BioC 3.6: CHECK report for rexposome on veracruz1

Package: rexposome

Version: 0.99.90

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rexposome_0.99.90.tar.gz

StartedAt: 2017-08-16 07:41:13 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 07:44:52 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 218.7 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 --no-vignettes --timings rexposome_0.99.90.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/rexposome.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘0.99.90’
* 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  8.3Mb
  sub-directories of 1Mb or more:
    data      2.8Mb
    doc       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 loading without being on the library search path ... 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
plotCorrelation-methods 16.851  0.079  17.368
clustering-methods      12.508  0.106  13.124
* 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-3.6-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	0.024	0.004	0.029
clustering-methods	12.508	0.106	13.124
correlation-methods	4.545	0.046	4.706
ex_imp	0.047	0.002	0.049
expo	0.022	0.004	0.027
expo_c	0.013	0.003	0.015
expos-methods	0.033	0.000	0.034
exposureNames-methods	0.016	0.004	0.020
exwas-methods	0.586	0.009	0.603
familyNames-methods	0.017	0.001	0.019
highAndLow-methods	0.553	0.003	0.572
ilod-methods	0.000	0.000	0.001
imputation-methods	0.000	0.000	0.001
imputeLOD	0	0	0
loadExposome	0.043	0.001	0.044
loadImputed	0.021	0.002	0.021
me	0.002	0.001	0.003
mexwas-methods	0.539	0.004	0.563
ndim-methods	0.051	0.001	0.052
normalityTest-methods	0.106	0.003	0.116
pca-methods	0.459	0.001	0.484
phenotypeNames-methods	0.016	0.000	0.016
plotClassification-methods	0.000	0.000	0.001
plotCorrelation-methods	16.851	0.079	17.368
plotEXP-methods	0.875	0.005	0.907
plotEffect-methods	1.654	0.010	1.694
plotExwas-methods	0.720	0.005	0.732
plotFamily-methods	3.612	0.069	3.733
plotHistogram-methods	0.302	0.006	0.328
plotLOD-methods	0.762	0.008	0.804
plotMissings-methods	0.636	0.004	0.653
plotPCA-methods	1.682	0.005	1.715
plotPHE-methods	0.342	0.003	0.353
readExposome	0.112	0.001	0.114
standardize-methods	0.205	0.007	0.218
tableLOD-methods	0.189	0.002	0.199
tableMissings-methods	0.039	0.001	0.040
tef-methods	0.315	0.011	0.327
toES	0.107	0.001	0.108
trans-methods	0.069	0.002	0.072
volcano_plot	0.724	0.006	0.751