BioC 3.5: CHECK report for minfi on veracruz2

Package: minfi

Version: 1.22.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings minfi_1.22.1.tar.gz

StartedAt: 2017-08-16 05:23:38 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 05:35:58 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 739.7 seconds

RetCode: 0

Status:  OK

CheckDir: minfi.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings minfi_1.22.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-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 ‘1.22.1’
* 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 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      61.748  3.122  66.695
bumphunter         31.864  6.784  39.723
densityBeanPlot     8.446  0.709   9.446
read.metharray.exp  8.813  0.264   9.306
densityPlot         6.163  0.704   7.056
preprocessIllumina  5.559  0.678   6.401
read.metharray      5.417  0.211   5.793
* 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-3.5-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	0.003	0.000	0.003
GenomicRatioSet-class	0.002	0.001	0.003
IlluminaMethylationManifest-class	2.747	0.121	2.954
MethylSet-class	0.002	0.000	0.002
RGChannelSet-class	0.001	0.000	0.001
RatioSet-class	0.000	0.001	0.001
bumphunter	31.864	6.784	39.723
combineArrays	61.748	3.122	66.695
compartments	4.230	0.563	4.949
controlStripPlot	3.323	0.297	3.726
convertArray	1.782	0.095	1.921
densityBeanPlot	8.446	0.709	9.446
densityPlot	6.163	0.704	7.056
detectionP	0.247	0.020	0.273
dmpFinder	0.343	0.034	0.379
estimateCellCounts	0.001	0.000	0.001
fixMethOutliers	1.484	0.330	1.854
gaphunter	0.110	0.002	0.118
getAnnotation	1.400	0.090	1.535
getGenomicRatioSetFromGEO	0.001	0.000	0.000
getQC	0.205	0.034	0.246
getSex	2.191	0.349	2.599
logit2	0.000	0.001	0.000
makeGenomicRatioSetFromMatrix	0.623	0.071	0.708
mapToGenome-methods	0.279	0.010	0.297
mdsPlot	1.027	0.215	1.274
minfiQC	3.145	0.570	3.849
plotBetasByType	0.001	0.000	0.001
plotCpg	0.152	0.005	0.161
preprocessFunnorm	4.163	0.250	4.530
preprocessIllumina	5.559	0.678	6.401
preprocessNoob	1.003	0.049	1.079
preprocessQuantile	0.619	0.029	0.671
preprocessRaw	4.186	0.462	4.828
preprocessSwan	0.503	0.027	0.546
qcReport	0.063	0.002	0.071
ratioConvert-methods	0.079	0.002	0.081
read.metharray	5.417	0.211	5.793
read.metharray.exp	8.813	0.264	9.306
read.metharray.sheet	0.056	0.002	0.057
readGEORawFile	0.001	0.000	0.001
readTCGA	0.001	0.000	0.000
subsetByLoci	0.475	0.033	0.517
utils	0.184	0.096	0.282