Kasper Daniel Hansen
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/minfi |
| Branch: RELEASE_3_10 |
| Last Commit: 2b177c3 |
| Last Changed Date: 2019-10-29 13:08:23 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
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 |
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### 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
###
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* 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 | |