Multiple platform build/check report for BioC 3.8 - CHECK report for rexposome on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:rexposome.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings rexposome_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/rexposome.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rexposome/DESCRIPTION’ ... OK
* this is package ‘rexposome’ version ‘1.4.0’
* 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      26.480  0.028  26.539
plotCorrelation-methods 11.044  0.036  11.094
correlation-methods      6.036  0.000   6.042
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/rexposome.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL rexposome
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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)

Tests output

Example timings

name	user	system	elapsed
classification-methods	0.016	0.004	0.021
clustering-methods	26.480	0.028	26.539
correlation-methods	6.036	0.000	6.042
ex_imp	0.048	0.000	0.047
expo	0.036	0.012	0.046
expo_c	0.016	0.004	0.019
expos-methods	0.364	0.004	0.371
exposureNames-methods	0.024	0.000	0.023
exwas-methods	0.496	0.000	0.495
familyNames-methods	0.020	0.000	0.019
highAndLow-methods	1.36	0.00	1.36
ilod-methods	0	0	0
imputation-methods	0	0	0
imputeLOD	0	0	0
loadExposome	0.064	0.000	0.080
loadImputed	0.024	0.000	0.022
me	0.004	0.000	0.004
mexwas-methods	0.272	0.000	0.273
ndim-methods	0.056	0.000	0.056
normalityTest-methods	0.328	0.008	0.339
pca-methods	0.088	0.000	0.088
phenotypeNames-methods	0.024	0.000	0.025
plotClassification-methods	0	0	0
plotCorrelation-methods	11.044	0.036	11.094
plotEXP-methods	0.428	0.004	0.434
plotEffect-methods	0.736	0.000	0.737
plotExwas-methods	0.468	0.000	0.471
plotFamily-methods	2.528	0.020	2.548
plotHistogram-methods	0.232	0.000	0.233
plotLOD-methods	0.420	0.004	0.422
plotMissings-methods	0.48	0.00	0.48
plotPCA-methods	1.316	0.000	1.320
plotPHE-methods	0.260	0.000	0.262
readExposome	0.036	0.000	0.035
standardize-methods	0.696	0.000	0.697
tableLOD-methods	0.204	0.000	0.205
tableMissings-methods	0.024	0.000	0.026
tef-methods	0.344	0.000	0.344
toES	0.136	0.000	0.135
trans-methods	0.272	0.000	0.269
volcano_plot	1.088	0.012	1.106

CHECK report for rexposome on malbec1

Summary

Command output

Installation output

Tests output

Example timings