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CHECK report for minfi on tokay1

This page was generated on 2018-04-12 13:21:17 -0400 (Thu, 12 Apr 2018).

Package 859/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
minfi 1.24.0
Kasper Daniel Hansen
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/minfi
Branch: RELEASE_3_6
Last Commit: a4df428
Last Changed Date: 2017-10-30 12:39:36 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: minfi
Version: 1.24.0
Command: rm -rf minfi.buildbin-libdir minfi.Rcheck && mkdir minfi.buildbin-libdir minfi.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=minfi.buildbin-libdir minfi_1.24.0.tar.gz >minfi.Rcheck\00install.out 2>&1 && cp minfi.Rcheck\00install.out minfi-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=minfi.buildbin-libdir --install="check:minfi-install.out" --force-multiarch --no-vignettes --timings minfi_1.24.0.tar.gz
StartedAt: 2018-04-12 01:28:29 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 01:48:30 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 1201.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: minfi.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf minfi.buildbin-libdir minfi.Rcheck && mkdir minfi.buildbin-libdir minfi.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=minfi.buildbin-libdir minfi_1.24.0.tar.gz >minfi.Rcheck\00install.out 2>&1 && cp minfi.Rcheck\00install.out minfi-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=minfi.buildbin-libdir --install="check:minfi-install.out" --force-multiarch --no-vignettes --timings minfi_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/minfi.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'minfi/DESCRIPTION' ... OK
* this is package 'minfi' version '1.24.0'
* 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 whether package 'minfi' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmS2Txy/R.INSTALL2bd416e5dc3/minfi/man/GenomicMethylSet-class.Rd:129: missing file link 'RangedSummarizedExperiment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmS2Txy/R.INSTALL2bd416e5dc3/minfi/man/GenomicRatioSet-class.Rd:121: missing file link 'RangedSummarizedExperiment'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/minfi.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 object imported by a ':::' call: 'bumphunter:::.getEstimate'
  See the note in ?`:::` about the use of this operator.
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
combineArrays      66.13   5.53   73.33
bumphunter         33.23   3.30   36.53
read.metharray.exp  7.35   0.25    7.60
preprocessRaw       5.89   0.47    6.36
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
combineArrays      69.82   4.17   74.02
bumphunter         38.07   5.41   43.51
read.metharray.exp  8.54   0.24    8.84
read.metharray      5.63   0.15    5.80
densityPlot         4.83   0.55    5.38
compartments        4.36   0.93    5.29
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/minfi.Rcheck/00check.log'
for details.

Installation output

minfi.Rcheck/00install.out


install for i386

* installing *source* package 'minfi' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'minfi'
    finding HTML links ... done
    GenomicMethylSet-class                  html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmS2Txy/R.INSTALL2bd416e5dc3/minfi/man/GenomicMethylSet-class.Rd:129: missing file link 'RangedSummarizedExperiment'
    GenomicRatioSet-class                   html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmS2Txy/R.INSTALL2bd416e5dc3/minfi/man/GenomicRatioSet-class.Rd:121: missing file link 'RangedSummarizedExperiment'
    IlluminaMethylationAnnotation-class     html  
    IlluminaMethylationManifest-class       html  
    MethylSet-class                         html  
    finding level-2 HTML links ... done

    RGChannelSet-class                      html  
    RatioSet-class                          html  
    blockFinder                             html  
    bumphunter                              html  
    combineArrays                           html  
    compartments                            html  
    controlStripPlot                        html  
    convertArray                            html  
    cpgCollapse                             html  
    densityBeanPlot                         html  
    densityPlot                             html  
    detectionP                              html  
    dmpFinder                               html  
    estimateCellCounts                      html  
    fixMethOutliers                         html  
    gaphunter                               html  
    getAnnotation                           html  
    getGenomicRatioSetFromGEO               html  
    getQC                                   html  
    getSex                                  html  
    logit2                                  html  
    makeGenomicRatioSetFromMatrix           html  
    mapToGenome-methods                     html  
    mdsPlot                                 html  
    minfi-defunct                           html  
    minfi-deprecated                        html  
    minfi-package                           html  
    minfiQC                                 html  
    plotBetasByType                         html  
    plotCpg                                 html  
    preprocessFunnorm                       html  
    preprocessIllumina                      html  
    preprocessNoob                          html  
    preprocessQuantile                      html  
    preprocessRaw                           html  
    preprocessSwan                          html  
    qcReport                                html  
    ratioConvert-methods                    html  
    read.metharray                          html  
    read.metharray.exp                      html  
    read.metharray.sheet                    html  
    readGEORawFile                          html  
    readTCGA                                html  
    subsetByLoci                            html  
    utils                                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'minfi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'minfi' as minfi_1.24.0.zip
* DONE (minfi)
In R CMD INSTALL
In R CMD INSTALL

Tests output

minfi.Rcheck/tests_i386/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, cbind, colMeans, colSums, colnames, 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


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:base':

