BioC 3.2: CHECK report for missMethyl on oaxaca

Package: missMethyl

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings missMethyl_1.4.0.tar.gz

StartedAt: 2016-04-23 02:13:27 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 02:24:10 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 643.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: missMethyl.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings missMethyl_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/missMethyl.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘missMethyl/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘missMethyl’ version ‘1.4.0’
* 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 ‘missMethyl’ can be installed ... [27s/27s] WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.2-bioc/meat/missMethyl.Rcheck/00install.out’ for details.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
SWAN.MethyLumiSet: no visible global function definition for
  ‘phenoData’
SWAN.default: no visible global function definition for ‘phenoData’
SWAN.default: no visible global function definition for
  ‘featureNames<-’
SWAN.default: no visible global function definition for ‘sampleNames<-’
gometh: no visible binding for global variable
  ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
gometh: no visible global function definition for ‘toTable’
* 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 ... [281s/365s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
gometh             82.357  7.154 133.249
SWAN               65.096  5.246  70.404
densityByProbeType 38.150  3.433  64.291
RUVadj             22.250  1.220  23.509
topRUV             21.364  1.528  38.354
RUVfit             15.547  1.147  16.702
* 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: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/missMethyl.Rcheck/00check.log’
for details.

* installing *source* package ‘missMethyl’ ...
** R
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** 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: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (missMethyl)

name	user	system	elapsed
RUVadj	22.250	1.220	23.509
RUVfit	15.547	1.147	16.702
SWAN	65.096	5.246	70.404
contrasts.varFit	0.085	0.001	0.138
densityByProbeType	38.150	3.433	64.291
getINCs	1.924	0.211	3.732
getLeveneResiduals	0.011	0.001	0.014
gometh	82.357	7.154	133.249
topRUV	21.364	1.528	38.354
topVar	0.016	0.000	0.031
varFit	0.016	0.000	0.027