Package: rexposome

Version: 1.6.0

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_1.6.0.tar.gz

StartedAt: 2019-10-16 06:10:40 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 06:15:06 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 265.6 seconds

RetCode: 0

Status:  OK

CheckDir: rexposome.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/rexposome.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.6.0’
* 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      29.390  0.332  30.602
plotCorrelation-methods 20.251  0.180  21.758
correlation-methods      9.176  0.215   9.859
* 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.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rexposome
###
##############################################################################
##############################################################################


* 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	0.017	0.008	0.025
clustering-methods	29.390	0.332	30.602
correlation-methods	9.176	0.215	9.859
ex_imp	0.048	0.004	0.055
expo	0.045	0.025	0.071
expo_c	0.017	0.007	0.026
expos-methods	0.390	0.013	0.445
exposureNames-methods	0.023	0.004	0.051
exwas-methods	0.742	0.010	0.982
familyNames-methods	0.025	0.005	0.035
highAndLow-methods	1.273	0.013	1.539
ilod-methods	0.000	0.000	0.001
imputation-methods	0.000	0.000	0.001
imputeLOD	0.000	0.000	0.001
loadExposome	0.151	0.005	0.188
loadImputed	0.028	0.003	0.036
me	0.005	0.004	0.013
mexwas-methods	0.609	0.009	0.740
ndim-methods	0.098	0.003	0.121
normalityTest-methods	0.559	0.014	0.690
pca-methods	0.090	0.002	0.110
phenotypeNames-methods	0.019	0.002	0.023
plotClassification-methods	0.001	0.000	0.001
plotCorrelation-methods	20.251	0.180	21.758
plotEXP-methods	0.497	0.009	0.542
plotEffect-methods	1.440	0.023	1.490
plotExwas-methods	1.379	0.031	1.441
plotFamily-methods	4.422	0.181	4.683
plotHistogram-methods	0.399	0.018	0.417
plotLOD-methods	0.722	0.021	0.744
plotMissings-methods	0.911	0.008	0.937
plotPCA-methods	2.340	0.012	2.658
plotPHE-methods	0.444	0.007	0.452
readExposome	0.125	0.003	0.128
standardize-methods	0.970	0.025	0.995
tableLOD-methods	0.281	0.010	0.294
tableMissings-methods	0.038	0.011	0.048
tef-methods	0.634	0.038	0.708
toES	0.165	0.005	0.169
trans-methods	0.369	0.003	0.372
volcano_plot	1.390	0.072	1.518