Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1266/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
minfi 1.52.1 (landing page) Kasper Daniel Hansen
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 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 | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the minfi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/minfi.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: minfi |
Version: 1.52.1 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:minfi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings minfi_1.52.1.tar.gz |
StartedAt: 2024-11-20 09:54:16 -0000 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 10:04:28 -0000 (Wed, 20 Nov 2024) |
EllapsedTime: 612.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: minfi.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:minfi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings minfi_1.52.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/minfi.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘minfi/DESCRIPTION’ ... OK * this is package ‘minfi’ version ‘1.52.1’ * 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 ‘minfi’ 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘DelayedArray:::get_verbose_block_processing’ ‘DelayedArray:::normarg_grid’ ‘bumphunter:::.getEstimate’ See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.guessArrayTypes’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE Found the following possibly unsafe calls: File ‘minfi/R/IlluminaMethylationManifest-class.R’: unlockBinding(name, env = object@data) * checking Rd files ... NOTE checkRd: (-1) gaphunter.Rd:19: Lost braces 19 | If one of the first two, code{\link{getBeta}} is used to calculate beta values. If a | ^ checkRd: (-1) ratioConvert-methods.Rd:35: Lost braces 35 | \code{\link{RatioSet}} or code{\link{GenomicRatioSet}} for the output | ^ checkRd: (-1) ratioConvert-methods.Rd:36: Lost braces 36 | object and \code{\link{MethylSet}} or code{\link{GenomicMethylSet}} | ^ * 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 combineArrays 71.650 1.541 73.867 bumphunter 34.500 0.424 34.896 read.metharray.exp 9.188 0.028 9.230 IlluminaMethylationManifest-class 6.283 0.151 6.446 densityPlot 6.212 0.008 6.229 read.metharray 6.018 0.116 6.143 preprocessIllumina 5.037 0.064 5.109 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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: 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/minfi.Rcheck/00check.log’ for details.
minfi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL minfi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘minfi’ ... ** 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 (minfi)
minfi.Rcheck/tests/runTests.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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("minfi") || stop("unable to load minfi") Loading required package: minfi 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: GenomicRanges Loading required package: stats4 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: 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: 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 Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: bumphunter Loading required package: foreach Loading required package: iterators Loading required package: parallel Loading required package: locfit locfit 1.5-9.10 2024-06-24 Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) [1] TRUE > BiocGenerics:::testPackage("minfi") Loading required package: minfiData Loading required package: IlluminaHumanMethylation450kmanifest Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19 Loading required package: digest Loading required package: DelayedArray Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Loading required package: S4Arrays Loading required package: abind Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: SparseArray Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep RUNIT TEST PROTOCOL -- Wed Nov 20 10:04:22 2024 *********************************************** Number of test functions: 10 Number of errors: 0 Number of failures: 0 1 Test Suite : minfi RUnit Tests - 10 test functions, 0 errors, 0 failures Number of test functions: 10 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 48.768 1.078 49.882
minfi.Rcheck/minfi-Ex.timings
name | user | system | elapsed | |
GenomicMethylSet-class | 0.002 | 0.000 | 0.002 | |
GenomicRatioSet-class | 0.001 | 0.000 | 0.001 | |
IlluminaMethylationManifest-class | 6.283 | 0.151 | 6.446 | |
MethylSet-class | 0.001 | 0.000 | 0.000 | |
RGChannelSet-class | 0.001 | 0.000 | 0.001 | |
RatioSet-class | 0.001 | 0.000 | 0.001 | |
bumphunter | 34.500 | 0.424 | 34.896 | |
combineArrays | 71.650 | 1.541 | 73.867 | |
compartments | 3.567 | 0.179 | 3.752 | |
controlStripPlot | 2.460 | 0.040 | 2.502 | |
convertArray | 1.777 | 0.004 | 1.785 | |
densityBeanPlot | 3.124 | 0.076 | 3.205 | |
densityPlot | 6.212 | 0.008 | 6.229 | |
detectionP | 0.533 | 0.004 | 0.538 | |
dmpFinder | 0.161 | 0.000 | 0.162 | |
estimateCellCounts | 0 | 0 | 0 | |
fixMethOutliers | 1.192 | 0.000 | 1.194 | |
gaphunter | 0.115 | 0.000 | 0.115 | |
getAnnotation | 1.032 | 0.004 | 1.037 | |
getGenomicRatioSetFromGEO | 0 | 0 | 0 | |
getQC | 0.275 | 0.000 | 0.276 | |
getSex | 2.295 | 0.008 | 2.307 | |
logit2 | 0 | 0 | 0 | |
makeGenomicRatioSetFromMatrix | 0.560 | 0.000 | 0.561 | |
mapToGenome-methods | 0.257 | 0.000 | 0.257 | |
mdsPlot | 0.337 | 0.000 | 0.339 | |
minfiQC | 3.569 | 0.004 | 3.581 | |
plotBetasByType | 0.001 | 0.000 | 0.000 | |
plotCpg | 0.137 | 0.000 | 0.137 | |
preprocessFunnorm | 4.241 | 0.048 | 4.297 | |
preprocessIllumina | 5.037 | 0.064 | 5.109 | |
preprocessNoob | 1.056 | 0.004 | 1.062 | |
preprocessQuantile | 1.074 | 0.008 | 1.083 | |
preprocessRaw | 3.778 | 0.028 | 3.810 | |
preprocessSwan | 0.761 | 0.000 | 0.763 | |
qcReport | 0.054 | 0.000 | 0.054 | |
ratioConvert-methods | 0.098 | 0.000 | 0.098 | |
read.metharray | 6.018 | 0.116 | 6.143 | |
read.metharray.exp | 9.188 | 0.028 | 9.230 | |
read.metharray.sheet | 0.064 | 0.000 | 0.064 | |
readGEORawFile | 0 | 0 | 0 | |
readTCGA | 0.000 | 0.001 | 0.000 | |
subsetByLoci | 0.912 | 0.001 | 0.914 | |
utils | 0.251 | 0.000 | 0.252 | |