BioC 3.2: CHECK report for minfi on linux1.bioconductor.org

Package: minfi

Version: 1.16.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings minfi_1.16.0.tar.gz

StartedAt: 2015-10-27 05:44:53 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:58:44 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 830.4 seconds

RetCode: 0

Status:  OK

CheckDir: minfi.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings minfi_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/minfi.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.16.0’
* 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 ... [21s/21s] 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.SummarizedExperiment0.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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [388s/388s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
gaphunter     265.398  0.085 265.730
bumphunter     38.085  1.187  39.328
compartments   28.600  0.027  28.684
detectionP      6.635  0.001   6.644
read.450k       5.812  0.012   5.829
read.450k.exp   5.139  0.020   5.165
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [205s/237s]
 [205s/237s] 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-3.2-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	0.002	0.000	0.002
GenomicRatioSet-class	0.001	0.000	0.001
IlluminaMethylationManifest-class	2.698	0.083	2.782
MethylSet-class	0.001	0.000	0.001
RGChannelSet-class	0.001	0.000	0.001
RatioSet-class	0.001	0.000	0.001
bumphunter	38.085	1.187	39.328
compartments	28.600	0.027	28.684
controlStripPlot	1.488	0.004	1.493
densityBeanPlot	3.486	0.028	3.527
densityPlot	2.268	0.012	2.283
detectionP	6.635	0.001	6.644
dmpFinder	0.192	0.000	0.191
estimateCellCounts	0.001	0.000	0.001
fixMethOutliers	2.274	0.011	2.287
gaphunter	265.398	0.085	265.730
getAnnotation	0.692	0.016	0.707
getGenomicRatioSetFromGEO	0.000	0.000	0.001
getQC	0.334	0.008	0.342
getSex	1.466	0.048	1.516
logit2	0	0	0
makeGenomicRatioSetFromMatrix	0.815	0.012	0.826
mdsPlot	0.451	0.000	0.452
minfiQC	4.553	0.004	4.561
plotBetasByType	0	0	0
plotCpg	0.19	0.00	0.19
preprocessFunnorm	0	0	0
preprocessIllumina	2.390	0.004	2.395
preprocessNoob	0	0	0
preprocessQuantile	0.000	0.000	0.001
preprocessRaw	1.762	0.000	1.762
preprocessSwan	0.001	0.000	0.000
qcReport	0.047	0.000	0.046
read.450k	5.812	0.012	5.829
read.450k.exp	5.139	0.020	5.165
read.450k.sheet	0.048	0.000	0.048
readGEORawFile	0.000	0.000	0.001
readTCGA	0	0	0
utils	1.083	0.172	1.256