Package: MethylMix

Version: 2.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MethylMix_2.8.0.tar.gz

StartedAt: 2018-04-12 06:16:45 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 06:18:58 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 132.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MethylMix.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 MethylMix_2.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/MethylMix.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MethylMix/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MethylMix’ version ‘2.8.0’
* package encoding: UTF-8
* 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 ‘MethylMix’ can be installed ... 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 ... NOTE
Namespace in Imports field not imported from: ‘digest’
  All declared Imports should be used.
* 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 ... WARNING
Codoc mismatches from documentation object 'ComBat_NoFiles':
ComBat_NoFiles
  Code: function(dat, saminfo, type = "txt", write = F, covariates =
                 "all", par.prior = F, filter = F, skip = 0,
                 prior.plots = T)
  Docs: function(dat, saminfo, type = "txt", write = F, covariates =
                 "all", par.prior = T, filter = F, skip = 0,
                 prior.plots = T)
  Mismatches in argument default values:
    Name: 'par.prior' Code: F Docs: T

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
MethylMix_PlotModel 27.311  0.081  27.897
MethylMix           21.329  0.074  21.828
MethylMix_Predict   20.735  0.048  21.117
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/MethylMix.Rcheck/00check.log’
for details.

* installing *source* package ‘MethylMix’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MethylMix)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(MethylMix)
> 
> test_check("MethylMix")
Found 251 samples with both methylation and expression data.
Correlating methylation data with gene expression...

Found 9 transcriptionally predictive genes.

Starting Beta mixture modeling.
Running Beta mixture model on 9 genes and on 251 samples.
ERBB2 :  2  components are best.
FAAH :  2  components are best.
FOXD1 :  2  components are best.
ME1 :  2  components are best.
MGMT :  2  components are best.
OAS1 :  2  components are best.
SOX10 :  2  components are best.
TRAF6 :  2  components are best.
ZNF217 :  2  components are best.
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 3 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 22.341   0.132  22.812 

name	user	system	elapsed
Download_DNAmethylation	0.001	0.000	0.002
Download_GeneExpression	0.001	0.000	0.002
GetData	0.001	0.001	0.001
MethylMix	21.329	0.074	21.828
MethylMix_ModelGeneExpression	0.093	0.002	0.096
MethylMix_PlotModel	27.311	0.081	27.897
MethylMix_Predict	20.735	0.048	21.117
Preprocess_DNAmethylation	0.002	0.000	0.002
Preprocess_GeneExpression	0.000	0.001	0.001