BioC 3.6: CHECK report for minfi on veracruz1

Package: minfi

Version: 1.23.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings minfi_1.23.3.tar.gz

StartedAt: 2017-08-16 05:39:43 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 05:50:33 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 650.1 seconds

RetCode: 0

Status:  OK

CheckDir: minfi.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings minfi_1.23.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/minfi.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.23.3’
* 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 sizes of PDF files under ‘inst/doc’ ... 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      61.407  3.290  66.700
bumphunter         30.234  6.299  41.976
read.metharray.exp  8.187  0.271   8.692
minfiQC             6.352  0.583   7.127
densityPlot         5.671  0.683   6.565
densityBeanPlot     5.279  0.604   6.031
preprocessIllumina  4.413  0.738   5.306
read.metharray      4.626  0.232   5.007
* 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-3.6-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	0.002	0.000	0.003
GenomicRatioSet-class	0.002	0.000	0.002
IlluminaMethylationManifest-class	2.657	0.128	2.873
MethylSet-class	0.002	0.000	0.002
RGChannelSet-class	0.001	0.000	0.001
RatioSet-class	0.001	0.001	0.002
bumphunter	30.234	6.299	41.976
combineArrays	61.407	3.290	66.700
compartments	4.152	0.575	4.882
controlStripPlot	3.195	0.321	3.647
convertArray	1.594	0.100	1.748
densityBeanPlot	5.279	0.604	6.031
densityPlot	5.671	0.683	6.565
detectionP	1.229	0.130	1.404
dmpFinder	0.348	0.008	0.360
estimateCellCounts	0.001	0.001	0.001
fixMethOutliers	0.663	0.166	0.847
gaphunter	0.103	0.002	0.113
getAnnotation	2.076	0.159	2.289
getGenomicRatioSetFromGEO	0.001	0.000	0.001
getQC	0.208	0.029	0.239
getSex	1.947	0.267	2.253
logit2	0.001	0.000	0.000
makeGenomicRatioSetFromMatrix	0.565	0.059	0.634
mapToGenome-methods	0.294	0.010	0.307
mdsPlot	1.165	0.200	1.396
minfiQC	6.352	0.583	7.127
plotBetasByType	0.000	0.000	0.001
plotCpg	0.148	0.005	0.156
preprocessFunnorm	4.153	0.340	4.644
preprocessIllumina	4.413	0.738	5.306
preprocessNoob	1.089	0.051	1.167
preprocessQuantile	0.629	0.030	0.674
preprocessRaw	3.034	0.322	3.456
preprocessSwan	0.517	0.028	0.554
qcReport	0.055	0.002	0.058
ratioConvert-methods	0.074	0.001	0.077
read.metharray	4.626	0.232	5.007
read.metharray.exp	8.187	0.271	8.692
read.metharray.sheet	0.060	0.001	0.068
readGEORawFile	0.000	0.000	0.001
readTCGA	0.000	0.000	0.001
subsetByLoci	0.431	0.029	0.474
utils	0.178	0.097	0.282