results > > library("edgeR") Loading required package: limma Attaching package: 'limma' The following object is masked from 'package:DESeq2': plotMA The following object is masked from 'package:BiocGenerics': plotMA > design <- model.matrix(~ cell + dex, data = coldata) > dl <- DGEList(counts = countdata, group = coldata$dex) > dl <- calcNormFactors(dl) > dl <- estimateDisp(dl, design=design) > DEreport(dl, countdata) The report has been generated in the "/Users/biocbuild/bbs-3.20-bioc/meat/Rvisdiff.Rcheck/tests/DEreport" path. > de <- exactTest(dl,pair=1:2) > DEreport(de, countdata, coldata$dex) The report has been generated in the "/Users/biocbuild/bbs-3.20-bioc/meat/Rvisdiff.Rcheck/tests/DEreport" path. > > ### Produce interactive DE reports from limma results > > library("limma") > design <- model.matrix(~ 0 + dex + cell, data = coldata) > contr <- makeContrasts(dextrt - dexuntrt,levels=colnames(design)) > limmaexprs <- voom(countdata, design) > fit <- lmFit(limmaexprs, design) > fit <- contrasts.fit(fit, contrasts=contr) > fit <- eBayes(fit) > DEreport(fit, countdata) The report has been generated in the "/Users/biocbuild/bbs-3.20-bioc/meat/Rvisdiff.Rcheck/tests/DEreport/dextrt - dexuntrt" path. The index has been generated in the "/Users/biocbuild/bbs-3.20-bioc/meat/Rvisdiff.Rcheck/tests/DEreport" path. > > ### Produce interactive DE reports from Differential test results > > untrt <- countdata[,coldata$dex=="untrt"] > trt <- countdata[,coldata$dex=="trt"] > library(matrixTests) > wilcox <- col_wilcoxon_twosample(t(untrt), t(trt)) Warning message: col_wilcoxon_twosample: 50597 of the columns had ties: cannot compute exact p-values with ties. First occurrence at column 2 > stat <- wilcox$statistic > p <- wilcox$pvalue > log2FoldChange <- log2(rowMeans(trt)+1) - log2(rowMeans(untrt)+1) > wilcox <- data.frame(genes = rownames(countdata), statistic = stat, + pValue = round(p, 6), pAdjust = p.adjust(wilcox[,2], method = "BH"), + expMean = rowMeans(countdata), log2FC = log2FoldChange) > normalized <- edgeR::cpm(countdata) > normalized <- as.data.frame(normalized) > normalized$genes <- rownames(normalized) > DEreport(wilcox, NULL, coldata$dex, normalized = normalized, genes="genes", + pvalue="pValue", padj = "pAdjust", stat = "statistic", + baseMean="expMean", log2FoldChange="log2FC") The report has been generated in the "/Users/biocbuild/bbs-3.20-bioc/meat/Rvisdiff.Rcheck/tests/DEreport" path. > > ### Missing columns tests > colnames(wilcox) <- c("genes","missing1","missing2","missing3","missing4","missing5") > DEreport(wilcox, NULL, coldata$dex, normalized = normalized, genes="genes") The report has been generated in the "/Users/biocbuild/bbs-3.20-bioc/meat/Rvisdiff.Rcheck/tests/DEreport" path. Warning messages: 1: In getColnamesJSON(colnames(DE)) : Missing pvalue in DE results. Valid names for pvalue are 'pvalue', 'P.Value', 'PValue' or you can especify a custom name in pvalue argument. 2: In getColnamesJSON(colnames(DE)) : Missing padj in DE results. Valid names for padj are 'padj', 'FDR', 'adj.P.Val' or you can especify a custom name in padj argument. 3: In getColnamesJSON(colnames(DE)) : Missing log2FoldChange in DE results. Valid names for log2FoldChange are 'log2FoldChange', 'logFC' or you can especify a custom name in log2FoldChange argument. 4: In getColnamesJSON(colnames(DE)) : Missing baseMean in DE results. Valid names for baseMean are 'baseMean', 'AveExpr', 'logCPM' or you can especify a custom name in baseMean argument. > > > proc.time() user system elapsed 101.698 4.037 106.477
Rvisdiff.Rcheck/Rvisdiff-Ex.timings
name | user | system | elapsed | |
DEreport | 37.162 | 1.011 | 38.398 | |