Package: rexposome

Version: 1.8.0

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_1.8.0.tar.gz

StartedAt: 2020-04-15 05:06:20 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:09:50 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 210.1 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 --install=check:rexposome.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rexposome_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/rexposome.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.8.0’
* 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 ‘rexposome’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.8Mb
  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      29.274  0.212  30.908
plotCorrelation-methods 13.889  0.148  14.377
correlation-methods      6.923  0.105   7.205
* 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-3.10-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/3.6/Resources/library’
* installing *source* package ‘rexposome’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rexposome)

name	user	system	elapsed
classification-methods	0.042	0.005	0.049
clustering-methods	29.274	0.212	30.908
correlation-methods	6.923	0.105	7.205
ex_imp	0.038	0.002	0.041
expo	0.048	0.010	0.058
expo_c	0.015	0.004	0.018
expos-methods	0.340	0.008	0.367
exposureNames-methods	0.051	0.007	0.061
exwas-methods	0.525	0.008	0.534
familyNames-methods	0.038	0.003	0.042
highAndLow-methods	1.065	0.013	1.103
ilod-methods	0	0	0
imputation-methods	0.000	0.000	0.001
imputeLOD	0	0	0
loadExposome	0.066	0.001	0.075
loadImputed	0.022	0.002	0.024
me	0.004	0.002	0.007
mexwas-methods	0.316	0.005	0.325
ndim-methods	0.070	0.002	0.071
normalityTest-methods	0.397	0.004	0.410
pca-methods	0.120	0.002	0.130
phenotypeNames-methods	0.018	0.001	0.019
plotClassification-methods	0	0	0
plotCorrelation-methods	13.889	0.148	14.377
plotEXP-methods	0.323	0.007	0.339
plotEffect-methods	0.809	0.010	0.822
plotExwas-methods	0.732	0.004	0.788
plotFamily-methods	3.557	0.145	3.811
plotHistogram-methods	0.326	0.006	0.335
plotLOD-methods	0.543	0.008	0.553
plotMissings-methods	0.646	0.004	0.658
plotPCA-methods	1.563	0.009	1.582
plotPHE-methods	0.372	0.003	0.378
readExposome	0.050	0.001	0.050
standardize-methods	1.070	0.011	1.151
tableLOD-methods	0.220	0.005	0.230
tableMissings-methods	0.057	0.004	0.062
tef-methods	0.377	0.018	0.397
toES	0.169	0.003	0.173
trans-methods	0.293	0.006	0.300
volcano_plot	1.331	0.042	1.422