Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-19 12:12 -0400 (Wed, 19 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4687 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4402 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4351 |
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 1242/2242 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
minfi 1.51.0 (landing page) Kasper Daniel Hansen
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | 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 | ![]() | ||||||||
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. |
Package: minfi |
Version: 1.51.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:minfi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings minfi_1.51.0.tar.gz |
StartedAt: 2024-06-18 22:15:43 -0400 (Tue, 18 Jun 2024) |
EndedAt: 2024-06-18 22:18:53 -0400 (Tue, 18 Jun 2024) |
EllapsedTime: 190.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: minfi.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:minfi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings minfi_1.51.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/minfi.Rcheck’ * using R version 4.4.1 RC (2024-06-06 r86719) * 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 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘minfi/DESCRIPTION’ ... OK * this is package ‘minfi’ version ‘1.51.0’ * 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 ‘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 dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘bumphunter:::.getEstimate’ ‘DelayedArray:::get_verbose_block_processing’ ‘DelayedArray:::normarg_grid’ 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 30.976 0.649 31.633 bumphunter 10.481 1.243 11.723 * 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/minfi.Rcheck/00check.log’ for details.
minfi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL minfi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 RC (2024-06-06 r86719) -- "Race for Your Life" 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. > 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': anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, 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': expand.grid, I, 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 1.5-9.9 2024-03-01 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 -- Tue Jun 18 22:18:49 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 14.141 0.412 14.554
minfi.Rcheck/minfi-Ex.timings
name | user | system | elapsed | |
GenomicMethylSet-class | 0.001 | 0.000 | 0.000 | |
GenomicRatioSet-class | 0.000 | 0.001 | 0.001 | |
IlluminaMethylationManifest-class | 1.988 | 0.022 | 2.011 | |
MethylSet-class | 0 | 0 | 0 | |
RGChannelSet-class | 0 | 0 | 0 | |
RatioSet-class | 0 | 0 | 0 | |
bumphunter | 10.481 | 1.243 | 11.723 | |
combineArrays | 30.976 | 0.649 | 31.633 | |
compartments | 0.502 | 0.055 | 0.556 | |
controlStripPlot | 0.879 | 0.038 | 0.917 | |
convertArray | 0.422 | 0.026 | 0.448 | |
densityBeanPlot | 0.673 | 0.057 | 0.731 | |
densityPlot | 1.324 | 0.098 | 1.422 | |
detectionP | 0.111 | 0.003 | 0.114 | |
dmpFinder | 0.034 | 0.004 | 0.039 | |
estimateCellCounts | 0 | 0 | 0 | |
fixMethOutliers | 0.280 | 0.019 | 0.299 | |
gaphunter | 0.026 | 0.001 | 0.027 | |
getAnnotation | 0.216 | 0.015 | 0.231 | |
getGenomicRatioSetFromGEO | 0 | 0 | 0 | |
getQC | 0.087 | 0.002 | 0.088 | |
getSex | 0.479 | 0.041 | 0.521 | |
logit2 | 0.000 | 0.000 | 0.001 | |
makeGenomicRatioSetFromMatrix | 0.112 | 0.008 | 0.119 | |
mapToGenome-methods | 0.040 | 0.002 | 0.042 | |
mdsPlot | 0.054 | 0.006 | 0.060 | |
minfiQC | 0.812 | 0.050 | 0.863 | |
plotBetasByType | 0.001 | 0.000 | 0.000 | |
plotCpg | 0.025 | 0.002 | 0.027 | |
preprocessFunnorm | 0.593 | 0.057 | 0.649 | |
preprocessIllumina | 1.504 | 0.119 | 1.625 | |
preprocessNoob | 0.198 | 0.004 | 0.202 | |
preprocessQuantile | 0.200 | 0.009 | 0.208 | |
preprocessRaw | 0.640 | 0.045 | 0.684 | |
preprocessSwan | 0.163 | 0.012 | 0.178 | |
qcReport | 0.013 | 0.002 | 0.015 | |
ratioConvert-methods | 0.021 | 0.002 | 0.023 | |
read.metharray | 1.897 | 0.035 | 1.933 | |
read.metharray.exp | 2.809 | 0.062 | 2.879 | |
read.metharray.sheet | 0.014 | 0.002 | 0.016 | |
readGEORawFile | 0.000 | 0.000 | 0.001 | |
readTCGA | 0 | 0 | 0 | |
subsetByLoci | 0.179 | 0.004 | 0.184 | |
utils | 0.037 | 0.009 | 0.046 | |