Kasper Daniel Hansen
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/minfi |
| Branch: RELEASE_3_8 |
| Last Commit: b5125b2 |
| Last Changed Date: 2019-03-08 11:12:11 -0400 (Fri, 08 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:56:07 -0400 (Tue, 16 Apr 2019).
| Package 961/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| minfi 1.28.4 Kasper Daniel Hansen
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: minfi |
| Version: 1.28.4 |
| 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_1.28.4.tar.gz |
| StartedAt: 2019-04-16 01:18:08 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:27:12 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 544.4 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_1.28.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/minfi.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.28.4’
* 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:::.normarg_grid’
‘DelayedArray:::get_verbose_block_processing’
‘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 72.030 4.051 76.919
bumphunter 33.230 7.433 41.156
read.metharray.exp 9.356 0.510 9.927
read.metharray 6.029 0.301 6.370
minfiQC 5.021 0.955 6.045
* 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-3.8-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/3.5/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 version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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, lengths, 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
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 16 01:27:04 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
54.549 2.763 58.725
minfi.Rcheck/minfi-Ex.timings
| name | user | system | elapsed | |
| GenomicMethylSet-class | 0.003 | 0.001 | 0.003 | |
| GenomicRatioSet-class | 0.001 | 0.000 | 0.002 | |
| IlluminaMethylationManifest-class | 3.488 | 0.149 | 3.682 | |
| 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 | 33.230 | 7.433 | 41.156 | |
| combineArrays | 72.030 | 4.051 | 76.919 | |
| compartments | 4.018 | 0.919 | 4.983 | |
| controlStripPlot | 2.611 | 0.273 | 2.902 | |
| convertArray | 1.267 | 0.115 | 1.389 | |
| densityBeanPlot | 3.424 | 0.538 | 3.981 | |
| densityPlot | 3.716 | 0.603 | 4.351 | |
| detectionP | 0.273 | 0.020 | 0.295 | |
| dmpFinder | 0.122 | 0.012 | 0.136 | |
| estimateCellCounts | 0 | 0 | 0 | |
| fixMethOutliers | 1.837 | 0.332 | 2.185 | |
| gaphunter | 0.121 | 0.002 | 0.123 | |
| getAnnotation | 1.114 | 0.121 | 1.251 | |
| getGenomicRatioSetFromGEO | 0.001 | 0.001 | 0.000 | |
| getQC | 0.227 | 0.055 | 0.288 | |
| getSex | 2.394 | 0.411 | 2.833 | |
| logit2 | 0 | 0 | 0 | |
| makeGenomicRatioSetFromMatrix | 0.388 | 0.053 | 0.445 | |
| mapToGenome-methods | 0.221 | 0.018 | 0.241 | |
| mdsPlot | 0.292 | 0.136 | 0.430 | |
| minfiQC | 5.021 | 0.955 | 6.045 | |
| plotBetasByType | 0 | 0 | 0 | |
| plotCpg | 0.117 | 0.005 | 0.123 | |
| preprocessFunnorm | 4.052 | 0.392 | 4.487 | |
| preprocessIllumina | 3.131 | 0.482 | 3.641 | |
| preprocessNoob | 0.774 | 0.076 | 0.855 | |
| preprocessQuantile | 0.778 | 0.077 | 0.860 | |
| preprocessRaw | 3.143 | 0.441 | 3.604 | |
| preprocessSwan | 0.342 | 0.020 | 0.366 | |
| qcReport | 0.037 | 0.001 | 0.038 | |
| ratioConvert-methods | 0.070 | 0.001 | 0.071 | |
| read.metharray | 6.029 | 0.301 | 6.370 | |
| read.metharray.exp | 9.356 | 0.510 | 9.927 | |
| read.metharray.sheet | 0.070 | 0.003 | 0.073 | |
| readGEORawFile | 0 | 0 | 0 | |
| readTCGA | 0.001 | 0.001 | 0.000 | |
| subsetByLoci | 0.477 | 0.030 | 0.529 | |
| utils | 0.253 | 0.147 | 0.414 | |