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CHECK report for minfi on merida2

This page was generated on 2019-04-09 13:26:36 -0400 (Tue, 09 Apr 2019).

Package 986/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
minfi 1.29.4
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)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

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

Command output

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### Running 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
###
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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.



Installation output

minfi.Rcheck/00install.out

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###
### 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)

Tests output

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 

Example timings

minfi.Rcheck/minfi-Ex.timings

nameusersystemelapsed
GenomicMethylSet-class0.0020.0010.003
GenomicRatioSet-class0.0010.0010.002
IlluminaMethylationManifest-class3.8760.1514.062
MethylSet-class0.0010.0000.002
RGChannelSet-class0.0020.0010.002
RatioSet-class0.0010.0000.001
bumphunter34.073 7.55541.992
combineArrays72.727 4.43677.879
compartments3.4890.5334.052
controlStripPlot2.6310.2552.910
convertArray2.7900.2423.054
densityBeanPlot2.6910.2973.011
densityPlot5.6250.5636.268
detectionP0.2330.0180.260
dmpFinder0.1420.0110.156
estimateCellCounts0.0000.0000.001
fixMethOutliers0.7890.1770.971
gaphunter0.0980.0030.101
getAnnotation2.9660.2363.230
getGenomicRatioSetFromGEO000
getQC0.2150.0150.233
getSex1.0060.1431.158
logit2000
makeGenomicRatioSetFromMatrix0.3520.0630.415
mapToGenome-methods0.1820.0180.202
mdsPlot4.7060.2194.975
minfiQC1.8410.3372.203
plotBetasByType000
plotCpg0.1150.0060.124
preprocessFunnorm3.7490.5564.351
preprocessIllumina3.1400.3513.522
preprocessNoob0.8030.0860.896
preprocessQuantile0.7960.0850.894
preprocessRaw2.570.242.83
preprocessSwan0.4190.0250.447
qcReport0.0450.0020.048
ratioConvert-methods0.0810.0010.083
read.metharray5.6810.4206.153
read.metharray.exp9.2300.2919.602
read.metharray.sheet0.0530.0020.056
readGEORawFile0.0010.0010.001
readTCGA0.0000.0000.001
subsetByLoci0.3680.0270.398
utils0.1550.0580.214