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CHECK report for minfi on malbec2

This page was generated on 2018-10-17 08:23:58 -0400 (Wed, 17 Oct 2018).

Package 909/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
minfi 1.26.2
Kasper Daniel Hansen
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/minfi
Branch: RELEASE_3_7
Last Commit: ebb07b7
Last Changed Date: 2018-06-15 16:54:00 -0400 (Fri, 15 Jun 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: minfi
Version: 1.26.2
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:minfi.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings minfi_1.26.2.tar.gz
StartedAt: 2018-10-16 02:01:38 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 02:12:46 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 667.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: minfi.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:minfi.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings minfi_1.26.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/minfi.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.26.2’
* 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 ... WARNING
Problems with news in ‘inst/NEWS.Rd’:
  inst/NEWS.Rd:6: unknown macro '\item'
  inst/NEWS.Rd:9: unknown macro '\item'
  inst/NEWS.Rd:13: unknown macro '\item'
  inst/NEWS.Rd:17: unexpected '}'
  Malformed NEWS.Rd file:
  Chunk starting
    \item Fix bug in \code{preprocessQuantile()} that arose when
  contains no \itemize.
* 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:::.as_array_or_matrix’ ‘DelayedArray:::.normarg_grid’
  ‘DelayedArray:::extract_block’ ‘DelayedArray:::get_max_block_length’
  ‘DelayedArray:::get_spacings_for_hypercube_capped_length_blocks’
  ‘DelayedArray:::get_spacings_for_linear_capped_length_blocks’
  ‘DelayedArray:::get_verbose_block_processing’
  ‘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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
preprocessFunnorm  96.788  0.004  96.840
bumphunter         64.992  0.916  66.139
combineArrays      62.276  2.124  67.307
preprocessNoob     46.260  0.016  46.297
preprocessQuantile 37.048  0.000  37.093
getAnnotation      30.916  0.020  30.949
compartments       19.772  0.160  19.943
read.metharray.exp  7.288  0.020   7.422
minfiQC             6.940  0.008   6.951
getSex              6.372  0.148   6.523
read.metharray      5.600  0.012   5.620
* 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 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/minfi.Rcheck/00check.log’
for details.



Installation output

minfi.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL minfi
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.7-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)

Tests output

minfi.Rcheck/tests/runTests.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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 Oct 16 02:12:41 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 
 45.448   1.048  46.646 

Example timings

minfi.Rcheck/minfi-Ex.timings

nameusersystemelapsed
GenomicMethylSet-class0.0000.0000.002
GenomicRatioSet-class0.0000.0000.001
IlluminaMethylationManifest-class3.3120.0803.395
MethylSet-class0.0000.0000.001
RGChannelSet-class0.0000.0040.001
RatioSet-class0.0000.0000.001
bumphunter64.992 0.91666.139
combineArrays62.276 2.12467.307
compartments19.772 0.16019.943
controlStripPlot3.1120.0923.667
convertArray1.1360.0001.133
densityBeanPlot3.9800.0884.071
densityPlot2.7440.0002.746
detectionP0.2040.0000.204
dmpFinder0.0880.0000.088
estimateCellCounts0.0000.0000.001
fixMethOutliers4.2040.0204.231
gaphunter0.0760.0000.078
getAnnotation30.916 0.02030.949
getGenomicRatioSetFromGEO0.0000.0000.001
getQC0.2080.0400.249
getSex6.3720.1486.523
logit20.0000.0000.001
makeGenomicRatioSetFromMatrix4.6800.0004.685
mapToGenome-methods4.3880.0004.391
mdsPlot0.1480.0080.156
minfiQC6.9400.0086.951
plotBetasByType0.0000.0040.001
plotCpg0.0800.0000.079
preprocessFunnorm96.788 0.00496.840
preprocessIllumina1.9680.0281.998
preprocessNoob46.260 0.01646.297
preprocessQuantile37.048 0.00037.093
preprocessRaw2.3200.0002.321
preprocessSwan0.3560.0000.354
qcReport0.0400.0000.038
ratioConvert-methods0.9480.0000.948
read.metharray5.6000.0125.620
read.metharray.exp7.2880.0207.422
read.metharray.sheet0.0320.0000.035
readGEORawFile0.0000.0000.001
readTCGA000
subsetByLoci0.3000.0040.303
utils0.1080.0000.108