BioC 2.13: CHECK report for minfi on zin1

Package: minfi

Version: 1.8.9

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings minfi_1.8.9.tar.gz

StartedAt: 2014-04-05 02:26:42 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:34:07 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 444.9 seconds

RetCode: 0

Status:  OK

CheckDir: minfi.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/minfi.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.8.9’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ... [145s/146s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
bumphunter         46.139  1.092  48.059
preprocessQuantile 21.709  0.432  22.176
densityBeanPlot     8.265  0.140   8.419
minfiQC             8.169  0.004   8.184
read.450k.exp       7.188  0.052   7.334
densityPlot         6.852  0.064   6.927
read.450k           6.201  0.052   6.302
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [130s/131s]
 [130s/131s] 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 was 1 note.
See
  ‘/home/biocbuild/bbs-2.13-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	0.004	0.000	0.005
GenomicRatioSet-class	0.004	0.000	0.004
IlluminaMethylationManifest-class	2.460	0.108	2.639
MethylSet-class	0.000	0.000	0.001
RGChannelSet-class	0.000	0.000	0.002
RatioSet-class	0.000	0.000	0.002
bumphunter	46.139	1.092	48.059
controlStripPlot	1.656	0.008	1.832
densityBeanPlot	8.265	0.140	8.419
densityPlot	6.852	0.064	6.927
detectionP	4.976	0.004	4.990
dmpFinder	0.392	0.012	0.405
estimateCellCounts	0.004	0.000	0.001
fixMethOutliers	2.405	0.004	2.411
getAnnotation	1.944	0.004	1.951
getQC	0.440	0.008	0.450
getSex	3.892	0.000	3.900
logit2	0.000	0.000	0.001
mdsPlot	0.940	0.004	0.945
minfiQC	8.169	0.004	8.184
plotBetasByType	0.004	0.000	0.001
plotCpg	0.160	0.004	0.164
preprocessIllumina	4.052	0.008	4.064
preprocessQuantile	21.709	0.432	22.176
preprocessRaw	4.340	0.016	4.369
preprocessSwan	0.000	0.000	0.001
qcReport	0.068	0.004	0.076
read.450k	6.201	0.052	6.302
read.450k.exp	7.188	0.052	7.334
read.450k.sheet	0.076	0.004	0.080
utils	1.788	0.188	1.978