Package: rexposome

Version: 1.5.0

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_1.5.0.tar.gz

StartedAt: 2019-04-09 03:17:05 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:20:22 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 196.7 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_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/rexposome.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.5.0’
* 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      28.436  0.162  29.128
plotCorrelation-methods 14.671  0.119  15.239
correlation-methods      7.724  0.127   8.088
* 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-3.9-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’ ...
** 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	0.021	0.007	0.028
clustering-methods	28.436	0.162	29.128
correlation-methods	7.724	0.127	8.088
ex_imp	0.035	0.002	0.036
expo	0.040	0.011	0.051
expo_c	0.016	0.004	0.020
expos-methods	0.306	0.009	0.321
exposureNames-methods	0.022	0.002	0.024
exwas-methods	0.734	0.021	0.763
familyNames-methods	0.023	0.003	0.026
highAndLow-methods	0.969	0.006	0.981
ilod-methods	0.001	0.000	0.000
imputation-methods	0	0	0
imputeLOD	0	0	0
loadExposome	0.108	0.002	0.111
loadImputed	0.017	0.002	0.018
me	0.003	0.002	0.006
mexwas-methods	0.243	0.002	0.247
ndim-methods	0.103	0.001	0.105
normalityTest-methods	0.414	0.007	0.422
pca-methods	0.068	0.002	0.070
phenotypeNames-methods	0.018	0.001	0.019
plotClassification-methods	0.000	0.001	0.000
plotCorrelation-methods	14.671	0.119	15.239
plotEXP-methods	0.455	0.006	0.532
plotEffect-methods	0.937	0.015	0.991
plotExwas-methods	0.700	0.013	0.722
plotFamily-methods	3.348	0.190	3.625
plotHistogram-methods	0.318	0.008	0.334
plotLOD-methods	0.563	0.005	0.576
plotMissings-methods	0.620	0.006	0.635
plotPCA-methods	2.085	0.025	2.154
plotPHE-methods	0.389	0.003	0.407
readExposome	0.049	0.001	0.050
standardize-methods	0.937	0.017	0.959
tableLOD-methods	0.241	0.006	0.249
tableMissings-methods	0.061	0.008	0.071
tef-methods	0.448	0.017	0.535
toES	0.123	0.003	0.126
trans-methods	0.337	0.002	0.348
volcano_plot	1.026	0.026	1.154