Package: rexposome

Version: 1.0.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings rexposome_1.0.0.tar.gz

StartedAt: 2018-04-12 02:21:34 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:24:54 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 199.4 seconds

RetCode: 0

Status:  OK

CheckDir: rexposome.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings rexposome_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/rexposome.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.0.0’
* 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 10.6Mb
  sub-directories of 1Mb or more:
    data      2.8Mb
    doc       5.1Mb
    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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
clustering-methods      20.608  0.016  20.644
plotCorrelation-methods 13.096  0.028  13.135
* 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-3.6-bioc/meat/rexposome.Rcheck/00check.log’
for details.

* installing *source* package ‘rexposome’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing 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	0.068	0.000	0.067
clustering-methods	20.608	0.016	20.644
correlation-methods	3.644	0.008	3.651
ex_imp	0.044	0.000	0.045
expo	0.016	0.008	0.028
expo_c	0.012	0.004	0.017
expos-methods	0.036	0.004	0.039
exposureNames-methods	0.024	0.000	0.024
exwas-methods	0.804	0.004	0.807
familyNames-methods	0.020	0.004	0.022
highAndLow-methods	0.564	0.000	0.564
ilod-methods	0	0	0
imputation-methods	0.000	0.000	0.001
imputeLOD	0	0	0
loadExposome	0.132	0.000	0.131
loadImputed	0.016	0.000	0.014
me	0.000	0.004	0.003
mexwas-methods	0.524	0.000	0.523
ndim-methods	0.068	0.000	0.068
normalityTest-methods	0.100	0.000	0.099
pca-methods	0.360	0.000	0.361
phenotypeNames-methods	0.028	0.000	0.030
plotClassification-methods	0.004	0.000	0.001
plotCorrelation-methods	13.096	0.028	13.135
plotEXP-methods	0.708	0.000	0.708
plotEffect-methods	1.372	0.000	1.373
plotExwas-methods	0.824	0.000	0.824
plotFamily-methods	2.980	0.012	2.995
plotHistogram-methods	0.300	0.004	0.304
plotLOD-methods	0.920	0.004	0.926
plotMissings-methods	0.540	0.000	0.541
plotPCA-methods	1.352	0.000	1.353
plotPHE-methods	0.296	0.000	0.297
readExposome	0.116	0.000	0.114
standardize-methods	0.556	0.000	0.556
tableLOD-methods	0.304	0.000	0.304
tableMissings-methods	0.064	0.000	0.063
tef-methods	0.628	0.000	0.628
toES	0.088	0.000	0.090
trans-methods	0.056	0.000	0.056
volcano_plot	0.592	0.004	0.597