Package: rexposome

Version: 1.5.0

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_1.5.0.tar.gz

StartedAt: 2019-04-09 03:09:46 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:12:47 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 181.1 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_1.5.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/rexposome.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.5.0’
* 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      26.972  0.019  27.008
plotCorrelation-methods 12.117  0.036  12.176
correlation-methods      6.721  0.010   6.759
* 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	0.023	0.004	0.026
clustering-methods	26.972	0.019	27.008
correlation-methods	6.721	0.010	6.759
ex_imp	0.040	0.001	0.041
expo	0.029	0.008	0.037
expo_c	0.019	0.000	0.019
expos-methods	0.757	0.004	0.764
exposureNames-methods	0.026	0.000	0.026
exwas-methods	0.603	0.004	0.623
familyNames-methods	0.022	0.000	0.022
highAndLow-methods	0.933	0.000	0.933
ilod-methods	0	0	0
imputation-methods	0	0	0
imputeLOD	0	0	0
loadExposome	0.082	0.003	0.112
loadImputed	0.014	0.000	0.014
me	0.000	0.002	0.002
mexwas-methods	0.196	0.000	0.196
ndim-methods	0.091	0.000	0.090
normalityTest-methods	0.411	0.000	0.411
pca-methods	0.074	0.000	0.075
phenotypeNames-methods	0.033	0.008	0.040
plotClassification-methods	0	0	0
plotCorrelation-methods	12.117	0.036	12.176
plotEXP-methods	0.381	0.012	0.393
plotEffect-methods	0.945	0.000	0.945
plotExwas-methods	0.541	0.000	0.540
plotFamily-methods	2.612	0.024	2.637
plotHistogram-methods	0.267	0.004	0.270
plotLOD-methods	0.557	0.004	0.561
plotMissings-methods	0.661	0.000	0.661
plotPCA-methods	1.847	0.004	1.851
plotPHE-methods	0.252	0.000	0.252
readExposome	0.037	0.000	0.036
standardize-methods	0.724	0.000	0.724
tableLOD-methods	0.258	0.000	0.258
tableMissings-methods	0.05	0.00	0.05
tef-methods	0.372	0.000	0.371
toES	0.111	0.004	0.115
trans-methods	0.213	0.000	0.213
volcano_plot	0.729	0.000	0.728