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: 2017-10-18 06:10:48 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 06:22:34 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 705.7 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_1.22.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/minfi.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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      61.455  3.520  67.616
bumphunter         32.835  7.096  41.269
read.metharray.exp  9.215  0.337   9.814
preprocessRaw       7.862  0.547   8.699
densityPlot         6.291  0.794   7.289
densityBeanPlot     6.177  0.680   7.090
preprocessIllumina  5.919  0.720   6.857
read.metharray      5.679  0.255   6.125
compartments        5.000  0.799   6.016
minfiQC             4.398  0.704   5.276
* 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	0.004
GenomicRatioSet-class	0.002	0.001	0.002
IlluminaMethylationManifest-class	2.811	0.144	3.027
MethylSet-class	0.001	0.000	0.002
RGChannelSet-class	0.002	0.000	0.002
RatioSet-class	0.002	0.000	0.002
bumphunter	32.835	7.096	41.269
combineArrays	61.455	3.520	67.616
compartments	5.000	0.799	6.016
controlStripPlot	2.360	0.276	2.728
convertArray	2.825	0.238	3.161
densityBeanPlot	6.177	0.680	7.090
densityPlot	6.291	0.794	7.289
detectionP	0.296	0.024	0.328
dmpFinder	0.356	0.014	0.379
estimateCellCounts	0.001	0.000	0.001
fixMethOutliers	1.726	0.292	2.085
gaphunter	0.122	0.002	0.129
getAnnotation	1.449	0.110	1.601
getGenomicRatioSetFromGEO	0.001	0.000	0.000
getQC	0.220	0.049	0.276
getSex	2.514	0.395	3.021
logit2	0.000	0.000	0.001
makeGenomicRatioSetFromMatrix	0.586	0.080	0.688
mapToGenome-methods	0.311	0.018	0.336
mdsPlot	1.202	0.224	1.477
minfiQC	4.398	0.704	5.276
plotBetasByType	0.001	0.000	0.001
plotCpg	0.122	0.006	0.133
preprocessFunnorm	4.503	0.297	4.955
preprocessIllumina	5.919	0.720	6.857
preprocessNoob	1.142	0.088	1.256
preprocessQuantile	0.631	0.032	0.679
preprocessRaw	7.862	0.547	8.699
preprocessSwan	0.546	0.033	0.606
qcReport	0.065	0.002	0.068
ratioConvert-methods	0.074	0.002	0.078
read.metharray	5.679	0.255	6.125
read.metharray.exp	9.215	0.337	9.814
read.metharray.sheet	0.063	0.002	0.067
readGEORawFile	0.000	0.000	0.001
readTCGA	0	0	0
subsetByLoci	0.469	0.032	0.513
utils	1.169	0.201	1.440