Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:39 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

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? 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 1584/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rexposome 1.16.0  (landing page)
Xavier Escribà Montagut
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/rexposome
git_branch: RELEASE_3_14
git_last_commit: 42df3c5
git_last_commit_date: 2021-10-26 12:36:52 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: 1.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rexposome.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rexposome_1.16.0.tar.gz
StartedAt: 2022-04-12 17:33:32 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 17:37:54 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 262.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: rexposome.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rexposome.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rexposome_1.16.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/rexposome.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.16.0’
* 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 ... 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      28.304  0.155  28.533
invExWAS-methods        20.600  0.157  21.146
plotCorrelation-methods 17.412  0.135  17.579
correlation-methods      7.332  0.096   7.434
* 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/rexposome.Rcheck/00check.log’
for details.



Installation output

rexposome.Rcheck/00install.out

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


* 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-methods0.0170.0030.020
clustering-methods28.304 0.15528.533
correlation-methods7.3320.0967.434
ex_imp0.0360.0020.039
expo0.0330.0250.127
expo_c0.0160.0040.019
expos-methods0.2890.0080.297
exposureNames-methods0.0270.0050.031
exwas-methods0.5180.0140.534
familyNames-methods0.0320.0060.037
highAndLow-methods0.8170.0110.831
ilod-methods000
imputation-methods0.0000.0010.000
imputeLOD000
invExWAS-methods20.600 0.15721.146
loadExposome0.0640.0020.067
loadExposome_plain0.0640.0020.067
loadImputed0.0270.0010.028
me0.0040.0030.007
mexwas-methods1.6740.0131.689
ndim-methods0.0860.0020.088
normalityTest-methods0.3210.0110.332
pca-methods0.1030.0030.106
phenotypeNames-methods0.0680.0080.077
plotClassification-methods000
plotCorrelation-methods17.412 0.13517.579
plotEXP-methods0.3210.0060.327
plotEffect-methods0.9640.0190.982
plotExwas-methods1.0500.0091.060
plotFamily-methods2.5800.0652.652
plotHistogram-methods0.3510.0060.357
plotLOD-methods0.5760.0070.583
plotMissings-methods0.5600.0080.568
plotPCA-methods1.4060.0161.463
plotPHE-methods0.3230.0030.327
readExposome0.0640.0010.065
standardize-methods0.7170.0070.725
tableLOD-methods0.2210.0050.226
tableMissings-methods0.0370.0060.043
tef-methods0.4510.0100.461
toES0.1370.0030.140
trans-methods0.2690.0060.276
volcano_plot0.9220.0140.940