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This page was generated on 2024-06-11 15:42 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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

Package 1694/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rexposome 1.27.0  (landing page)
Xavier Escribà Montagut
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/rexposome
git_branch: devel
git_last_commit: 03f5c48
git_last_commit_date: 2024-04-30 10:59:30 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for rexposome on merida1

To the developers/maintainers of the rexposome package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: rexposome
Version: 1.27.0
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_1.27.0.tar.gz
StartedAt: 2024-06-10 08:45:48 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 08:52:12 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 383.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: rexposome.Rcheck
Warnings: 5

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_1.27.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/rexposome.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rexposome/DESCRIPTION’ ... OK
* this is package ‘rexposome’ version ‘1.27.0’
* 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 ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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:
  ‘missMDA’ ‘nnet’ ‘sandwich’
* 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 : <anonymous>: no visible global function
  definition for ‘confint’
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.. confint reformulate terms
Consider adding
  importFrom("stats", "confint", "reformulate", "terms")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) exwas-methods.Rd:50: Lost braces
    50 | An code{ExWAS} object with the result of the association study
       |        ^
checkRd: (-1) invExWAS-methods.Rd:31: Lost braces
    31 | An code{ExWAS} object with the result of the association study
       |        ^
checkRd: (-1) standardize-methods.Rd:13: Lost braces
    13 | #' @param object code{ExposomeSet} with 'set' will be summarized.
       |                      ^
* checking Rd metadata ... WARNING
Rd files with duplicated alias 'extract':
  ‘extract-methods.Rd’ ‘get_robust_sd-methods.Rd’
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
S4 class codoc mismatches from Rd file 'ExWAS-class.Rd':
Slots for class 'ExWAS'
  Code: comparison description effective formula robust.std.err
  Docs: comparison description effective formula

* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'ExposomeSet-class.Rd'
  ‘robust’

Undocumented arguments in Rd file 'exwas-methods.Rd'
  ‘robust’

Undocumented arguments in Rd file 'imExposomeSet-class.Rd'
  ‘robust’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
invExWAS-methods        27.369  0.208  31.313
clustering-methods      26.797  0.248  28.975
plotCorrelation-methods 24.913  0.209  27.327
correlation-methods      9.517  0.117  10.520
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-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/4.4-x86_64/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-methods0.0230.0090.034
clustering-methods26.797 0.24828.975
correlation-methods 9.517 0.11710.520
ex_imp0.0350.0030.039
expo0.0330.0290.069
expo_c0.0150.0040.022
expos-methods0.3570.0060.395
exposureNames-methods0.0530.0110.065
exwas-methods0.7370.0120.874
familyNames-methods0.0240.0090.039
highAndLow-methods1.2540.0141.478
ilod-methods0.0000.0010.001
imputation-methods0.0000.0010.000
imputeLOD0.0000.0010.000
invExWAS-methods27.369 0.20831.313
loadExposome0.0850.0040.094
loadExposome_plain0.0850.0040.094
loadImputed0.0340.0040.038
me0.0040.0050.009
mexwas-methods1.5900.0181.650
ndim-methods0.0990.0040.130
normalityTest-methods0.4230.0210.528
pca-methods0.1270.0040.162
phenotypeNames-methods0.0230.0070.035
plotClassification-methods0.0000.0010.000
plotCorrelation-methods24.913 0.20927.327
plotEXP-methods0.5070.0100.580
plotEffect-methods1.2070.0201.372
plotExwas-methods0.8970.0131.031
plotFamily-methods4.2750.1004.620
plotHistogram-methods0.8700.0160.939
plotLOD-methods0.8450.0120.904
plotMissings-methods1.0050.0111.048
plotPCA-methods2.5900.0282.798
plotPHE-methods0.5350.0090.597
readExposome0.0860.0030.101
standardize-methods1.0660.0171.174
tableLOD-methods0.2890.0130.331
tableMissings-methods0.0340.0090.049
tef-methods0.5120.0140.581
toES0.2960.0100.335
trans-methods0.3420.0070.380
volcano_plot1.3880.0231.552