Kasper Daniel Hansen
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/minfi |
| Branch: master |
| Last Commit: b38c8da |
| Last Changed Date: 2019-03-08 09:54:51 -0400 (Fri, 08 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:26:36 -0400 (Tue, 09 Apr 2019).
| Package 986/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| minfi 1.29.4 Kasper Daniel Hansen
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
| Package: minfi |
| Version: 1.29.4 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:minfi.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings minfi_1.29.4.tar.gz |
| StartedAt: 2019-04-09 02:14:27 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 02:23:55 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 568.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: minfi.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:minfi.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings minfi_1.29.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/minfi.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘minfi/DESCRIPTION’ ... OK
* this is package ‘minfi’ version ‘1.29.4’
* 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 72.727 4.436 77.879
bumphunter 34.073 7.555 41.992
read.metharray.exp 9.230 0.291 9.602
densityPlot 5.625 0.563 6.268
read.metharray 5.681 0.420 6.153
* 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
‘/Users/biocbuild/bbs-3.9-bioc/meat/minfi.Rcheck/00check.log’
for details.
minfi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL minfi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘minfi’ ... ** 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 * DONE (minfi)
minfi.Rcheck/tests/runTests.Rout
R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, colMeans, colSums, 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, rowMeans, rowSums,
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:DelayedArray':
type
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 1.5-9.1 2013-03-22
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 -- Tue Apr 9 02:23:38 2019
***********************************************
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
45.630 2.365 48.432
minfi.Rcheck/minfi-Ex.timings
| name | user | system | elapsed | |
| GenomicMethylSet-class | 0.002 | 0.001 | 0.003 | |
| GenomicRatioSet-class | 0.001 | 0.001 | 0.002 | |
| IlluminaMethylationManifest-class | 3.876 | 0.151 | 4.062 | |
| MethylSet-class | 0.001 | 0.000 | 0.002 | |
| RGChannelSet-class | 0.002 | 0.001 | 0.002 | |
| RatioSet-class | 0.001 | 0.000 | 0.001 | |
| bumphunter | 34.073 | 7.555 | 41.992 | |
| combineArrays | 72.727 | 4.436 | 77.879 | |
| compartments | 3.489 | 0.533 | 4.052 | |
| controlStripPlot | 2.631 | 0.255 | 2.910 | |
| convertArray | 2.790 | 0.242 | 3.054 | |
| densityBeanPlot | 2.691 | 0.297 | 3.011 | |
| densityPlot | 5.625 | 0.563 | 6.268 | |
| detectionP | 0.233 | 0.018 | 0.260 | |
| dmpFinder | 0.142 | 0.011 | 0.156 | |
| estimateCellCounts | 0.000 | 0.000 | 0.001 | |
| fixMethOutliers | 0.789 | 0.177 | 0.971 | |
| gaphunter | 0.098 | 0.003 | 0.101 | |
| getAnnotation | 2.966 | 0.236 | 3.230 | |
| getGenomicRatioSetFromGEO | 0 | 0 | 0 | |
| getQC | 0.215 | 0.015 | 0.233 | |
| getSex | 1.006 | 0.143 | 1.158 | |
| logit2 | 0 | 0 | 0 | |
| makeGenomicRatioSetFromMatrix | 0.352 | 0.063 | 0.415 | |
| mapToGenome-methods | 0.182 | 0.018 | 0.202 | |
| mdsPlot | 4.706 | 0.219 | 4.975 | |
| minfiQC | 1.841 | 0.337 | 2.203 | |
| plotBetasByType | 0 | 0 | 0 | |
| plotCpg | 0.115 | 0.006 | 0.124 | |
| preprocessFunnorm | 3.749 | 0.556 | 4.351 | |
| preprocessIllumina | 3.140 | 0.351 | 3.522 | |
| preprocessNoob | 0.803 | 0.086 | 0.896 | |
| preprocessQuantile | 0.796 | 0.085 | 0.894 | |
| preprocessRaw | 2.57 | 0.24 | 2.83 | |
| preprocessSwan | 0.419 | 0.025 | 0.447 | |
| qcReport | 0.045 | 0.002 | 0.048 | |
| ratioConvert-methods | 0.081 | 0.001 | 0.083 | |
| read.metharray | 5.681 | 0.420 | 6.153 | |
| read.metharray.exp | 9.230 | 0.291 | 9.602 | |
| read.metharray.sheet | 0.053 | 0.002 | 0.056 | |
| readGEORawFile | 0.001 | 0.001 | 0.001 | |
| readTCGA | 0.000 | 0.000 | 0.001 | |
| subsetByLoci | 0.368 | 0.027 | 0.398 | |
| utils | 0.155 | 0.058 | 0.214 | |