BioC 3.3: CHECK report for minfi on morelia

Package: minfi

Version: 1.17.10

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings minfi_1.17.10.tar.gz

StartedAt: 2016-04-21 05:03:29 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 05:13:39 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 609.8 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 minfi_1.17.10.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/minfi.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘minfi/DESCRIPTION’ ... OK
* this is package ‘minfi’ version ‘1.17.10’
* 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 ... [22s/22s] 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.SummarizedExperiment.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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [189s/190s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
gaphunter          44.291  0.406  44.741
bumphunter         34.867  8.039  42.966
compartments       33.288  1.759  35.064
detectionP          9.278  0.507   9.787
read.metharray.exp  6.613  0.283   6.905
preprocessIllumina  5.380  0.450   5.839
read.metharray      5.254  0.262   5.523
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [210s/210s]
 [210s/210s] 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
  ‘/Users/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	0.002	0.001	0.002
GenomicRatioSet-class	0.001	0.000	0.001
IlluminaMethylationManifest-class	2.234	0.108	2.341
MethylSet-class	0.001	0.000	0.001
RGChannelSet-class	0.001	0.000	0.001
RatioSet-class	0.001	0.000	0.002
bumphunter	34.867	8.039	42.966
compartments	33.288	1.759	35.064
controlStripPlot	1.438	0.079	1.791
densityBeanPlot	4.255	0.286	4.545
densityPlot	3.264	0.384	3.650
detectionP	9.278	0.507	9.787
dmpFinder	0.113	0.008	0.122
estimateCellCounts	0.000	0.000	0.001
fixMethOutliers	0.798	0.204	1.003
gaphunter	44.291	0.406	44.741
getAnnotation	1.824	0.100	1.926
getGenomicRatioSetFromGEO	0.001	0.000	0.000
getQC	0.394	0.055	0.449
getSex	2.909	0.210	3.123
logit2	0	0	0
makeGenomicRatioSetFromMatrix	1.245	0.151	1.398
mdsPlot	0.476	0.011	0.487
minfiQC	4.196	0.513	4.711
plotBetasByType	0.001	0.001	0.001
plotCpg	0.218	0.006	0.225
preprocessFunnorm	0.001	0.000	0.001
preprocessIllumina	5.380	0.450	5.839
preprocessNoob	0.001	0.000	0.000
preprocessQuantile	0.001	0.000	0.001
preprocessRaw	2.754	0.148	2.904
preprocessSwan	0.001	0.000	0.000
qcReport	0.057	0.001	0.060
read.450k	0.000	0.000	0.001
read.450k.exp	0.001	0.000	0.000
read.450k.sheet	0	0	0
read.metharray	5.254	0.262	5.523
read.metharray.exp	6.613	0.283	6.905
read.metharray.sheet	0.072	0.002	0.074
readGEORawFile	0.000	0.000	0.001
readTCGA	0.001	0.001	0.001
utils	0.147	0.066	0.213