BioC 3.5: CHECK report for minfi on malbec2

Package: minfi

Version: 1.22.1

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings minfi_1.22.1.tar.gz

StartedAt: 2017-10-18 00:51:08 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:00:47 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 579.0 seconds

RetCode: 0

Status:  OK

CheckDir: minfi.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings minfi_1.22.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/minfi.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.22.1’
* 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 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 ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
combineArrays      61.624  7.816  72.158
bumphunter         29.432  2.528  32.104
read.metharray.exp  7.548  0.016   7.566
densityBeanPlot     5.440  0.316   5.758
* 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-3.5-bioc/meat/minfi.Rcheck/00check.log’
for details.

* installing *source* package ‘minfi’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (minfi)

name	user	system	elapsed
GenomicMethylSet-class	0.004	0.000	0.003
GenomicRatioSet-class	0.004	0.000	0.001
IlluminaMethylationManifest-class	2.764	0.052	2.819
MethylSet-class	0.000	0.000	0.001
RGChannelSet-class	0.000	0.000	0.001
RatioSet-class	0	0	0
bumphunter	29.432	2.528	32.104
combineArrays	61.624	7.816	72.158
compartments	2.932	0.356	3.286
controlStripPlot	2.884	0.248	3.747
convertArray	1.260	0.004	1.264
densityBeanPlot	5.440	0.316	5.758
densityPlot	4.668	0.004	4.671
detectionP	0.236	0.000	0.235
dmpFinder	0.288	0.000	0.289
estimateCellCounts	0	0	0
fixMethOutliers	1.632	0.000	1.633
gaphunter	0.084	0.000	0.084
getAnnotation	0.972	0.000	0.969
getGenomicRatioSetFromGEO	0.000	0.000	0.001
getQC	0.240	0.000	0.238
getSex	4.712	0.004	4.721
logit2	0	0	0
makeGenomicRatioSetFromMatrix	0.396	0.000	0.395
mapToGenome-methods	0.172	0.000	0.170
mdsPlot	1.084	0.052	1.136
minfiQC	2.940	0.024	2.969
plotBetasByType	0.000	0.000	0.001
plotCpg	0.104	0.000	0.103
preprocessFunnorm	3.292	0.000	3.312
preprocessIllumina	4.484	0.156	4.645
preprocessNoob	0.736	0.000	0.736
preprocessQuantile	0.496	0.004	0.501
preprocessRaw	2.972	0.072	3.048
preprocessSwan	0.424	0.020	0.446
qcReport	0.060	0.000	0.063
ratioConvert-methods	0.060	0.000	0.059
read.metharray	4.812	0.020	4.832
read.metharray.exp	7.548	0.016	7.566
read.metharray.sheet	0.068	0.000	0.066
readGEORawFile	0	0	0
readTCGA	0.000	0.000	0.001
subsetByLoci	0.376	0.000	0.376
utils	0.944	0.196	1.142