BioC 2.13: CHECK report for minfi on perceval

Package: minfi

Version: 1.8.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch minfi_1.8.9.tar.gz

StartedAt: 2014-04-05 02:38:01 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:59:47 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 1305.9 seconds

RetCode: 0

Status:  OK

CheckDir: minfi.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/minfi.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [32s/32s] 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’ ‘bumphunter:::.getEstimate’
  ‘GenomicRanges:::.ShallowSimpleListAssays’
  ‘GenomicRanges:::.valid.SummarizedExperiment.colData_dims’
  ‘GenomicRanges:::clone’
  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 ... [8m/10m] OK
Examples with CPU or elapsed time > 5s
                                     user system elapsed
bumphunter                        114.769 31.539 148.911
preprocessQuantile                 66.865 13.401 147.723
detectionP                         36.152  2.496  39.035
minfiQC                            19.504  5.765  47.337
densityBeanPlot                    19.080  1.985  21.409
densityPlot                        18.647  2.306  21.318
getSex                             15.275  3.930  21.643
read.450k.exp                      15.371  1.948  19.671
preprocessIllumina                 14.306  2.175  31.127
preprocessRaw                      14.648  1.453  22.811
read.450k                          13.580  1.464  17.154
getAnnotation                      10.909  1.546  12.767
IlluminaMethylationManifest-class   5.783  0.556   6.395
fixMethOutliers                     4.906  1.299   6.277
utils                               3.329  0.966   5.007
mdsPlot                             2.898  0.636   6.592
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [308s/393s]
 [309s/393s] 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
  ‘/Users/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	0.504	0.006	0.643
GenomicRatioSet-class	0.509	0.006	0.520
IlluminaMethylationManifest-class	5.783	0.556	6.395
MethylSet-class	0.003	0.006	0.008
RGChannelSet-class	0.004	0.007	0.011
RatioSet-class	0.004	0.008	0.012
bumphunter	114.769	31.539	148.911
controlStripPlot	4.133	0.552	4.866
densityBeanPlot	19.080	1.985	21.409
densityPlot	18.647	2.306	21.318
detectionP	36.152	2.496	39.035
dmpFinder	0.468	0.083	0.551
estimateCellCounts	0.003	0.009	0.012
fixMethOutliers	4.906	1.299	6.277
getAnnotation	10.909	1.546	12.767
getQC	0.395	0.039	0.445
getSex	15.275	3.930	21.643
logit2	0.002	0.004	0.016
mdsPlot	2.898	0.636	6.592
minfiQC	19.504	5.765	47.337
plotBetasByType	0.003	0.007	0.010
plotCpg	0.733	0.070	1.490
preprocessIllumina	14.306	2.175	31.127
preprocessQuantile	66.865	13.401	147.723
preprocessRaw	14.648	1.453	22.811
preprocessSwan	0.003	0.006	0.010
qcReport	0.194	0.014	0.276
read.450k	13.580	1.464	17.154
read.450k.exp	15.371	1.948	19.671
read.450k.sheet	0.211	0.014	0.325
utils	3.329	0.966	5.007