Package: rexposome

Version: 1.4.0

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_1.4.0.tar.gz

StartedAt: 2019-04-16 02:18:37 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:22:00 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 203.5 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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/rexposome.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.4.0’
* 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      29.691  0.196  30.589
plotCorrelation-methods 13.557  0.116  13.950
correlation-methods      6.797  0.131   7.007
* 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-3.8-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/3.5/Resources/library’
* installing *source* package ‘rexposome’ ...
** 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
* DONE (rexposome)

name	user	system	elapsed
classification-methods	0.018	0.006	0.025
clustering-methods	29.691	0.196	30.589
correlation-methods	6.797	0.131	7.007
ex_imp	0.032	0.002	0.035
expo	0.032	0.006	0.039
expo_c	0.015	0.003	0.018
expos-methods	0.268	0.007	0.275
exposureNames-methods	0.021	0.002	0.024
exwas-methods	0.594	0.007	0.604
familyNames-methods	0.021	0.002	0.024
highAndLow-methods	1.461	0.010	1.489
ilod-methods	0	0	0
imputation-methods	0.000	0.000	0.001
imputeLOD	0.000	0.001	0.000
loadExposome	0.068	0.001	0.069
loadImputed	0.015	0.002	0.016
me	0.002	0.001	0.004
mexwas-methods	0.237	0.006	0.245
ndim-methods	0.072	0.004	0.076
normalityTest-methods	0.354	0.008	0.370
pca-methods	0.072	0.001	0.073
phenotypeNames-methods	0.020	0.001	0.021
plotClassification-methods	0	0	0
plotCorrelation-methods	13.557	0.116	13.950
plotEXP-methods	0.422	0.005	0.464
plotEffect-methods	0.958	0.026	1.012
plotExwas-methods	0.707	0.010	0.725
plotFamily-methods	3.649	0.107	4.026
plotHistogram-methods	0.359	0.008	0.409
plotLOD-methods	0.614	0.004	0.627
plotMissings-methods	0.657	0.006	0.671
plotPCA-methods	1.946	0.010	2.106
plotPHE-methods	0.415	0.004	0.426
readExposome	0.053	0.001	0.059
standardize-methods	0.986	0.011	1.003
tableLOD-methods	0.221	0.003	0.228
tableMissings-methods	0.095	0.008	0.103
tef-methods	0.452	0.011	0.475
toES	0.155	0.002	0.158
trans-methods	0.368	0.001	0.374
volcano_plot	1.094	0.024	1.128