BioC 3.3: CHECK report for minfi on linux2.bioconductor.org

Package: minfi

Version: 1.17.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings minfi_1.17.0.tar.gz

StartedAt: 2015-10-27 05:49:48 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:02:44 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 775.3 seconds

RetCode: 0

Status:  OK

CheckDir: minfi.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings minfi_1.17.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/minfi.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.17.0’
* 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 ... [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:
  ‘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 ... [394s/394s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
gaphunter     263.864  0.200 264.245
bumphunter     38.854  1.650  40.557
compartments   31.546  0.025  31.607
read.450k.exp   6.427  0.016   6.444
detectionP      6.313  0.000   6.324
read.450k       5.820  0.024   5.848
minfiQC         5.331  0.008   5.339
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [180s/209s]
 [180s/209s] 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-3.3-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	0.000	0.003
GenomicRatioSet-class	0.001	0.000	0.002
IlluminaMethylationManifest-class	2.454	0.079	2.541
MethylSet-class	0.001	0.001	0.001
RGChannelSet-class	0.001	0.000	0.001
RatioSet-class	0	0	0
bumphunter	38.854	1.650	40.557
compartments	31.546	0.025	31.607
controlStripPlot	1.461	0.023	1.486
densityBeanPlot	3.618	0.036	3.659
densityPlot	3.486	0.005	3.496
detectionP	6.313	0.000	6.324
dmpFinder	0.164	0.000	0.164
estimateCellCounts	0.001	0.000	0.001
fixMethOutliers	1.693	0.004	1.697
gaphunter	263.864	0.200	264.245
getAnnotation	0.823	0.032	0.854
getGenomicRatioSetFromGEO	0	0	0
getQC	0.483	0.000	0.483
getSex	2.194	0.060	2.253
logit2	0.000	0.000	0.001
makeGenomicRatioSetFromMatrix	1.228	0.004	1.232
mdsPlot	0.346	0.008	0.353
minfiQC	5.331	0.008	5.339
plotBetasByType	0.001	0.000	0.001
plotCpg	0.163	0.000	0.164
preprocessFunnorm	0.001	0.000	0.000
preprocessIllumina	2.511	0.000	2.511
preprocessNoob	0.001	0.000	0.001
preprocessQuantile	0.001	0.000	0.001
preprocessRaw	1.683	0.000	1.683
preprocessSwan	0.001	0.000	0.000
qcReport	0.036	0.000	0.036
read.450k	5.820	0.024	5.848
read.450k.exp	6.427	0.016	6.444
read.450k.sheet	0.037	0.000	0.037
readGEORawFile	0	0	0
readTCGA	0.001	0.000	0.001
utils	1.387	0.200	1.593