Package: rexposome

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rexposome.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rexposome_1.2.0.tar.gz

StartedAt: 2018-05-25 02:09:33 -0400 (Fri, 25 May 2018)

EndedAt: 2018-05-25 02:13:41 -0400 (Fri, 25 May 2018)

EllapsedTime: 247.9 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 --install=check:rexposome.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rexposome_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/rexposome.Rcheck’
* using R version 3.5.0 (2018-04-23)
* 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 ‘1.2.0’
* 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  5.9Mb
  sub-directories of 1Mb or more:
    data      2.8Mb
    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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
clustering-methods      27.303  0.234  27.756
plotCorrelation-methods 18.376  0.114  18.602
correlation-methods      5.801  0.099   5.941
* 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-3.7-bioc/meat/rexposome.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rexposome
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘rexposome’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare 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	0.016	0.005	0.021
clustering-methods	27.303	0.234	27.756
correlation-methods	5.801	0.099	5.941
ex_imp	0.034	0.002	0.036
expo	0.035	0.009	0.044
expo_c	0.026	0.002	0.028
expos-methods	0.052	0.005	0.056
exposureNames-methods	0.024	0.007	0.031
exwas-methods	0.435	0.018	0.455
familyNames-methods	0.022	0.002	0.023
highAndLow-methods	0.557	0.005	0.566
ilod-methods	0.001	0.000	0.001
imputation-methods	0.001	0.000	0.002
imputeLOD	0.002	0.000	0.001
loadExposome	0.057	0.001	0.059
loadImputed	0.024	0.002	0.026
me	0.005	0.002	0.007
mexwas-methods	0.293	0.003	0.295
ndim-methods	0.150	0.003	0.153
normalityTest-methods	0.080	0.006	0.087
pca-methods	0.078	0.003	0.080
phenotypeNames-methods	0.019	0.001	0.020
plotClassification-methods	0.001	0.000	0.002
plotCorrelation-methods	18.376	0.114	18.602
plotEXP-methods	0.356	0.005	0.368
plotEffect-methods	0.770	0.022	0.801
plotExwas-methods	0.535	0.007	0.549
plotFamily-methods	2.901	0.100	3.024
plotHistogram-methods	0.285	0.005	0.292
plotLOD-methods	0.542	0.009	0.557
plotMissings-methods	0.691	0.010	0.709
plotPCA-methods	1.700	0.006	1.718
plotPHE-methods	0.337	0.003	0.344
readExposome	0.056	0.001	0.057
standardize-methods	0.142	0.011	0.153
tableLOD-methods	0.152	0.003	0.155
tableMissings-methods	0.078	0.005	0.083
tef-methods	0.300	0.022	0.326
toES	0.136	0.003	0.141
trans-methods	0.082	0.008	0.092
volcano_plot	0.777	0.034	0.817