Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1290/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MLP 1.54.0 (landing page) Tobias Verbeke
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
To the developers/maintainers of the MLP package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MLP.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: MLP |
Version: 1.54.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MLP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MLP_1.54.0.tar.gz |
StartedAt: 2024-12-20 06:11:15 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 06:24:20 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 784.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MLP.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MLP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MLP_1.54.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MLP.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MLP/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MLP’ version ‘1.54.0’ * 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 ‘MLP’ 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 ... NOTE checkRd: (-1) getGeneSets.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) getGeneSets.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed getGeneSets 127.856 2.945 159.001 addGeneSetDescription 109.310 11.154 128.642 MLP 40.044 2.111 45.895 plot.MLP 6.024 0.148 6.233 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test.KEGG.R’ Running ‘test.MLP.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: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/MLP.Rcheck/00check.log’ for details.
MLP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MLP ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘MLP’ ... ** 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 (MLP)
MLP.Rcheck/tests/test.KEGG.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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(MLP) > > pathPValues <- system.file("exampleFiles", "examplePValues.rda", package = "MLP") > load(pathPValues) > > pvalues <- examplePValues[seq.int(1000)] > > system.time(geneSet <- getGeneSets( + species = "Mouse", + geneSetSource = "KEGG", + entrezIdentifiers = names(pvalues) + )) user system elapsed 87.044 0.547 112.920 > > set.seed(111) > mlpOut <- MLP( + geneSet = geneSet, + geneStatistic = pvalues + ) > > mlpOutWithGeneSetDescr <- addGeneSetDescription(object = mlpOut, geneSetSource = "KEGG") Warning message: In addGeneSetDescription(object = mlpOut, geneSetSource = "KEGG") : The MLP object already contains a column 'geneSetDescription' > > > > proc.time() user system elapsed 95.761 1.087 148.989
MLP.Rcheck/tests/test.MLP.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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. > require(MLP) Loading required package: MLP > set.seed(479) > > # This is just the expressionset for this experiment. > > pathExampleData <- system.file("exampleFiles", "expressionSetGcrma.rda", package = "MLP") > load(pathExampleData) > > # Libraries needed > library(limma) > library(org.Mm.eg.db) # for mouse Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following object is masked from 'package:limma': plotMA 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, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min 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")'. Loading required package: IRanges 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 > > exprs(expressionSetGcrma)[1:2,] 2760 2763 2765 2766 2768 2769 2761 100009600 2.371111 2.170060 2.233383 2.180717 2.325886 2.239441 2.297301 100012 2.176163 2.318876 2.419263 2.223307 2.585125 2.346060 2.292061 2762 2764 2767 2770 2771 100009600 2.409001 2.49458 2.115814 2.371262 2.267459 100012 2.336415 2.47979 2.361981 2.330418 2.520918 > # 2760 2763 2765 2766 2768 2769 2761 2762 2764 2767 > #100009600 2.371111 2.170060 2.233383 2.180717 2.325886 2.239441 2.297301 2.409001 2.49458 2.115814 > #100012 2.176163 2.318876 2.419263 2.223307 2.585125 2.346060 2.292061 2.336415 2.47979 2.361981 > # 2770 2771 > #100009600 2.371262 2.267459 > #100012 2.330418 2.520918 > > pData(expressionSetGcrma) sample subGroup sampleColor subGroup1 2760 1 1 #FF0000 WT 2763 4 1 #FF0000 WT 2765 6 1 #FF0000 WT 2766 7 1 #FF0000 WT 2768 9 1 #FF0000 WT 2769 10 1 #FF0000 WT 2761 2 2 #0000FF KO 2762 3 2 #0000FF KO 2764 5 2 #0000FF KO 2767 8 2 #0000FF KO 2770 11 2 #0000FF KO 2771 12 2 #0000FF KO > # sample subGroup sampleColor > #2760 1 1 #FF0000 > #2763 4 1 #FF0000 > #2765 6 1 #FF0000 > #2766 7 1 #FF0000 > #2768 9 1 #FF0000 > #2769 10 1 #FF0000 > #2761 2 2 #0000FF > #2762 3 2 #0000FF > #2764 5 2 #0000FF > #2767 8 2 #0000FF > #2770 11 2 #0000FF > #2771 12 2 #0000FF > > pData(expressionSetGcrma)$subGroup1 <- ifelse(pData(expressionSetGcrma)$subGroup==1,"WT","KO") > > ###==============================================GENERATING LIMMA p-VALUES================================= > > # boxplot(data.frame(exprs(expressionSetGcrma)) > normDat <- normalizeQuantiles(exprs(expressionSetGcrma), ties=TRUE) > subGroup <- pData(expressionSetGcrma)$subGroup > design <- model.matrix(~ -1 +factor(subGroup )) > > colnames(design) <- c("group1", "group2") > contrast.matrix <- makeContrasts(group1-group2, levels=design) > fit <- lmFit(normDat,design) > fit2 <- contrasts.fit(fit, contrast.matrix) > fit2 <- eBayes(fit2) > normDat.p <- fit2$p.value > > normDat.p[1:5] [1] 0.4328583 0.7448996 0.6088859 0.1845008 0.2312761 > #[1] 0.4328583 0.7448996 0.6088859 0.1845008 0.2312761 > > system.time(goGeneSet <- getGeneSets(species = "Mouse", geneSetSource = "GOBP", entrezIdentifiers = featureNames(expressionSetGcrma))) Loading required namespace: GO.db user system elapsed 51.460 6.090 61.034 > goGeneSet[1:3] $`GO:0000002` [1] "11545" "12628" "13804" "16882" "17258" "17527" "18975" "19819" [9] "20133" "21975" "22059" "23797" "27393" "27395" "27397" "50776" [17] "57813" "70556" "72170" "72962" "74143" "74244" "74528" "76781" [25] "83408" "83945" "192287" "208084" "216021" "216860" "226153" "230784" [33] "276852" "327762" "381760" "382985" "408022" $`GO:0000012` [1] "11545" "14211" "21958" "22064" "22594" "66408" "70099" "71991" [9] "72103" "93759" "104884" "234258" "319583" "319955" $`GO:0000017` [1] "20537" "246787" > # output changes with annotation version ! > > y <- normDat.p[,1] > names(y) <- featureNames(expressionSetGcrma) > > y[1:10] 100009600 100012 100017 100019 100034251 100036521 100037258 100037278 0.4328583 0.7448996 0.6088859 0.1845008 0.2312761 0.7865153 0.7772888 0.1037431 100038570 100038635 0.1368744 0.3272610 > # 100009600 100012 100017 100019 100034251 100036521 100037258 100037278 > # 0.4328583 0.7448996 0.6088859 0.1845008 0.2312761 0.7865153 0.7772888 0.1037431 > # 100038570 100038635 > # 0.1368744 0.3272610 > > mlpObject <- MLP(geneSet = goGeneSet, geneStatistic = y, minGenes = 5, maxGenes = 100, rowPermutations = TRUE, + nPermutations = 6, smoothPValues = TRUE) > > > > mlpObject[1:10, ] totalGeneSetSize testedGeneSetSize geneSetStatistic geneSetPValue GO:0098700 11 9 1.6077152 9.928398e-06 GO:0002478 34 29 0.9941643 5.186240e-05 GO:0002468 17 12 1.2692571 1.196260e-04 GO:0019884 41 34 0.9093627 1.257672e-04 GO:0019886 22 19 1.0530544 2.086268e-04 GO:0002282 5 5 1.6379883 2.107123e-04 GO:0048002 87 52 0.7697129 3.498831e-04 GO:0002495 26 23 0.9693229 3.535690e-04 GO:0002504 28 25 0.9087814 7.747836e-04 GO:1905146 21 21 0.9127922 1.420942e-03 geneSetDescription GO:0098700 neurotransmitter loading into synaptic vesicle GO:0002478 antigen processing and presentation of exogenous peptide antigen GO:0002468 dendritic cell antigen processing and presentation GO:0019884 antigen processing and presentation of exogenous antigen GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II GO:0002282 microglial cell activation involved in immune response GO:0048002 antigen processing and presentation of peptide antigen GO:0002495 antigen processing and presentation of peptide antigen via MHC class II GO:0002504 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II GO:1905146 lysosomal protein catabolic process > # output changes with annotation version ! > > plotGOgraph(object = mlpObject, main = "test of main") Loading required namespace: Rgraphviz Loading required namespace: GOstats Loading required namespace: gplots > > pdf(file = "test10.pdf", width = 10, height = 10) > # x11(width = 10, height = 10) > plot(mlpObject, nRow = 10) # by default: type = "barplot" > dev.off() pdf 2 > > unlink("test10.pdf") > > if (FALSE){ + pdf(file = "test5.pdf", width =10, height = 10) + mlpBarplot(object = mlpObject, geneSetSource = "GOBP", nRow = 10, descriptionLength = 5) + dev.off() + + unlink("test5.pdf") + + pdf(file = "test100.pdf", width =10, height = 20) + mlpBarplot(object = mlpObject, geneSetSource = "GOBP", nRow = 10, descriptionLength = 100) + dev.off() + + unlink("test100.pdf") + } > > plot(mlpObject, type = "quantileCurves") > plot(mlpObject, type = "GOgraph") > > proc.time() user system elapsed 92.727 10.451 107.656
MLP.Rcheck/MLP-Ex.timings
name | user | system | elapsed | |
MLP | 40.044 | 2.111 | 45.895 | |
addGeneSetDescription | 109.310 | 11.154 | 128.642 | |
getGeneSets | 127.856 | 2.945 | 159.001 | |
mlpBarplot | 0.030 | 0.004 | 0.035 | |
plot.MLP | 6.024 | 0.148 | 6.233 | |
plotGOgraph | 1.094 | 0.024 | 1.120 | |
plotGeneSetSignificance | 1.165 | 0.048 | 1.223 | |