BioC 3.5: CHECK report for minfi on toluca2

Package: minfi

Version: 1.21.7

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings minfi_1.21.7.tar.gz

StartedAt: 2017-04-23 06:45:31 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 06:58:43 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 791.8 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_1.21.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/minfi.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘minfi/DESCRIPTION’ ... OK
* this is package ‘minfi’ version ‘1.21.7’
* 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      66.476  3.561  71.048
bumphunter         34.990  7.568  42.937
read.metharray.exp 13.935  0.305  14.368
densityPlot        12.137  0.868  13.154
densityBeanPlot    12.181  0.804  13.200
preprocessIllumina 11.405  0.729  12.239
preprocessRaw       9.691  0.480  10.273
preprocessFunnorm   8.689  0.381   9.151
read.metharray      6.740  0.210   7.007
compartments        5.501  0.643   6.288
controlStripPlot    5.588  0.397   6.261
minfiQC             5.034  0.736   5.799
* 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	0.000	0.002
IlluminaMethylationManifest-class	2.786	0.148	2.966
MethylSet-class	0.001	0.000	0.002
RGChannelSet-class	0.001	0.000	0.002
RatioSet-class	0.002	0.000	0.002
bumphunter	34.990	7.568	42.937
combineArrays	66.476	3.561	71.048
compartments	5.501	0.643	6.288
controlStripPlot	5.588	0.397	6.261
convertArray	4.449	0.251	4.760
densityBeanPlot	12.181	0.804	13.200
densityPlot	12.137	0.868	13.154
detectionP	0.315	0.029	0.346
dmpFinder	0.446	0.018	0.467
estimateCellCounts	0.001	0.000	0.001
fixMethOutliers	1.766	0.271	2.059
gaphunter	0.131	0.002	0.134
getAnnotation	2.035	0.105	2.153
getGenomicRatioSetFromGEO	0.000	0.000	0.001
getQC	0.226	0.044	0.271
getSex	3.187	0.381	3.604
logit2	0.001	0.001	0.000
makeGenomicRatioSetFromMatrix	1.889	0.186	2.089
mapToGenome-methods	0.431	0.011	0.444
mdsPlot	0.239	0.112	0.353
minfiQC	5.034	0.736	5.799
plotBetasByType	0.001	0.000	0.001
plotCpg	0.194	0.005	0.201
preprocessFunnorm	8.689	0.381	9.151
preprocessIllumina	11.405	0.729	12.239
preprocessNoob	1.449	0.065	1.518
preprocessQuantile	1.608	0.171	1.794
preprocessRaw	9.691	0.480	10.273
preprocessSwan	0.578	0.034	0.614
qcReport	0.062	0.002	0.063
ratioConvert-methods	0.075	0.001	0.077
read.metharray	6.740	0.210	7.007
read.metharray.exp	13.935	0.305	14.368
read.metharray.sheet	0.072	0.003	0.074
readGEORawFile	0.001	0.000	0.001
readTCGA	0.001	0.000	0.001
subsetByLoci	0.532	0.040	0.577
utils	0.193	0.118	0.315