BioC 3.3: CHECK report for minfi on oaxaca

Package: minfi

Version: 1.18.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings minfi_1.18.6.tar.gz

StartedAt: 2016-10-13 03:43:06 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 03:54:11 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 665.8 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_1.18.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/minfi.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.18.6’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘Biobase’ ‘lattice’ ‘GenomicRanges’
  ‘SummarizedExperiment’ ‘Biostrings’ ‘bumphunter’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 objects imported by ':::' calls:
  ‘BiocGenerics:::replaceSlots’
  ‘SummarizedExperiment:::.valid.SummarizedExperiment.assays_ncol’
  ‘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
gaphunter          50.546  0.343  50.973
bumphunter         35.149  5.710  40.952
compartments       31.753  2.045  33.854
detectionP         24.303  0.623  24.965
read.metharray.exp 15.803  0.415  16.311
read.metharray     11.078  0.436  11.532
preprocessIllumina  8.231  0.327   8.589
densityBeanPlot     6.294  0.253   6.558
densityPlot         5.758  0.526   6.531
preprocessRaw       4.981  0.157   5.156
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-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	0.002	0.000	0.002
GenomicRatioSet-class	0.002	0.000	0.003
IlluminaMethylationManifest-class	2.632	0.135	2.770
MethylSet-class	0.002	0.000	0.003
RGChannelSet-class	0.002	0.000	0.001
RatioSet-class	0.002	0.000	0.002
bumphunter	35.149	5.710	40.952
compartments	31.753	2.045	33.854
controlStripPlot	2.348	0.088	2.701
densityBeanPlot	6.294	0.253	6.558
densityPlot	5.758	0.526	6.531
detectionP	24.303	0.623	24.965
dmpFinder	0.137	0.009	0.146
estimateCellCounts	0.001	0.000	0.001
fixMethOutliers	2.234	0.298	2.535
gaphunter	50.546	0.343	50.973
getAnnotation	1.788	0.102	1.896
getGenomicRatioSetFromGEO	0.001	0.001	0.001
getQC	0.182	0.007	0.189
getSex	3.388	0.375	3.775
logit2	0.000	0.000	0.001
makeGenomicRatioSetFromMatrix	1.114	0.075	1.189
mdsPlot	0.860	0.154	1.762
minfiQC	4.386	0.501	4.894
plotBetasByType	0.001	0.000	0.001
plotCpg	0.287	0.002	0.290
preprocessFunnorm	0.000	0.000	0.001
preprocessIllumina	8.231	0.327	8.589
preprocessNoob	0	0	0
preprocessQuantile	0.001	0.000	0.001
preprocessRaw	4.981	0.157	5.156
preprocessSwan	0.001	0.000	0.001
qcReport	0.059	0.001	0.060
read.450k	0.001	0.000	0.001
read.450k.exp	0.001	0.000	0.001
read.450k.sheet	0	0	0
read.metharray	11.078	0.436	11.532
read.metharray.exp	15.803	0.415	16.311
read.metharray.sheet	0.082	0.002	0.085
readGEORawFile	0	0	0
readTCGA	0.000	0.000	0.001
utils	0.661	0.198	0.861