BioC 3.3: CHECK report for minfi on morelia

Package: minfi

Version: 1.17.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings minfi_1.17.0.tar.gz

StartedAt: 2015-10-22 08:27:04 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 08:37:25 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 620.7 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_1.17.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/minfi.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.17.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [282s/283s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
gaphunter     154.782  1.581 156.476
bumphunter     31.055  7.147  38.215
compartments   26.287  1.596  27.890
detectionP      8.780  0.599   9.386
read.450k.exp   5.861  0.353   6.225
read.450k       5.589  0.258   5.850
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [171s/171s]
 [172s/172s] 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
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : Error in 'rgl_init'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : Error in 'rgl_init'
* DONE (minfi)

name	user	system	elapsed
GenomicMethylSet-class	0.002	0.001	0.002
GenomicRatioSet-class	0.001	0.000	0.001
IlluminaMethylationManifest-class	2.153	0.129	2.283
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	31.055	7.147	38.215
compartments	26.287	1.596	27.890
controlStripPlot	1.223	0.062	1.749
densityBeanPlot	3.844	0.296	4.144
densityPlot	4.071	0.520	4.596
detectionP	8.780	0.599	9.386
dmpFinder	0.104	0.007	0.111
estimateCellCounts	0	0	0
fixMethOutliers	0.559	0.105	0.664
gaphunter	154.782	1.581	156.476
getAnnotation	1.519	0.107	1.627
getGenomicRatioSetFromGEO	0	0	0
getQC	0.139	0.007	0.146
getSex	2.541	0.290	2.836
logit2	0.000	0.000	0.001
makeGenomicRatioSetFromMatrix	1.070	0.129	1.199
mdsPlot	0.493	0.063	0.557
minfiQC	3.683	0.434	4.119
plotBetasByType	0	0	0
plotCpg	0.182	0.009	0.193
preprocessFunnorm	0.001	0.000	0.000
preprocessIllumina	3.016	0.233	3.253
preprocessNoob	0.000	0.000	0.001
preprocessQuantile	0.000	0.000	0.001
preprocessRaw	2.361	0.223	2.585
preprocessSwan	0.001	0.000	0.001
qcReport	0.056	0.002	0.058
read.450k	5.589	0.258	5.850
read.450k.exp	5.861	0.353	6.225
read.450k.sheet	0.046	0.001	0.048
readGEORawFile	0	0	0
readTCGA	0.001	0.000	0.001
utils	1.348	0.265	1.613