BioC 3.6: CHECK report for rexposome on malbec1

Package: rexposome

Version: 0.99.90

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings rexposome_0.99.90.tar.gz

StartedAt: 2017-08-16 01:54:31 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:57:53 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 201.4 seconds

RetCode: 0

Status:  OK

CheckDir: rexposome.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings rexposome_0.99.90.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/rexposome.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘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  7.3Mb
  sub-directories of 1Mb or more:
    data      2.8Mb
    doc       1.8Mb
    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 14.024  0.016  14.047
clustering-methods      10.956  0.040  11.169
* 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	0.016	0.004	0.018
clustering-methods	10.956	0.040	11.169
correlation-methods	4.14	0.00	4.14
ex_imp	0.044	0.000	0.043
expo	0.020	0.004	0.024
expo_c	0.012	0.004	0.016
expos-methods	0.032	0.000	0.034
exposureNames-methods	0.020	0.000	0.021
exwas-methods	0.512	0.004	0.517
familyNames-methods	0.024	0.004	0.025
highAndLow-methods	0.604	0.000	0.604
ilod-methods	0.000	0.000	0.001
imputation-methods	0.000	0.000	0.001
imputeLOD	0	0	0
loadExposome	0.04	0.00	0.04
loadImputed	0.012	0.000	0.013
me	0.000	0.000	0.002
mexwas-methods	0.480	0.000	0.482
ndim-methods	0.052	0.000	0.052
normalityTest-methods	0.100	0.000	0.102
pca-methods	0.352	0.000	0.353
phenotypeNames-methods	0.036	0.000	0.037
plotClassification-methods	0.000	0.000	0.001
plotCorrelation-methods	14.024	0.016	14.047
plotEXP-methods	0.676	0.004	0.680
plotEffect-methods	1.252	0.004	1.257
plotExwas-methods	0.512	0.000	0.516
plotFamily-methods	2.568	0.020	2.591
plotHistogram-methods	0.204	0.000	0.206
plotLOD-methods	0.936	0.000	0.934
plotMissings-methods	0.752	0.000	0.754
plotPCA-methods	1.200	0.000	1.201
plotPHE-methods	0.276	0.000	0.275
readExposome	0.076	0.000	0.078
standardize-methods	0.164	0.000	0.165
tableLOD-methods	0.220	0.004	0.225
tableMissings-methods	0.060	0.000	0.061
tef-methods	0.320	0.000	0.319
toES	0.092	0.000	0.093
trans-methods	0.452	0.000	0.453
volcano_plot	0.516	0.000	0.518