Package: rexposome

Version: 1.6.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:rexposome.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings rexposome_1.6.0.tar.gz

StartedAt: 2019-10-16 04:28:57 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:31:48 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 171.1 seconds

RetCode: 0

Status:  OK

CheckDir: rexposome.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:rexposome.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings rexposome_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/rexposome.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.6.0’
* 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  5.9Mb
  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      25.675  0.032  25.708
plotCorrelation-methods  9.598  0.008   9.606
correlation-methods      5.377  0.008   5.385
* 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-3.9-bioc/meat/rexposome.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL rexposome
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* installing to library ‘/home/biocbuild/bbs-3.9-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	0.015	0.004	0.019
clustering-methods	25.675	0.032	25.708
correlation-methods	5.377	0.008	5.385
ex_imp	0.027	0.000	0.027
expo	0.021	0.004	0.025
expo_c	0.010	0.004	0.014
expos-methods	0.545	0.000	0.545
exposureNames-methods	0.018	0.000	0.018
exwas-methods	0.358	0.000	0.358
familyNames-methods	0.019	0.000	0.019
highAndLow-methods	0.829	0.000	0.829
ilod-methods	0.001	0.000	0.000
imputation-methods	0	0	0
imputeLOD	0	0	0
loadExposome	0.079	0.008	0.102
loadImputed	0.010	0.004	0.014
me	0.002	0.000	0.003
mexwas-methods	0.211	0.000	0.211
ndim-methods	0.049	0.000	0.049
normalityTest-methods	0.337	0.004	0.341
pca-methods	0.081	0.000	0.081
phenotypeNames-methods	0.023	0.000	0.023
plotClassification-methods	0.001	0.000	0.000
plotCorrelation-methods	9.598	0.008	9.606
plotEXP-methods	0.273	0.000	0.272
plotEffect-methods	0.693	0.004	0.697
plotExwas-methods	0.615	0.000	0.615
plotFamily-methods	3.899	0.032	3.930
plotHistogram-methods	0.337	0.012	0.349
plotLOD-methods	0.653	0.020	0.673
plotMissings-methods	0.678	0.004	0.682
plotPCA-methods	1.842	0.000	1.842
plotPHE-methods	0.272	0.000	0.272
readExposome	0.034	0.000	0.034
standardize-methods	0.698	0.000	0.698
tableLOD-methods	0.328	0.000	0.328
tableMissings-methods	0.035	0.000	0.035
tef-methods	0.622	0.004	0.626
toES	0.088	0.000	0.087
trans-methods	0.22	0.00	0.22
volcano_plot	0.674	0.000	0.675