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This page was generated on 2022-06-24 12:07:46 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for minfi on merida1


To the developers/maintainers of the minfi package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/minfi.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1186/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
minfi 1.42.0  (landing page)
Kasper Daniel Hansen
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/minfi
git_branch: RELEASE_3_15
git_last_commit: 30fc705
git_last_commit_date: 2022-04-26 11:09:22 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: minfi
Version: 1.42.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:minfi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings minfi_1.42.0.tar.gz
StartedAt: 2022-06-24 05:17:32 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 05:31:29 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 836.8 seconds
RetCode: 0
Status:   OK  
CheckDir: minfi.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:minfi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings minfi_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/minfi.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘minfi/DESCRIPTION’ ... OK
* this is package ‘minfi’ version ‘1.42.0’
* 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 ... NOTE
Found the following possibly unsafe calls:
File ‘minfi/R/IlluminaMethylationManifest-class.R’:
  unlockBinding(name, env = object@data)
* 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 (user + system) or elapsed time > 5s
                                    user system elapsed
combineArrays                     94.748  2.816 100.253
bumphunter                        39.131  4.876  45.488
read.metharray.exp                12.542  0.103  13.802
read.metharray                     7.961  0.130   8.779
preprocessFunnorm                  6.388  0.309   7.050
preprocessIllumina                 6.504  0.134   6.970
densityPlot                        6.165  0.177   6.400
preprocessRaw                      5.337  0.083   5.707
IlluminaMethylationManifest-class  5.149  0.163   5.368
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/minfi.Rcheck/00check.log’
for details.



Installation output

minfi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL minfi
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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)

Tests output

minfi.Rcheck/tests/runTests.Rout


R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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

Attaching package: 'BiocGenerics'

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.max, which.min

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

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: parallel
Loading required package: locfit
locfit 1.5-9.5 	 2022-03-01
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
Loading required package: DelayedArray
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand


Attaching package: 'DelayedArray'

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

    aperm, apply, rowsum, scale, sweep



RUNIT TEST PROTOCOL -- Fri Jun 24 05:31:15 2022 
*********************************************** 
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 
 65.487   2.193  71.655 

Example timings

minfi.Rcheck/minfi-Ex.timings

nameusersystemelapsed
GenomicMethylSet-class0.0040.0000.004
GenomicRatioSet-class0.0020.0000.002
IlluminaMethylationManifest-class5.1490.1635.368
MethylSet-class0.0010.0000.002
RGChannelSet-class0.0020.0000.002
RatioSet-class0.0010.0010.002
bumphunter39.131 4.87645.488
combineArrays 94.748 2.816100.253
compartments3.3130.2423.698
controlStripPlot3.6620.1183.815
convertArray2.4870.0262.530
densityBeanPlot4.1060.0784.210
densityPlot6.1650.1776.400
detectionP0.7550.0070.770
dmpFinder1.7280.0981.845
estimateCellCounts000
fixMethOutliers0.9930.0041.003
gaphunter0.1830.0030.187
getAnnotation1.4180.0071.436
getGenomicRatioSetFromGEO000
getQC0.3110.0030.329
getSex1.4910.0091.510
logit20.0010.0000.001
makeGenomicRatioSetFromMatrix2.0450.0762.148
mapToGenome-methods0.3510.0040.368
mdsPlot0.3120.0040.371
minfiQC2.6280.0082.756
plotBetasByType000
plotCpg0.2060.0040.222
preprocessFunnorm6.3880.3097.050
preprocessIllumina6.5040.1346.970
preprocessNoob1.5130.0071.583
preprocessQuantile1.580.011.68
preprocessRaw5.3370.0835.707
preprocessSwan1.1160.0061.172
qcReport0.0960.0040.107
ratioConvert-methods0.1630.0040.174
read.metharray7.9610.1308.779
read.metharray.exp12.542 0.10313.802
read.metharray.sheet0.0950.0040.106
readGEORawFile0.0000.0010.000
readTCGA0.0010.0000.000
subsetByLoci1.3830.0071.515
utils0.2190.0040.247