BioC 3.1: CHECK report for missMethyl on morelia

Package: missMethyl

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings missMethyl_1.2.0.tar.gz

StartedAt: 2015-10-09 04:00:21 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 04:07:15 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 414.0 seconds

RetCode: 0

Status:  OK

CheckDir: missMethyl.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 missMethyl_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/missMethyl.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.2.0’
* 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 ... [20s/20s] 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 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 ... [214s/214s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
gometh             59.347  6.281  65.696
SWAN               47.846  6.752  54.611
densityByProbeType 25.128  3.530  28.702
RUVadj             18.072  1.792  19.895
topRUV             16.648  1.911  18.568
RUVfit             14.221  1.801  16.029
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/missMethyl.Rcheck/00check.log’
for details.

* installing *source* package ‘missMethyl’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (missMethyl)

name	user	system	elapsed
RUVadj	18.072	1.792	19.895
RUVfit	14.221	1.801	16.029
SWAN	47.846	6.752	54.611
contrasts.varFit	0.079	0.005	0.092
densityByProbeType	25.128	3.530	28.702
getINCs	0.639	0.058	0.698
getLeveneResiduals	0.008	0.000	0.010
gometh	59.347	6.281	65.696
topRUV	16.648	1.911	18.568
topVar	0.011	0.000	0.010
varFit	0.010	0.000	0.011