BioC 2.14: CHECK report for minfi on zin2

Package: minfi

Version: 1.10.2

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings minfi_1.10.2.tar.gz

StartedAt: 2014-10-08 01:05:52 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 01:12:35 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 402.9 seconds

RetCode: 0

Status:  OK

CheckDir: minfi.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings minfi_1.10.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/minfi.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘minfi/DESCRIPTION’ ... OK
* this is package ‘minfi’ version ‘1.10.2’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘Biobase’ ‘lattice’ ‘GenomicRanges’ ‘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 ... [17s/17s] 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:
  ‘Biobase:::.showAnnotatedDataFrame’
  ‘GenomicRanges:::.ShallowSimpleListAssays’
  ‘GenomicRanges:::.valid.SummarizedExperiment.colData_dims’
  ‘GenomicRanges:::clone’ ‘bumphunter:::.getEstimate’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 ... [128s/129s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
bumphunter         40.275  1.816  42.306
preprocessFunnorm  17.369  0.216  17.622
preprocessQuantile 12.629  0.100  13.082
read.450k.exp       7.088  0.008   7.111
read.450k           5.669  0.032   5.712
detectionP          5.061  0.000   5.070
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [113s/114s]
 [114s/114s] 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.14-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	2.500	0.112	2.615
MethylSet-class	0.004	0.000	0.001
RGChannelSet-class	0.000	0.000	0.001
RatioSet-class	0.000	0.000	0.002
bumphunter	40.275	1.816	42.306
controlStripPlot	1.360	0.008	1.371
densityBeanPlot	4.620	0.052	4.679
densityPlot	3.584	0.008	3.625
detectionP	5.061	0.000	5.070
dmpFinder	0.184	0.000	0.184
estimateCellCounts	0.000	0.000	0.001
fixMethOutliers	2.156	0.024	2.184
getAnnotation	1.284	0.004	1.292
getQC	0.444	0.000	0.445
getSex	2.152	0.068	2.223
logit2	0.000	0.000	0.001
mdsPlot	0.816	0.016	0.835
minfiQC	4.664	0.036	4.707
plotBetasByType	0.000	0.000	0.001
plotCpg	0.148	0.004	0.153
preprocessFunnorm	17.369	0.216	17.622
preprocessIllumina	1.816	0.000	1.816
preprocessQuantile	12.629	0.100	13.082
preprocessRaw	1.716	0.004	1.755
preprocessSwan	0.000	0.000	0.001
qcReport	0.040	0.008	0.049
read.450k	5.669	0.032	5.712
read.450k.exp	7.088	0.008	7.111
read.450k.sheet	0.056	0.004	0.063
utils	1.440	0.240	1.682