Package: rexposome

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rexposome_1.0.0.tar.gz

StartedAt: 2018-04-12 08:36:31 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 08:40:18 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 227.1 seconds

RetCode: 0

Status:  OK

CheckDir: rexposome.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 rexposome_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/rexposome.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 ‘rexposome/DESCRIPTION’ ... OK
* this is package ‘rexposome’ version ‘1.0.0’
* 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 ‘rexposome’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.5Mb
  sub-directories of 1Mb or more:
    data      2.8Mb
    doc       7.0Mb
    extdata   2.2Mb
* 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 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
imputeLOD: multiple local function definitions for ‘faux’ with
  different formal arguments
plotHistogram,ExposomeSet: no visible binding for global variable
  ‘..density..’
Undefined global functions or variables:
  ..density..
* 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 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
clustering-methods      22.546  0.130  23.047
plotCorrelation-methods 17.462  0.128  18.612
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/rexposome.Rcheck/00check.log’
for details.

* installing *source* package ‘rexposome’ ...
** 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 (rexposome)

name	user	system	elapsed
classification-methods	0.271	0.006	0.282
clustering-methods	22.546	0.130	23.047
correlation-methods	4.437	0.032	4.528
ex_imp	0.053	0.001	0.055
expo	0.033	0.008	0.042
expo_c	0.019	0.003	0.021
expos-methods	0.042	0.002	0.044
exposureNames-methods	0.260	0.002	0.264
exwas-methods	0.568	0.015	0.596
familyNames-methods	0.016	0.002	0.019
highAndLow-methods	0.597	0.008	0.620
ilod-methods	0.000	0.000	0.001
imputation-methods	0.001	0.000	0.001
imputeLOD	0.001	0.001	0.001
loadExposome	0.370	0.002	0.377
loadImputed	0.015	0.001	0.015
me	0.003	0.002	0.005
mexwas-methods	0.664	0.015	0.696
ndim-methods	0.056	0.002	0.059
normalityTest-methods	0.092	0.008	0.102
pca-methods	0.45	0.01	0.48
phenotypeNames-methods	0.014	0.001	0.016
plotClassification-methods	0.001	0.000	0.001
plotCorrelation-methods	17.462	0.128	18.612
plotEXP-methods	0.903	0.006	0.928
plotEffect-methods	1.739	0.015	1.788
plotExwas-methods	0.903	0.006	0.936
plotFamily-methods	2.825	0.053	2.953
plotHistogram-methods	0.281	0.005	0.291
plotLOD-methods	1.058	0.019	1.097
plotMissings-methods	0.676	0.005	0.700
plotPCA-methods	1.688	0.007	1.741
plotPHE-methods	0.332	0.004	0.346
readExposome	0.105	0.002	0.108
standardize-methods	0.193	0.010	0.203
tableLOD-methods	0.196	0.002	0.201
tableMissings-methods	0.044	0.002	0.047
tef-methods	0.593	0.009	0.607
toES	0.125	0.004	0.130
trans-methods	0.065	0.002	0.067
volcano_plot	0.717	0.009	0.737