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 11:49:24 -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: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:minfi.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings minfi_1.28.4.tar.gz |
| StartedAt: 2019-04-16 01:26:51 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:35:00 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 488.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: minfi.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:minfi.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings minfi_1.28.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/minfi.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.28.4’
* 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 79.152 2.664 85.230
bumphunter 36.968 1.384 38.873
read.metharray.exp 8.304 0.028 8.342
read.metharray 5.716 0.032 5.767
* 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-3.8-bioc/meat/minfi.Rcheck/00check.log’
for details.
minfi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL minfi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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-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, 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 01:34:55 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
46.264 1.080 47.471
minfi.Rcheck/minfi-Ex.timings
| name | user | system | elapsed | |
| GenomicMethylSet-class | 0.004 | 0.000 | 0.002 | |
| GenomicRatioSet-class | 0.000 | 0.000 | 0.001 | |
| IlluminaMethylationManifest-class | 4.092 | 0.116 | 4.223 | |
| MethylSet-class | 0.000 | 0.000 | 0.001 | |
| RGChannelSet-class | 0.000 | 0.004 | 0.001 | |
| RatioSet-class | 0 | 0 | 0 | |
| bumphunter | 36.968 | 1.384 | 38.873 | |
| combineArrays | 79.152 | 2.664 | 85.230 | |
| compartments | 3.880 | 0.336 | 4.220 | |
| controlStripPlot | 2.480 | 0.020 | 2.719 | |
| convertArray | 1.636 | 0.008 | 1.647 | |
| densityBeanPlot | 3.632 | 0.060 | 3.695 | |
| densityPlot | 4.068 | 0.024 | 4.095 | |
| detectionP | 0.264 | 0.000 | 0.262 | |
| dmpFinder | 0.088 | 0.000 | 0.087 | |
| estimateCellCounts | 0 | 0 | 0 | |
| fixMethOutliers | 1.820 | 0.060 | 1.883 | |
| gaphunter | 0.096 | 0.000 | 0.106 | |
| getAnnotation | 1.280 | 0.000 | 1.282 | |
| getGenomicRatioSetFromGEO | 0 | 0 | 0 | |
| getQC | 0.212 | 0.004 | 0.215 | |
| getSex | 2.492 | 0.008 | 2.504 | |
| logit2 | 0 | 0 | 0 | |
| makeGenomicRatioSetFromMatrix | 0.408 | 0.000 | 0.409 | |
| mapToGenome-methods | 0.276 | 0.000 | 0.275 | |
| mdsPlot | 0.276 | 0.072 | 0.351 | |
| minfiQC | 4.372 | 0.060 | 4.437 | |
| plotBetasByType | 0 | 0 | 0 | |
| plotCpg | 0.108 | 0.000 | 0.109 | |
| preprocessFunnorm | 2.872 | 0.004 | 2.891 | |
| preprocessIllumina | 3.008 | 0.024 | 3.036 | |
| preprocessNoob | 0.700 | 0.036 | 0.738 | |
| preprocessQuantile | 0.620 | 0.048 | 0.673 | |
| preprocessRaw | 2.988 | 0.000 | 2.991 | |
| preprocessSwan | 0.380 | 0.000 | 0.381 | |
| qcReport | 0.044 | 0.000 | 0.044 | |
| ratioConvert-methods | 0.064 | 0.000 | 0.064 | |
| read.metharray | 5.716 | 0.032 | 5.767 | |
| read.metharray.exp | 8.304 | 0.028 | 8.342 | |
| read.metharray.sheet | 0.052 | 0.000 | 0.051 | |
| readGEORawFile | 0 | 0 | 0 | |
| readTCGA | 0 | 0 | 0 | |
| subsetByLoci | 0.340 | 0.000 | 0.343 | |
| utils | 0.148 | 0.000 | 0.150 | |