Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:45 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the minfi package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1140/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
minfi 1.38.0 (landing page) Kasper Daniel Hansen
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: minfi |
Version: 1.38.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:minfi.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings minfi_1.38.0.tar.gz |
StartedAt: 2021-10-14 10:36:31 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 10:44:21 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 469.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: minfi.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:minfi.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings minfi_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/minfi.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘minfi/DESCRIPTION’ ... OK * this is package ‘minfi’ version ‘1.38.0’ * 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 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 ... 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 ... 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed combineArrays 68.716 4.436 73.175 bumphunter 30.061 2.908 32.973 read.metharray.exp 12.196 0.088 12.285 read.metharray 7.396 0.060 7.456 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.13-bioc/meat/minfi.Rcheck/00check.log’ for details.
minfi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL minfi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-pc-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("minfi") || stop("unable to load minfi") Loading required package: minfi Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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, 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: GenomicRanges Loading required package: stats4 Loading required package: S4Vectors Attaching package: 'S4Vectors' 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: locfit locfit 1.5-9.4 2020-03-24 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 Attaching package: 'DelayedArray' The following objects are masked from 'package:base': aperm, apply, rowsum, scale, sweep RUNIT TEST PROTOCOL -- Thu Oct 14 10:44:16 2021 *********************************************** 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 Warning messages: 1: 'colGrid' is deprecated. Use 'colAutoGrid' instead. See help("Deprecated") 2: 'colGrid' is deprecated. Use 'colAutoGrid' instead. See help("Deprecated") > > proc.time() user system elapsed 41.938 1.516 43.445
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 | 4.301 | 0.164 | 4.464 | |
MethylSet-class | 0.001 | 0.000 | 0.001 | |
RGChannelSet-class | 0.001 | 0.000 | 0.001 | |
RatioSet-class | 0.001 | 0.000 | 0.001 | |
bumphunter | 30.061 | 2.908 | 32.973 | |
combineArrays | 68.716 | 4.436 | 73.175 | |
compartments | 3.058 | 0.332 | 3.390 | |
controlStripPlot | 1.820 | 0.054 | 1.874 | |
convertArray | 1.507 | 0.004 | 1.512 | |
densityBeanPlot | 2.871 | 0.056 | 2.927 | |
densityPlot | 3.220 | 0.012 | 3.232 | |
detectionP | 0.392 | 0.000 | 0.393 | |
dmpFinder | 0.11 | 0.00 | 0.11 | |
estimateCellCounts | 0.000 | 0.000 | 0.001 | |
fixMethOutliers | 1.602 | 0.044 | 1.647 | |
gaphunter | 0.084 | 0.000 | 0.084 | |
getAnnotation | 0.649 | 0.004 | 0.652 | |
getGenomicRatioSetFromGEO | 0.000 | 0.000 | 0.001 | |
getQC | 0.219 | 0.004 | 0.222 | |
getSex | 2.002 | 0.039 | 2.041 | |
logit2 | 0.000 | 0.001 | 0.000 | |
makeGenomicRatioSetFromMatrix | 0.284 | 0.003 | 0.287 | |
mapToGenome-methods | 0.188 | 0.000 | 0.188 | |
mdsPlot | 0.152 | 0.000 | 0.152 | |
minfiQC | 2.400 | 0.092 | 2.492 | |
plotBetasByType | 0.000 | 0.000 | 0.001 | |
plotCpg | 0.102 | 0.004 | 0.107 | |
preprocessFunnorm | 3.251 | 0.036 | 3.286 | |
preprocessIllumina | 2.491 | 0.032 | 2.523 | |
preprocessNoob | 1.740 | 0.028 | 1.768 | |
preprocessQuantile | 1.005 | 0.012 | 1.015 | |
preprocessRaw | 1.866 | 0.000 | 1.867 | |
preprocessSwan | 1.254 | 0.000 | 1.254 | |
qcReport | 0.038 | 0.004 | 0.042 | |
ratioConvert-methods | 0.081 | 0.000 | 0.080 | |
read.metharray | 7.396 | 0.060 | 7.456 | |
read.metharray.exp | 12.196 | 0.088 | 12.285 | |
read.metharray.sheet | 0.049 | 0.004 | 0.052 | |
readGEORawFile | 0.000 | 0.001 | 0.001 | |
readTCGA | 0.000 | 0.001 | 0.000 | |
subsetByLoci | 0.751 | 0.002 | 0.754 | |
utils | 0.132 | 0.000 | 0.132 | |