BioC 3.5: CHECK report for minfi on oaxaca

Package: minfi

Version: 1.21.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings minfi_1.21.5.tar.gz

StartedAt: 2017-03-04 05:52:43 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 06:04:14 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 690.4 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_1.21.5.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 r72177)
* 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 ‘1.21.5’
* 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      59.405  3.336  67.281
bumphunter         32.908  7.383  41.125
read.metharray.exp  9.613  0.297   9.914
densityBeanPlot     8.517  0.718   9.240
densityPlot         7.306  0.772   8.080
minfiQC             6.989  0.659   7.652
preprocessIllumina  5.473  0.748   6.223
preprocessNoob      5.078  0.431   5.510
read.metharray      4.959  0.249   5.209
* 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	0.001	0.003
GenomicRatioSet-class	0.002	0.001	0.003
IlluminaMethylationManifest-class	2.621	0.126	2.748
MethylSet-class	0.001	0.000	0.002
RGChannelSet-class	0.001	0.001	0.002
RatioSet-class	0.001	0.000	0.002
bumphunter	32.908	7.383	41.125
combineArrays	59.405	3.336	67.281
compartments	4.298	0.533	4.834
controlStripPlot	3.427	0.310	4.150
convertArray	1.998	0.103	2.102
densityBeanPlot	8.517	0.718	9.240
densityPlot	7.306	0.772	8.080
detectionP	1.399	0.174	1.575
dmpFinder	0.358	0.013	0.371
estimateCellCounts	0.001	0.000	0.001
fixMethOutliers	0.797	0.212	1.009
gaphunter	0.124	0.002	0.179
getAnnotation	2.915	0.211	3.127
getGenomicRatioSetFromGEO	0.000	0.000	0.001
getQC	0.231	0.031	0.262
getSex	2.985	0.337	3.324
logit2	0.000	0.000	0.001
makeGenomicRatioSetFromMatrix	0.738	0.074	0.812
mapToGenome-methods	0.396	0.010	0.405
mdsPlot	1.035	0.192	1.227
minfiQC	6.989	0.659	7.652
plotBetasByType	0.000	0.000	0.001
plotCpg	0.173	0.006	0.178
preprocessFunnorm	3.329	0.260	3.613
preprocessIllumina	5.473	0.748	6.223
preprocessNoob	5.078	0.431	5.510
preprocessQuantile	0.715	0.030	0.746
preprocessRaw	4.121	0.394	4.517
preprocessSwan	0.597	0.046	0.645
qcReport	0.060	0.001	0.062
ratioConvert-methods	0.085	0.002	0.088
read.metharray	4.959	0.249	5.209
read.metharray.exp	9.613	0.297	9.914
read.metharray.sheet	0.065	0.002	0.066
readGEORawFile	0.001	0.000	0.000
readTCGA	0.001	0.000	0.001
subsetByLoci	0.469	0.036	0.505
utils	0.189	0.108	0.298