BioC 3.3: CHECK report for minfi on zin2

Package: minfi

Version: 1.18.6

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings minfi_1.18.6.tar.gz

StartedAt: 2016-10-13 04:19:38 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 04:27:44 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 486.4 seconds

RetCode: 0

Status:  OK

CheckDir: minfi.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings minfi_1.18.6.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/minfi.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.18.6’
* 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          44.900  0.008  44.968
bumphunter         33.552  0.887  34.478
compartments       26.076  0.032  26.112
read.metharray.exp  6.577  0.032   6.612
detectionP          5.725  0.000   5.735
read.metharray      5.028  0.016   5.040
densityBeanPlot     4.968  0.047   5.022
* 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-3.3-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	0.003	0.000	0.002
GenomicRatioSet-class	0.001	0.000	0.001
IlluminaMethylationManifest-class	2.536	0.048	2.583
MethylSet-class	0.002	0.000	0.001
RGChannelSet-class	0.001	0.000	0.001
RatioSet-class	0.001	0.000	0.002
bumphunter	33.552	0.887	34.478
compartments	26.076	0.032	26.112
controlStripPlot	1.451	0.024	1.612
densityBeanPlot	4.968	0.047	5.022
densityPlot	2.631	0.008	2.643
detectionP	5.725	0.000	5.735
dmpFinder	0.129	0.000	0.129
estimateCellCounts	0.001	0.000	0.000
fixMethOutliers	3.034	0.004	3.042
gaphunter	44.900	0.008	44.968
getAnnotation	0.895	0.028	0.924
getGenomicRatioSetFromGEO	0.001	0.000	0.000
getQC	0.369	0.000	0.369
getSex	1.809	0.092	1.902
logit2	0.000	0.000	0.001
makeGenomicRatioSetFromMatrix	0.710	0.000	0.711
mdsPlot	0.7	0.0	0.7
minfiQC	3.881	0.000	3.883
plotBetasByType	0	0	0
plotCpg	0.136	0.000	0.136
preprocessFunnorm	0.000	0.000	0.001
preprocessIllumina	3.235	0.000	3.237
preprocessNoob	0	0	0
preprocessQuantile	0.000	0.000	0.001
preprocessRaw	1.104	0.004	1.175
preprocessSwan	0.001	0.000	0.001
qcReport	0.030	0.008	0.037
read.450k	0	0	0
read.450k.exp	0.001	0.000	0.001
read.450k.sheet	0	0	0
read.metharray	5.028	0.016	5.040
read.metharray.exp	6.577	0.032	6.612
read.metharray.sheet	0.041	0.000	0.040
readGEORawFile	0.000	0.000	0.001
readTCGA	0.001	0.000	0.001
utils	0.558	0.004	0.563