Package: rexposome

Version: 1.9.0

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_1.9.0.tar.gz

StartedAt: 2020-01-16 08:08:13 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 08:12:40 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 267.2 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_1.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/rexposome.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.9.0’
* 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 (user + system) or elapsed time > 5s
                          user system elapsed
clustering-methods      28.361  0.318  29.499
plotCorrelation-methods 16.777  0.480  17.701
correlation-methods      8.454  0.358   9.085
* 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-3.11-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/4.0/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	0.023	0.010	0.034
clustering-methods	28.361	0.318	29.499
correlation-methods	8.454	0.358	9.085
ex_imp	0.036	0.003	0.038
expo	0.031	0.013	0.043
expo_c	0.014	0.005	0.019
expos-methods	0.391	0.014	0.406
exposureNames-methods	0.021	0.004	0.024
exwas-methods	0.806	0.047	0.875
familyNames-methods	0.025	0.004	0.029
highAndLow-methods	1.280	0.011	1.318
ilod-methods	0.000	0.000	0.001
imputation-methods	0.001	0.001	0.001
imputeLOD	0.000	0.000	0.001
loadExposome	0.134	0.004	0.140
loadImputed	0.028	0.003	0.030
me	0.005	0.004	0.008
mexwas-methods	0.455	0.006	0.461
ndim-methods	0.213	0.003	0.217
normalityTest-methods	0.330	0.013	0.344
pca-methods	0.100	0.004	0.105
phenotypeNames-methods	0.017	0.003	0.020
plotClassification-methods	0.000	0.000	0.001
plotCorrelation-methods	16.777	0.480	17.701
plotEXP-methods	0.505	0.020	0.529
plotEffect-methods	1.138	0.042	1.180
plotExwas-methods	0.973	0.035	1.007
plotFamily-methods	3.408	0.124	3.544
plotHistogram-methods	0.384	0.010	0.395
plotLOD-methods	1.147	0.043	1.191
plotMissings-methods	0.854	0.033	0.889
plotPCA-methods	1.977	0.008	1.987
plotPHE-methods	0.344	0.007	0.351
readExposome	0.048	0.002	0.049
standardize-methods	0.881	0.028	0.909
tableLOD-methods	0.270	0.018	0.289
tableMissings-methods	0.034	0.012	0.046
tef-methods	0.588	0.035	0.623
toES	0.228	0.006	0.234
trans-methods	0.537	0.032	0.569
volcano_plot	1.176	0.066	1.245