Package: rexposome

Version: 1.8.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:rexposome.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings rexposome_1.8.0.tar.gz

StartedAt: 2020-04-15 05:00:31 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:03:56 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 205.5 seconds

RetCode: 0

Status:  OK

CheckDir: rexposome.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:rexposome.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings rexposome_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/rexposome.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.8.0’
* 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      34.616  0.028  36.418
plotCorrelation-methods 12.872  0.000  12.945
correlation-methods      6.604  0.000   6.674
* 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-3.10-bioc/meat/rexposome.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL rexposome
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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	0.024	0.000	0.027
clustering-methods	34.616	0.028	36.418
correlation-methods	6.604	0.000	6.674
ex_imp	0.024	0.000	0.025
expo	0.024	0.004	0.026
expo_c	0.012	0.000	0.013
expos-methods	0.280	0.004	0.283
exposureNames-methods	0.024	0.004	0.029
exwas-methods	0.644	0.000	0.643
familyNames-methods	0.028	0.000	0.025
highAndLow-methods	1.352	0.004	1.367
ilod-methods	0.000	0.000	0.001
imputation-methods	0	0	0
imputeLOD	0	0	0
loadExposome	0.124	0.000	0.125
loadImputed	0.024	0.000	0.021
me	0.004	0.000	0.003
mexwas-methods	0.264	0.008	0.279
ndim-methods	0.084	0.000	0.082
normalityTest-methods	0.288	0.004	0.292
pca-methods	0.06	0.00	0.06
phenotypeNames-methods	0.044	0.000	0.043
plotClassification-methods	0	0	0
plotCorrelation-methods	12.872	0.000	12.945
plotEXP-methods	0.356	0.004	0.364
plotEffect-methods	1.072	0.000	1.075
plotExwas-methods	0.696	0.000	0.704
plotFamily-methods	3.664	0.036	3.706
plotHistogram-methods	0.408	0.000	0.406
plotLOD-methods	0.656	0.000	0.659
plotMissings-methods	0.716	0.004	0.722
plotPCA-methods	1.652	0.000	1.652
plotPHE-methods	0.448	0.000	0.450
readExposome	0.056	0.000	0.059
standardize-methods	0.908	0.000	0.909
tableLOD-methods	0.288	0.000	0.289
tableMissings-methods	0.064	0.000	0.065
tef-methods	0.456	0.000	0.453
toES	0.224	0.000	0.224
trans-methods	0.4	0.0	0.4
volcano_plot	1.028	0.000	1.038