Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:15 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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To the developers/maintainers of the MLP package: - Please 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 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 1219/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MLP 1.47.0 (landing page) Tobias Verbeke
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: MLP |
Version: 1.47.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MLP.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MLP_1.47.0.tar.gz |
StartedAt: 2023-02-07 08:34:15 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 08:41:30 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 435.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: MLP.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MLP.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MLP_1.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MLP.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘MLP/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MLP’ version ‘1.47.0’ * 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 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 ... 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 ... ERROR Running examples in ‘MLP-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: addGeneSetDescription > ### Title: Utility function which adds the biological description of the > ### gene sets as a column to the return value of the MLP function (data > ### frame) > ### Aliases: addGeneSetDescription > > ### ** Examples > > if (require(GO.db)){ + pathExamplePValues <- system.file("exampleFiles", "examplePValues.rda", package = "MLP") + load(pathExamplePValues) + geneSet <- getGeneSets(species = "Mouse", geneSetSource = "GOBP", entrezIdentifiers = names(examplePValues)) + mlpResult <- MLP(geneSet = geneSet, geneStatistic = examplePValues, addGeneSetDescription = FALSE) + head(mlpResult) + mlpResultsWithGSDescr <- addGeneSetDescription(object = mlpResult, geneSetSource = "GOBP") + head(mlpResultsWithGSDescr) + } Loading required package: GO.db Loading required package: AnnotationDbi 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, sort, 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 objects are masked from ‘package:base’: I, expand.grid, unname Loading required namespace: org.Mm.eg.db Killed * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test.KEGG.R’ Running ‘test.MLP.R’ ERROR Running the tests in ‘tests/test.MLP.R’ failed. Last 13 lines of output: > 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 Killed * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘UsingMLP.Rnw’... failed to complete the test ERROR Errors in running code in vignettes: when running code in ‘UsingMLP.Rnw’ ... > geneSet <- getGeneSets(species = "Mouse", geneSetSource = "GOCC", + entrezIdentifiers = names(pvalues)) Loading required namespace: GO.db Loading required namespace: org.Mm.eg.db Killed ... incomplete output. Crash? * checking re-building of vignette outputs ... NOTE Error(s) in re-building vignettes: --- re-building ‘UsingMLP.Rnw’ using Sweave Loading required package: MLP Loading required package: limma 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, setdiff, sort, 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 objects are masked from ‘package:base’: I, expand.grid, unname Loading required namespace: GO.db Loading required namespace: org.Mm.eg.db Killed * checking PDF version of manual ... OK * DONE Status: 3 ERRORs, 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/MLP.Rcheck/00check.log’ for details.
MLP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MLP ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (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(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 46.710 1.237 82.309 > > 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 52.598 1.689 117.698
MLP.Rcheck/tests/test.MLP.Rout.fail
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (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. > 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, setdiff, sort, 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 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 Killed
MLP.Rcheck/MLP-Ex.timings
name | user | system | elapsed | |
MLP | 32.566 | 0.541 | 36.183 | |