Back to Multiple platform build/check report for BioC 3.9
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

CHECK report for rexposome on merida2

This page was generated on 2019-04-09 13:35:27 -0400 (Tue, 09 Apr 2019).

Package 1333/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rexposome 1.5.0
Carles Hernandez-Ferrer
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/rexposome
Branch: master
Last Commit: 8850ab7
Last Changed Date: 2018-10-30 11:54:38 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: rexposome
Version: 1.5.0
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_1.5.0.tar.gz
StartedAt: 2019-04-09 03:17:05 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:20:22 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 196.7 seconds
RetCode: 0
Status:  OK 
CheckDir: rexposome.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/rexposome.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.5.0’
* 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  5.8Mb
  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      28.436  0.162  29.128
plotCorrelation-methods 14.671  0.119  15.239
correlation-methods      7.724  0.127   8.088
* 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-3.9-bioc/meat/rexposome.Rcheck/00check.log’
for details.



Installation output

rexposome.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rexposome
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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

rexposome.Rcheck/rexposome-Ex.timings

nameusersystemelapsed
classification-methods0.0210.0070.028
clustering-methods28.436 0.16229.128
correlation-methods7.7240.1278.088
ex_imp0.0350.0020.036
expo0.0400.0110.051
expo_c0.0160.0040.020
expos-methods0.3060.0090.321
exposureNames-methods0.0220.0020.024
exwas-methods0.7340.0210.763
familyNames-methods0.0230.0030.026
highAndLow-methods0.9690.0060.981
ilod-methods0.0010.0000.000
imputation-methods000
imputeLOD000
loadExposome0.1080.0020.111
loadImputed0.0170.0020.018
me0.0030.0020.006
mexwas-methods0.2430.0020.247
ndim-methods0.1030.0010.105
normalityTest-methods0.4140.0070.422
pca-methods0.0680.0020.070
phenotypeNames-methods0.0180.0010.019
plotClassification-methods0.0000.0010.000
plotCorrelation-methods14.671 0.11915.239
plotEXP-methods0.4550.0060.532
plotEffect-methods0.9370.0150.991
plotExwas-methods0.7000.0130.722
plotFamily-methods3.3480.1903.625
plotHistogram-methods0.3180.0080.334
plotLOD-methods0.5630.0050.576
plotMissings-methods0.6200.0060.635
plotPCA-methods2.0850.0252.154
plotPHE-methods0.3890.0030.407
readExposome0.0490.0010.050
standardize-methods0.9370.0170.959
tableLOD-methods0.2410.0060.249
tableMissings-methods0.0610.0080.071
tef-methods0.4480.0170.535
toES0.1230.0030.126
trans-methods0.3370.0020.348
volcano_plot1.0260.0261.154