    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
[preprocessFunnorm] Background and dye bias correction with noob
[preprocessNoob] Applying R/G ratio flip to fix dye bias...
[preprocessFunnorm] Mapping to genome
[preprocessFunnorm] Quantile extraction
[preprocessFunnorm] Normalization
[preprocessNoob] Applying R/G ratio flip to fix dye bias...
[preprocessQuantile] Mapping to genome.
[preprocessQuantile] Fixing outliers.
[preprocessQuantile] Quantile normalizing.
[preprocessNoob] Applying R/G ratio flip to fix dye bias...
[preprocessFunnorm] Background and dye bias correction with noob
[preprocessNoob] Applying R/G ratio flip to fix dye bias...
[preprocessFunnorm] Mapping to genome
[preprocessFunnorm] Quantile extraction
[preprocessFunnorm] Normalization


RUNIT TEST PROTOCOL -- Thu Apr 12 01:44:10 2018 
*********************************************** 
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 
 245.46   21.62  267.09

minfi.Rcheck/tests_x64/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, cbind, colMeans, colSums, colnames, 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


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:base':

    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
[preprocessFunnorm] Background and dye bias correction with noob
[preprocessNoob] Applying R/G ratio flip to fix dye bias...
[preprocessFunnorm] Mapping to genome
[preprocessFunnorm] Quantile extraction
[preprocessFunnorm] Normalization
[preprocessNoob] Applying R/G ratio flip to fix dye bias...
[preprocessQuantile] Mapping to genome.
[preprocessQuantile] Fixing outliers.
[preprocessQuantile] Quantile normalizing.
[preprocessNoob] Applying R/G ratio flip to fix dye bias...
[preprocessFunnorm] Background and dye bias correction with noob
[preprocessNoob] Applying R/G ratio flip to fix dye bias...
[preprocessFunnorm] Mapping to genome
[preprocessFunnorm] Quantile extraction
[preprocessFunnorm] Normalization


RUNIT TEST PROTOCOL -- Thu Apr 12 01:48:22 2018 
*********************************************** 
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 
 233.70   17.79  251.71

Example timings

minfi.Rcheck/examples_i386/minfi-Ex.timings

nameusersystemelapsed
GenomicMethylSet-class000
GenomicRatioSet-class000
IlluminaMethylationManifest-class3.050.153.20
MethylSet-class000
RGChannelSet-class000
RatioSet-class000
bumphunter33.23 3.3036.53
combineArrays66.13 5.5373.33
compartments2.921.464.38
controlStripPlot2.910.153.06
convertArray1.200.051.25
densityBeanPlot3.660.514.23
densityPlot4.310.444.75
detectionP0.220.000.22
dmpFinder0.300.020.32
estimateCellCounts000
fixMethOutliers1.280.081.36
gaphunter0.070.040.25
getAnnotation1.590.221.81
getGenomicRatioSetFromGEO000
getQC0.300.020.32
getSex1.090.141.23
logit2000
makeGenomicRatioSetFromMatrix1.350.141.48
mapToGenome-methods0.230.000.24
mdsPlot0.190.110.30
minfiQC4.290.374.67
plotBetasByType000
plotCpg0.090.000.09
preprocessFunnorm4.140.164.30
preprocessIllumina3.500.343.84
preprocessNoob0.720.130.84
preprocessQuantile0.470.030.50
preprocessRaw5.890.476.36
preprocessSwan0.370.000.39
qcReport0.060.000.07
ratioConvert-methods0.070.000.06
read.metharray4.320.014.34
read.metharray.exp7.350.257.60
read.metharray.sheet0.030.020.04
readGEORawFile000
readTCGA000
subsetByLoci0.340.000.35
utils0.110.080.18

minfi.Rcheck/examples_x64/minfi-Ex.timings

nameusersystemelapsed
GenomicMethylSet-class000
GenomicRatioSet-class000
IlluminaMethylationManifest-class3.310.133.44
MethylSet-class000
RGChannelSet-class000
RatioSet-class000
bumphunter38.07 5.4143.51
combineArrays69.82 4.1774.02
compartments4.360.935.29
controlStripPlot3.140.243.38
convertArray1.500.061.56
densityBeanPlot3.390.503.92
densityPlot4.830.555.38
detectionP0.200.000.21
dmpFinder0.330.000.33
estimateCellCounts000
fixMethOutliers0.890.111.00
gaphunter0.090.000.09
getAnnotation1.800.141.94
getGenomicRatioSetFromGEO000
getQC0.200.030.23
getSex1.250.121.38
logit2000
makeGenomicRatioSetFromMatrix4.710.274.97
mapToGenome-methods0.310.020.32
mdsPlot0.200.070.28
minfiQC3.300.573.88
plotBetasByType000
plotCpg0.140.000.14
preprocessFunnorm3.910.254.16
preprocessIllumina3.320.653.98
preprocessNoob0.880.080.95
preprocessQuantile0.470.030.50
preprocessRaw2.690.363.05
preprocessSwan0.420.000.42
qcReport0.050.000.05
ratioConvert-methods0.040.000.05
read.metharray5.630.155.80
read.metharray.exp8.540.248.84
read.metharray.sheet0.050.000.05
readGEORawFile000
readTCGA000
subsetByLoci0.340.000.34
utils0.110.060.17