Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 1259/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
minfi 1.53.1 (landing page) Kasper Daniel Hansen
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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: 1.53.1 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:minfi.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings minfi_1.53.1.tar.gz |
StartedAt: 2024-12-23 23:50:38 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 23:59:01 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 503.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: minfi.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:minfi.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings minfi_1.53.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/minfi.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘minfi/DESCRIPTION’ ... OK * this is package ‘minfi’ version ‘1.53.1’ * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 24 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: MethylSet-class.Rd: eSet-class RGChannelSet-class.Rd: SummarizedExperiment-class RatioSet-class.Rd: eSet-class blockFinder.Rd: clusterMaker, bumphunter bumphunter.Rd: clusterMaker Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 57.093 3.821 60.931 bumphunter 25.741 0.624 26.396 read.metharray.exp 6.630 0.070 6.701 IlluminaMethylationManifest-class 4.967 0.190 5.156 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/minfi.Rcheck/00check.log’ for details.
minfi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL minfi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/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 Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-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 Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 -- Mon Dec 23 23:58:03 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 38.036 1.589 39.623
minfi.Rcheck/minfi-Ex.timings
name | user | system | elapsed | |
GenomicMethylSet-class | 0.002 | 0.000 | 0.002 | |
GenomicRatioSet-class | 0.000 | 0.001 | 0.001 | |
IlluminaMethylationManifest-class | 4.967 | 0.190 | 5.156 | |
MethylSet-class | 0.001 | 0.000 | 0.001 | |
RGChannelSet-class | 0.001 | 0.000 | 0.001 | |
RatioSet-class | 0.000 | 0.001 | 0.000 | |
bumphunter | 25.741 | 0.624 | 26.396 | |
combineArrays | 57.093 | 3.821 | 60.931 | |
compartments | 1.699 | 0.313 | 2.012 | |
controlStripPlot | 1.828 | 0.120 | 1.948 | |
convertArray | 1.396 | 0.005 | 1.402 | |
densityBeanPlot | 2.471 | 0.154 | 2.624 | |
densityPlot | 2.781 | 0.025 | 2.806 | |
detectionP | 0.360 | 0.001 | 0.360 | |
dmpFinder | 0.093 | 0.000 | 0.093 | |
estimateCellCounts | 0 | 0 | 0 | |
fixMethOutliers | 0.539 | 0.001 | 0.539 | |
gaphunter | 0.093 | 0.001 | 0.095 | |
getAnnotation | 0.725 | 0.002 | 0.726 | |
getGenomicRatioSetFromGEO | 0 | 0 | 0 | |
getQC | 0.157 | 0.000 | 0.156 | |
getSex | 1.261 | 0.003 | 1.265 | |
logit2 | 0 | 0 | 0 | |
makeGenomicRatioSetFromMatrix | 0.334 | 0.000 | 0.334 | |
mapToGenome-methods | 0.172 | 0.001 | 0.173 | |
mdsPlot | 0.168 | 0.001 | 0.169 | |
minfiQC | 2.147 | 0.041 | 2.188 | |
plotBetasByType | 0 | 0 | 0 | |
plotCpg | 0.106 | 0.002 | 0.107 | |
preprocessFunnorm | 2.196 | 0.012 | 2.211 | |
preprocessIllumina | 2.930 | 0.137 | 3.067 | |
preprocessNoob | 0.683 | 0.027 | 0.709 | |
preprocessQuantile | 0.771 | 0.044 | 0.817 | |
preprocessRaw | 2.342 | 0.037 | 2.379 | |
preprocessSwan | 0.509 | 0.003 | 0.512 | |
qcReport | 0.036 | 0.001 | 0.037 | |
ratioConvert-methods | 0.064 | 0.001 | 0.065 | |
read.metharray | 4.650 | 0.212 | 4.862 | |
read.metharray.exp | 6.630 | 0.070 | 6.701 | |
read.metharray.sheet | 0.037 | 0.000 | 0.037 | |
readGEORawFile | 0.001 | 0.000 | 0.000 | |
readTCGA | 0 | 0 | 0 | |
subsetByLoci | 0.587 | 0.003 | 0.590 | |
utils | 0.095 | 0.030 | 0.125 | |