Multiple platform build/check report for BioC 3.7 - CHECK report for rexposome on malbec2

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:rexposome.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings rexposome_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/rexposome.Rcheck’
* using R version 3.5.0 (2018-04-23)
* 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 ‘1.2.0’
* 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      19.6  0.008  19.623
plotCorrelation-methods 11.9  0.012  11.933
* 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-3.7-bioc/meat/rexposome.Rcheck/00check.log’
for details.

Installation output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL rexposome
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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)

Tests output

Example timings

name	user	system	elapsed
classification-methods	0.020	0.000	0.018
clustering-methods	19.600	0.008	19.623
correlation-methods	3.788	0.012	3.805
ex_imp	0.024	0.000	0.025
expo	0.024	0.008	0.034
expo_c	0.012	0.000	0.013
expos-methods	0.040	0.000	0.038
exposureNames-methods	0.020	0.004	0.023
exwas-methods	0.320	0.004	0.326
familyNames-methods	0.020	0.000	0.021
highAndLow-methods	0.504	0.004	0.508
ilod-methods	0	0	0
imputation-methods	0.004	0.000	0.000
imputeLOD	0	0	0
loadExposome	0.06	0.00	0.08
loadImputed	0.024	0.000	0.023
me	0.008	0.000	0.005
mexwas-methods	0.288	0.000	0.288
ndim-methods	0.048	0.000	0.049
normalityTest-methods	0.088	0.000	0.087
pca-methods	0.056	0.000	0.055
phenotypeNames-methods	0.016	0.000	0.017
plotClassification-methods	0	0	0
plotCorrelation-methods	11.900	0.012	11.933
plotEXP-methods	0.236	0.000	0.233
plotEffect-methods	0.828	0.004	0.832
plotExwas-methods	0.340	0.000	0.341
plotFamily-methods	1.956	0.032	1.991
plotHistogram-methods	0.196	0.000	0.200
plotLOD-methods	0.412	0.016	0.428
plotMissings-methods	0.396	0.000	0.397
plotPCA-methods	1.112	0.004	1.119
plotPHE-methods	0.248	0.000	0.251
readExposome	0.036	0.000	0.036
standardize-methods	0.124	0.004	0.128
tableLOD-methods	0.180	0.000	0.179
tableMissings-methods	0.048	0.000	0.047
tef-methods	0.284	0.000	0.283
toES	0.100	0.000	0.101
trans-methods	0.044	0.000	0.044
volcano_plot	0.576	0.000	0.576

CHECK report for rexposome on malbec2

Summary

Command output

Installation output

Tests output

Example timings