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CHECK report for rexposome on machv2

This page was generated on 2020-10-17 11:59:23 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE rexposome PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1469/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rexposome 1.10.0
Carles Hernandez-Ferrer
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/rexposome
Branch: RELEASE_3_11
Last Commit: ff660bc
Last Changed Date: 2020-04-27 15:09:11 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: rexposome
Version: 1.10.0
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_1.10.0.tar.gz
StartedAt: 2020-10-17 04:32:41 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:36:41 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 240.5 seconds
RetCode: 0
Status:  OK 
CheckDir: rexposome.Rcheck
Warnings: 0

Command output

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### Running 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_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/rexposome.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rexposome/DESCRIPTION’ ... OK
* this is package ‘rexposome’ version ‘1.10.0’
* 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  6.0Mb
  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 (user + system) or elapsed time > 5s
                          user system elapsed
clustering-methods      29.572  0.167  30.743
plotCorrelation-methods 16.799  0.119  17.208
correlation-methods      6.819  0.110   6.934
* 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-3.11-bioc/meat/rexposome.Rcheck/00check.log’
for details.



Installation output

rexposome.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rexposome
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘rexposome’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rexposome)

Tests output


Example timings

rexposome.Rcheck/rexposome-Ex.timings

nameusersystemelapsed
classification-methods0.0250.0070.032
clustering-methods29.572 0.16730.743
correlation-methods6.8190.1106.934
ex_imp0.0290.0020.030
expo0.0350.0190.054
expo_c0.0150.0020.018
expos-methods0.3440.0140.357
exposureNames-methods0.0300.0060.035
exwas-methods0.4670.0220.488
familyNames-methods0.0230.0030.025
highAndLow-methods1.0700.0121.083
ilod-methods000
imputation-methods0.0010.0000.001
imputeLOD000
loadExposome0.0590.0020.062
loadImputed0.0210.0020.023
me0.0050.0030.007
mexwas-methods1.8600.0101.874
ndim-methods0.1150.0050.121
normalityTest-methods0.3590.0070.367
pca-methods0.1170.0050.122
phenotypeNames-methods0.0270.0030.030
plotClassification-methods0.0000.0000.001
plotCorrelation-methods16.799 0.11917.208
plotEXP-methods0.3310.0060.339
plotEffect-methods1.0630.0171.081
plotExwas-methods0.6710.0100.682
plotFamily-methods3.0530.0623.125
plotHistogram-methods0.3840.0040.388
plotLOD-methods0.6590.0060.667
plotMissings-methods0.7680.0070.914
plotPCA-methods1.8860.0151.905
plotPHE-methods0.3520.0110.364
readExposome0.0720.0020.083
standardize-methods1.0550.0161.316
tableLOD-methods0.2690.0100.345
tableMissings-methods0.0420.0100.111
tef-methods0.4830.0240.528
toES0.2060.0050.212
trans-methods0.3530.0070.362
volcano_plot1.0410.0351.083