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This page was generated on 2021-09-24 15:06:54 -0400 (Fri, 24 Sep 2021).

CHECK results for rexposome on machv2

To the developers/maintainers of the rexposome package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rexposome.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1560/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rexposome 1.14.1  (landing page)
Xavier Escribà Montagut
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/rexposome
git_branch: RELEASE_3_13
git_last_commit: 8a968e3
git_last_commit_date: 2021-07-12 06:24:53 -0400 (Mon, 12 Jul 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: rexposome
Version: 1.14.1
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_1.14.1.tar.gz
StartedAt: 2021-09-23 22:45:37 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 22:49:18 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 220.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: rexposome.Rcheck
Warnings: 2

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_1.14.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/rexposome.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.14.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... WARNING
Found the following file with a non-portable file name:
  vignettes/rsconnect/documents/exposome_data_analysis.Rmd/rpubs.com/rpubs/Publish Document.dcf
These are not fully portable file names.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Found the following non-portable file path:
  rexposome/vignettes/rsconnect/documents/exposome_data_analysis.Rmd/rpubs.com/rpubs/Publish Document.dcf

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* 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 ... WARNING
'::' or ':::' imports not declared from:
  ‘ggridges’ ‘missMDA’ ‘nnet’
* 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
invExWAS,ExposomeSet : <anonymous>: no visible global function
  definition for ‘reformulate’
invExWAS,ExposomeSet : <anonymous>: no visible global function
  definition for ‘terms’
invExWAS,ExposomeSet: no visible global function definition for
  ‘reformulate’
invExWAS,ExposomeSet: no visible global function definition for ‘terms’
plotHistogram,ExposomeSet: no visible binding for global variable
  ‘..density..’
Undefined global functions or variables:
  ..density.. reformulate terms
Consider adding
  importFrom("stats", "reformulate", "terms")
to your NAMESPACE file.
* 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 LazyData ... 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      25.583  0.126  25.737
invExWAS-methods        17.156  0.129  17.306
plotCorrelation-methods 15.255  0.102  15.378
correlation-methods      5.536  0.107   5.647
* 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 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-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/4.1/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-methods0.0200.0060.025
clustering-methods25.583 0.12625.737
correlation-methods5.5360.1075.647
ex_imp0.0290.0020.030
expo0.0260.0130.038
expo_c0.0130.0020.016
expos-methods0.2010.0050.207
exposureNames-methods0.0220.0050.028
exwas-methods0.4770.0140.492
familyNames-methods0.0240.0050.029
highAndLow-methods0.9450.0110.957
ilod-methods000
imputation-methods0.0000.0000.001
imputeLOD0.0000.0000.001
invExWAS-methods17.156 0.12917.306
loadExposome0.0570.0020.060
loadExposome_plain0.0570.0020.060
loadImputed0.0170.0020.019
me0.0030.0020.004
mexwas-methods1.6140.0091.629
ndim-methods0.0940.0030.099
normalityTest-methods0.4300.0110.444
pca-methods0.1230.0030.126
phenotypeNames-methods0.0670.0040.071
plotClassification-methods0.0000.0010.000
plotCorrelation-methods15.255 0.10215.378
plotEXP-methods0.2290.0050.236
plotEffect-methods0.8320.0130.846
plotExwas-methods0.5210.0060.528
plotFamily-methods2.7910.0572.855
plotHistogram-methods0.3830.0040.388
plotLOD-methods0.4540.0040.458
plotMissings-methods0.4720.0040.478
plotPCA-methods1.1450.0181.164
plotPHE-methods0.2760.0090.285
readExposome0.0510.0010.052
standardize-methods0.9370.0080.946
tableLOD-methods0.1840.0080.192
tableMissings-methods0.0310.0040.034
tef-methods0.3520.0100.362
toES0.1760.0040.180
trans-methods0.2470.0040.251
volcano_plot0.8360.0200.857