BioC 3.3: CHECK report for missMethyl on linux2.bioconductor.org

Package: missMethyl

Version: 1.5.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings missMethyl_1.5.0.tar.gz

StartedAt: 2015-10-27 05:54:02 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:59:23 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 321.5 seconds

RetCode: 0

Status:  OK

CheckDir: missMethyl.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings missMethyl_1.5.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/missMethyl.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.5.0’
* 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 ... [16s/16s] 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’
Undefined global functions or variables:
  IlluminaHumanMethylation450kanno.ilmn12.hg19 featureNames<- phenoData
  sampleNames<- 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [146s/146s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
gometh             53.131  0.736  53.915
SWAN               29.805  0.096  29.931
RUVadj             15.651  0.204  15.861
densityByProbeType 13.623  0.040  13.678
topRUV             11.997  0.008  12.023
RUVfit             10.124  0.048  10.173
* 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-3.3-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	15.651	0.204	15.861
RUVfit	10.124	0.048	10.173
SWAN	29.805	0.096	29.931
contrasts.varFit	0.041	0.000	0.041
densityByProbeType	13.623	0.040	13.678
getINCs	0.265	0.008	0.273
getLeveneResiduals	0.007	0.000	0.007
gometh	53.131	0.736	53.915
topRUV	11.997	0.008	12.023
topVar	0.01	0.00	0.01
varFit	0.01	0.00	0.01