BioC 3.2: CHECK report for missMethyl on zin1

Package: missMethyl

Version: 1.3.2

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings missMethyl_1.3.2.tar.gz

StartedAt: 2015-08-24 01:45:54 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 01:51:40 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 345.7 seconds

RetCode: 0

Status:  OK

CheckDir: missMethyl.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings missMethyl_1.3.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/missMethyl.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ‘1.3.2’
* 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 ... [19s/19s] 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 ... [163s/163s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
gometh             55.612  1.610  57.362
SWAN               33.116  0.235  33.423
RUVadj             18.192  0.467  18.689
densityByProbeType 16.280  0.097  16.379
RUVfit             13.558  0.012  13.617
topRUV             13.456  0.023  13.528
* 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
  ‘/home/biocbuild/bbs-3.2-bioc/meat/missMethyl.Rcheck/00check.log’
for details.

* installing *source* package ‘missMethyl’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (missMethyl)

name	user	system	elapsed
RUVadj	18.192	0.467	18.689
RUVfit	13.558	0.012	13.617
SWAN	33.116	0.235	33.423
contrasts.varFit	0.055	0.000	0.055
densityByProbeType	16.280	0.097	16.379
getINCs	0.451	0.007	0.460
getLeveneResiduals	0.008	0.000	0.012
gometh	55.612	1.610	57.362
topRUV	13.456	0.023	13.528
topVar	0.012	0.000	0.012
varFit	0.012	0.000	0.012