BioC 3.4: CHECK report for minfi on malbec1

Package: minfi

Version: 1.20.2

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings minfi_1.20.2.tar.gz

StartedAt: 2017-04-14 23:52:18 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-15 00:01:14 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 536.0 seconds

RetCode: 0

Status:  OK

CheckDir: minfi.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings minfi_1.20.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/minfi.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘minfi/DESCRIPTION’ ... OK
* this is package ‘minfi’ version ‘1.20.2’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘Biobase’ ‘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 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      56.716  3.604  60.959
bumphunter         30.716  0.772  31.602
read.metharray.exp  8.212  0.016   8.233
densityBeanPlot     6.964  0.140   7.108
read.metharray      5.680  0.016   5.700
preprocessIllumina  5.236  0.184   5.429
* 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
  ‘/home/biocbuild/bbs-3.4-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	0.000	0.000	0.002
GenomicRatioSet-class	0.000	0.000	0.001
IlluminaMethylationManifest-class	2.780	0.068	2.846
MethylSet-class	0.000	0.000	0.001
RGChannelSet-class	0.000	0.000	0.001
RatioSet-class	0.000	0.000	0.002
bumphunter	30.716	0.772	31.602
combineArrays	56.716	3.604	60.959
compartments	3.116	0.008	3.127
controlStripPlot	2.116	0.072	2.394
convertArray	1.104	0.000	1.107
densityBeanPlot	6.964	0.140	7.108
densityPlot	3.080	0.064	3.143
detectionP	0.220	0.000	0.218
dmpFinder	0.128	0.000	0.131
estimateCellCounts	0.000	0.000	0.001
fixMethOutliers	2.116	0.000	2.120
gaphunter	0.080	0.000	0.095
getAnnotation	0.920	0.004	0.926
getGenomicRatioSetFromGEO	0.004	0.000	0.000
getQC	0.208	0.000	0.208
getSex	2.316	0.024	2.340
logit2	0	0	0
makeGenomicRatioSetFromMatrix	0.652	0.000	0.652
mapToGenome-methods	0.200	0.000	0.201
mdsPlot	1.240	0.024	1.265
minfiQC	4.316	0.024	4.343
plotBetasByType	0.000	0.000	0.001
plotCpg	0.164	0.000	0.166
preprocessFunnorm	1.868	0.072	1.956
preprocessIllumina	5.236	0.184	5.429
preprocessNoob	0.612	0.000	0.614
preprocessQuantile	0.332	0.000	0.331
preprocessRaw	2.860	0.000	2.864
preprocessSwan	0.500	0.000	0.501
qcReport	0.072	0.000	0.073
ratioConvert-methods	0.1	0.0	0.1
read.metharray	5.680	0.016	5.700
read.metharray.exp	8.212	0.016	8.233
read.metharray.sheet	0.068	0.000	0.069
readGEORawFile	0	0	0
readTCGA	0.000	0.000	0.001
subsetByLoci	0.348	0.000	0.349
utils	0.104	0.024	0.129