BioC 2.14: CHECK report for minfi on morelia

Package: minfi

Version: 1.10.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch minfi_1.10.2.tar.gz

StartedAt: 2014-10-08 00:02:32 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:12:19 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 586.7 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 --no-multiarch minfi_1.10.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/minfi.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (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 ... [19s/19s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [180s/185s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
bumphunter         46.664  9.481  57.489
preprocessFunnorm  22.803  2.576  25.443
preprocessQuantile 15.649  1.784  17.457
detectionP         11.151  0.862  12.044
read.450k.exp       8.360  0.306   9.188
read.450k           6.820  0.354   7.512
densityPlot         5.451  0.676   6.159
minfiQC             5.132  0.854   6.001
densityBeanPlot     4.861  0.411   5.286
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [150s/181s]
 [150s/181s] 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
  ‘/Users/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	0.003	0.001	0.003
GenomicRatioSet-class	0.001	0.000	0.002
IlluminaMethylationManifest-class	2.825	0.190	3.336
MethylSet-class	0.002	0.000	0.001
RGChannelSet-class	0.002	0.000	0.002
RatioSet-class	0.001	0.000	0.002
bumphunter	46.664	9.481	57.489
controlStripPlot	1.666	0.109	2.116
densityBeanPlot	4.861	0.411	5.286
densityPlot	5.451	0.676	6.159
detectionP	11.151	0.862	12.044
dmpFinder	0.220	0.012	0.240
estimateCellCounts	0.001	0.000	0.001
fixMethOutliers	1.351	0.304	1.658
getAnnotation	2.432	0.257	2.722
getQC	0.218	0.009	0.227
getSex	4.036	0.422	4.476
logit2	0.000	0.000	0.001
mdsPlot	1.019	0.065	1.084
minfiQC	5.132	0.854	6.001
plotBetasByType	0.001	0.000	0.001
plotCpg	0.281	0.004	0.303
preprocessFunnorm	22.803	2.576	25.443
preprocessIllumina	3.433	0.334	3.777
preprocessQuantile	15.649	1.784	17.457
preprocessRaw	3.438	0.287	3.745
preprocessSwan	0.001	0.000	0.001
qcReport	0.084	0.003	0.086
read.450k	6.820	0.354	7.512
read.450k.exp	8.360	0.306	9.188
read.450k.sheet	0.098	0.005	0.144
utils	2.076	0.358	2.759