Back to Multiple platform build/check report for BioC 3.10 |
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This page was generated on 2020-04-15 12:06:37 -0400 (Wed, 15 Apr 2020).
Package 1047/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
minfi 1.32.0 Kasper Daniel Hansen
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: minfi |
Version: 1.32.0 |
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:minfi.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings minfi_1.32.0.tar.gz |
StartedAt: 2020-04-15 01:07:28 -0400 (Wed, 15 Apr 2020) |
EndedAt: 2020-04-15 01:16:47 -0400 (Wed, 15 Apr 2020) |
EllapsedTime: 559.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: minfi.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:minfi.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings minfi_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/minfi.Rcheck’ * using R version 3.6.3 (2020-02-29) * 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 ‘1.32.0’ * 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 or elapsed time > 5s user system elapsed combineArrays 77.060 2.860 103.999 bumphunter 36.492 1.796 38.789 read.metharray.exp 9.728 0.032 9.919 minfiQC 7.188 0.032 7.229 read.metharray 5.884 0.000 6.010 controlStripPlot 2.708 0.040 9.432 * 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-3.10-bioc/meat/minfi.Rcheck/00check.log’ for details.
minfi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL minfi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-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 3.6.3 (2020-02-29) -- "Holding the Windsock" Copyright (C) 2020 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, 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:base': expand.grid Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment 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")'. Loading required package: DelayedArray Loading required package: matrixStats Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians Loading required package: BiocParallel Attaching package: 'DelayedArray' The following objects are masked from 'package:matrixStats': colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following objects are masked from 'package:base': aperm, apply, rowsum 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 RUNIT TEST PROTOCOL -- Wed Apr 15 01:16:41 2020 *********************************************** 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 52.932 1.264 56.677
minfi.Rcheck/minfi-Ex.timings
name | user | system | elapsed | |
GenomicMethylSet-class | 0.004 | 0.000 | 0.002 | |
GenomicRatioSet-class | 0.000 | 0.000 | 0.002 | |
IlluminaMethylationManifest-class | 4.552 | 0.128 | 4.874 | |
MethylSet-class | 0.000 | 0.000 | 0.001 | |
RGChannelSet-class | 0.000 | 0.000 | 0.001 | |
RatioSet-class | 0.000 | 0.000 | 0.001 | |
bumphunter | 36.492 | 1.796 | 38.789 | |
combineArrays | 77.060 | 2.860 | 103.999 | |
compartments | 3.284 | 0.216 | 4.081 | |
controlStripPlot | 2.708 | 0.040 | 9.432 | |
convertArray | 1.612 | 0.040 | 2.001 | |
densityBeanPlot | 3.808 | 0.000 | 4.587 | |
densityPlot | 3.312 | 0.016 | 3.330 | |
detectionP | 0.184 | 0.004 | 0.188 | |
dmpFinder | 0.092 | 0.000 | 0.092 | |
estimateCellCounts | 0 | 0 | 0 | |
fixMethOutliers | 1.992 | 0.020 | 2.020 | |
gaphunter | 0.124 | 0.000 | 0.187 | |
getAnnotation | 0.856 | 0.000 | 0.859 | |
getGenomicRatioSetFromGEO | 0 | 0 | 0 | |
getQC | 0.324 | 0.012 | 0.336 | |
getSex | 2.400 | 0.012 | 2.417 | |
logit2 | 0 | 0 | 0 | |
makeGenomicRatioSetFromMatrix | 0.396 | 0.000 | 0.402 | |
mapToGenome-methods | 0.204 | 0.000 | 0.202 | |
mdsPlot | 0.144 | 0.000 | 0.144 | |
minfiQC | 7.188 | 0.032 | 7.229 | |
plotBetasByType | 0 | 0 | 0 | |
plotCpg | 0.176 | 0.000 | 0.178 | |
preprocessFunnorm | 2.884 | 0.008 | 3.022 | |
preprocessIllumina | 2.816 | 0.276 | 3.096 | |
preprocessNoob | 1.496 | 0.056 | 1.553 | |
preprocessQuantile | 0.700 | 0.004 | 0.704 | |
preprocessRaw | 2.228 | 0.000 | 2.227 | |
preprocessSwan | 0.324 | 0.000 | 0.325 | |
qcReport | 0.040 | 0.004 | 0.043 | |
ratioConvert-methods | 0.096 | 0.000 | 0.096 | |
read.metharray | 5.884 | 0.000 | 6.010 | |
read.metharray.exp | 9.728 | 0.032 | 9.919 | |
read.metharray.sheet | 0.060 | 0.000 | 0.513 | |
readGEORawFile | 0 | 0 | 0 | |
readTCGA | 0 | 0 | 0 | |
subsetByLoci | 0.408 | 0.004 | 0.420 | |
utils | 0.152 | 0.000 | 0.150 | |