Multiple platform build/check report for BioC 3.9 - CHECK report for rexposome on celaya2

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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) (2019-03-18 r76245)
* 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      28.903  0.318  30.069
plotCorrelation-methods 17.911  0.426  19.071
correlation-methods      8.443  0.449   8.894
* 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.

Installation output

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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)

Tests output

Example timings

name	user	system	elapsed
classification-methods	0.026	0.013	0.040
clustering-methods	28.903	0.318	30.069
correlation-methods	8.443	0.449	8.894
ex_imp	0.046	0.003	0.049
expo	0.040	0.017	0.057
expo_c	0.012	0.005	0.018
expos-methods	0.372	0.012	0.382
exposureNames-methods	0.023	0.012	0.035
exwas-methods	0.912	0.031	0.943
familyNames-methods	0.030	0.009	0.039
highAndLow-methods	1.105	0.011	1.115
ilod-methods	0.000	0.000	0.001
imputation-methods	0	0	0
imputeLOD	0.000	0.001	0.000
loadExposome	0.153	0.006	0.203
loadImputed	0.031	0.003	0.037
me	0.005	0.004	0.011
mexwas-methods	0.427	0.008	0.516
ndim-methods	0.090	0.005	0.122
normalityTest-methods	0.621	0.016	0.667
pca-methods	0.102	0.005	0.107
phenotypeNames-methods	0.021	0.004	0.025
plotClassification-methods	0	0	0
plotCorrelation-methods	17.911	0.426	19.071
plotEXP-methods	0.481	0.008	0.598
plotEffect-methods	1.250	0.089	1.356
plotExwas-methods	0.898	0.022	0.920
plotFamily-methods	3.426	0.120	3.610
plotHistogram-methods	0.373	0.008	0.381
plotLOD-methods	0.683	0.015	0.698
plotMissings-methods	0.765	0.008	0.786
plotPCA-methods	2.490	0.071	2.625
plotPHE-methods	0.549	0.007	0.556
readExposome	0.070	0.001	0.072
standardize-methods	0.940	0.024	0.966
tableLOD-methods	0.249	0.005	0.264
tableMissings-methods	0.038	0.018	0.057
tef-methods	0.601	0.039	0.677
toES	0.181	0.004	0.185
trans-methods	0.393	0.005	0.399
volcano_plot	1.365	0.070	1.462

CHECK report for rexposome on celaya2

Summary

Command output

Installation output

Tests output

Example timings