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: 2017-08-16 00:38:51 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:48:55 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 604.2 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 3.4.1 (2017-06-30)
* 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      62.120 10.700  77.482
bumphunter         31.276  7.460  38.893
densityPlot         8.412  0.056   8.475
read.metharray.exp  7.828  0.028   7.863
read.metharray      5.116  0.012   5.135
densityBeanPlot     4.888  0.212   5.108
* 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	0.000	0.000	0.002
GenomicRatioSet-class	0.000	0.000	0.001
IlluminaMethylationManifest-class	2.768	0.068	2.834
MethylSet-class	0.000	0.000	0.001
RGChannelSet-class	0.000	0.000	0.001
RatioSet-class	0	0	0
bumphunter	31.276	7.460	38.893
combineArrays	62.120	10.700	77.482
compartments	3.132	0.616	3.750
controlStripPlot	3.112	0.512	4.198
convertArray	1.212	0.004	1.216
densityBeanPlot	4.888	0.212	5.108
densityPlot	8.412	0.056	8.475
detectionP	0.340	0.004	0.354
dmpFinder	0.284	0.020	0.306
estimateCellCounts	0.000	0.000	0.001
fixMethOutliers	0.852	0.684	1.537
gaphunter	0.132	0.000	0.157
getAnnotation	1.708	0.168	1.875
getGenomicRatioSetFromGEO	0.000	0.000	0.001
getQC	0.232	0.004	0.235
getSex	1.360	0.012	1.374
logit2	0.000	0.000	0.001
makeGenomicRatioSetFromMatrix	0.488	0.000	0.487
mapToGenome-methods	0.180	0.000	0.181
mdsPlot	0.168	0.000	0.168
minfiQC	3.072	0.140	3.217
plotBetasByType	0.000	0.000	0.001
plotCpg	0.100	0.000	0.098
preprocessFunnorm	3.180	0.012	3.200
preprocessIllumina	3.240	0.000	3.243
preprocessNoob	0.844	0.000	0.850
preprocessQuantile	0.508	0.000	0.510
preprocessRaw	2.248	0.004	2.253
preprocessSwan	0.42	0.00	0.42
qcReport	0.048	0.004	0.050
ratioConvert-methods	0.064	0.000	0.063
read.metharray	5.116	0.012	5.135
read.metharray.exp	7.828	0.028	7.863
read.metharray.sheet	0.068	0.000	0.067
readGEORawFile	0.000	0.000	0.001
readTCGA	0	0	0
subsetByLoci	0.388	0.000	0.387
utils	0.132	0.004	0.138