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 12:07 -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 1362/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MultiAssayExperiment 1.32.0 (landing page) Marcel Ramos
| 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 | OK | OK | |||||||||
To the developers/maintainers of the MultiAssayExperiment package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MultiAssayExperiment.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: MultiAssayExperiment |
Version: 1.32.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MultiAssayExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MultiAssayExperiment_1.32.0.tar.gz |
StartedAt: 2024-12-21 02:41:18 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 02:45:31 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 253.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MultiAssayExperiment.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MultiAssayExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MultiAssayExperiment_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MultiAssayExperiment.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-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 Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MultiAssayExperiment/DESCRIPTION’ ... OK * this is package ‘MultiAssayExperiment’ version ‘1.32.0’ * 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 ‘MultiAssayExperiment’ 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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
MultiAssayExperiment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MultiAssayExperiment ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘MultiAssayExperiment’ ... ** using staged installation ** R ** data ** 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 (MultiAssayExperiment)
MultiAssayExperiment.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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(testthat) > library(MultiAssayExperiment) 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, saveRDS, 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 > > example("MultiAssayExperiment") MltAsE> ## Run the example ExperimentList MltAsE> example("ExperimentList") ExprmL> ## Create an empty ExperimentList instance ExprmL> ExperimentList() ExperimentList class object of length 0: ExprmL> ## Create array matrix and AnnotatedDataFrame to create an ExpressionSet class ExprmL> arraydat <- matrix(data = seq(101, length.out = 20), ncol = 4, ExprmL+ dimnames = list( ExprmL+ c("ENST00000294241", "ENST00000355076", ExprmL+ "ENST00000383706","ENST00000234812", "ENST00000383323"), ExprmL+ c("array1", "array2", "array3", "array4") ExprmL+ )) ExprmL> colDat <- data.frame(slope53 = rnorm(4), ExprmL+ row.names = c("array1", "array2", "array3", "array4")) ExprmL> ## SummarizedExperiment constructor ExprmL> exprdat <- SummarizedExperiment::SummarizedExperiment(arraydat, ExprmL+ colData = colDat) ExprmL> ## Create a sample methylation dataset ExprmL> methyldat <- matrix(data = seq(1, length.out = 25), ncol = 5, ExprmL+ dimnames = list( ExprmL+ c("ENST00000355076", "ENST00000383706", ExprmL+ "ENST00000383323", "ENST00000234812", "ENST00000294241"), ExprmL+ c("methyl1", "methyl2", "methyl3", ExprmL+ "methyl4", "methyl5") ExprmL+ )) ExprmL> ## Create a sample RNASeqGene dataset ExprmL> rnadat <- matrix( ExprmL+ data = sample(c(46851, 5, 19, 13, 2197, 507, ExprmL+ 84318, 126, 17, 21, 23979, 614), size = 20, replace = TRUE), ExprmL+ ncol = 4, ExprmL+ dimnames = list( ExprmL+ c("XIST", "RPS4Y1", "KDM5D", "ENST00000383323", "ENST00000234812"), ExprmL+ c("samparray1", "samparray2", "samparray3", "samparray4") ExprmL+ )) ExprmL> ## Create a mock RangedSummarizedExperiment from a data.frame ExprmL> rangedat <- data.frame(chr="chr2", start = 11:15, end = 12:16, ExprmL+ strand = c("+", "-", "+", "*", "."), ExprmL+ samp0 = c(0,0,1,1,1), samp1 = c(1,0,1,0,1), samp2 = c(0,1,0,1,0), ExprmL+ row.names = c(paste0("ENST", "00000", 135411:135414), "ENST00000383323")) ExprmL> rangeSE <- SummarizedExperiment::makeSummarizedExperimentFromDataFrame(rangedat) ExprmL> ## Combine to a named list and call the ExperimentList constructor function ExprmL> assayList <- list(Affy = exprdat, Methyl450k = methyldat, RNASeqGene = rnadat, ExprmL+ GISTIC = rangeSE) ExprmL> ## Use the ExperimentList constructor ExprmL> ExpList <- ExperimentList(assayList) MltAsE> ## Create sample maps for each experiment MltAsE> exprmap <- data.frame( MltAsE+ primary = c("Jack", "Jill", "Barbara", "Bob"), MltAsE+ colname = c("array1", "array2", "array3", "array4"), MltAsE+ stringsAsFactors = FALSE) MltAsE> methylmap <- data.frame( MltAsE+ primary = c("Jack", "Jack", "Jill", "Barbara", "Bob"), MltAsE+ colname = c("methyl1", "methyl2", "methyl3", "methyl4", "methyl5"), MltAsE+ stringsAsFactors = FALSE) MltAsE> rnamap <- data.frame( MltAsE+ primary = c("Jack", "Jill", "Bob", "Barbara"), MltAsE+ colname = c("samparray1", "samparray2", "samparray3", "samparray4"), MltAsE+ stringsAsFactors = FALSE) MltAsE> gistmap <- data.frame( MltAsE+ primary = c("Jack", "Bob", "Jill"), MltAsE+ colname = c("samp0", "samp1", "samp2"), MltAsE+ stringsAsFactors = FALSE) MltAsE> ## Combine as a named list and convert to a DataFrame MltAsE> maplist <- list(Affy = exprmap, Methyl450k = methylmap, MltAsE+ RNASeqGene = rnamap, GISTIC = gistmap) MltAsE> ## Create a sampleMap MltAsE> sampMap <- listToMap(maplist) MltAsE> ## Create an example phenotype data MltAsE> colDat <- data.frame(sex = c("M", "F", "M", "F"), age = 38:41, MltAsE+ row.names = c("Jack", "Jill", "Bob", "Barbara")) MltAsE> ## Create a MultiAssayExperiment instance MltAsE> mae <- MultiAssayExperiment(experiments = ExpList, colData = colDat, MltAsE+ sampleMap = sampMap) > > test_check("MultiAssayExperiment") [ FAIL 0 | WARN 45 | SKIP 1 | PASS 288 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-listToMap.R:3:1' [ FAIL 0 | WARN 45 | SKIP 1 | PASS 288 ] > > proc.time() user system elapsed 39.133 1.763 40.919
MultiAssayExperiment.Rcheck/MultiAssayExperiment-Ex.timings
name | user | system | elapsed | |
ExperimentList-class | 0.145 | 0.002 | 0.146 | |
ExperimentList | 0.122 | 0.003 | 0.125 | |
HDF5MultiAssayExperiment | 2.091 | 0.154 | 2.248 | |
MatchedAssayExperiment-class | 0.671 | 0.012 | 0.683 | |
MultiAssayExperiment-class | 1.309 | 0.034 | 1.343 | |
MultiAssayExperiment-helpers | 0.863 | 0.016 | 0.878 | |
MultiAssayExperiment-methods | 0.268 | 0.007 | 0.277 | |
MultiAssayExperiment | 0.177 | 0.002 | 0.179 | |
hasAssay | 0.006 | 0.000 | 0.006 | |
mapToList | 0.231 | 0.004 | 0.240 | |
miniACC | 1.370 | 0.046 | 1.416 | |
prepMultiAssay | 1.236 | 0.012 | 1.248 | |
reexports | 0.001 | 0.000 | 0.001 | |
subsetBy | 1.195 | 0.039 | 1.234 | |
upsetSamples | 1.359 | 0.031 | 1.392 | |