##############################################################################
##############################################################################
###
### 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_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/rexposome.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rexposome/DESCRIPTION’ ... OK
* this is package ‘rexposome’ version ‘1.30.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ... INFO
  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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ExposomeCorr-class.Rd: eSet-class, eSet, AssayData,
    AnnotatedDataFrame
  ExposomePCA-class.Rd: eSet, AnnotatedDataFrame
  ExposomeSet-class.Rd: eSet, AssayData, AnnotatedDataFrame
  correlation-methods.Rd: cramersV
  exposureNames-methods.Rd: featureNames, eSet
  ilod-methods.Rd: impute.MinProb
  pca-methods.Rd: FactoMineR
  plotCorrelation-methods.Rd: corrplot
  rexposome.Rd: impute
  volcano_plot.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
clustering-methods      16.023  0.184  16.324
invExWAS-methods        12.957  0.127  13.195
plotCorrelation-methods 11.067  0.118  11.253
* 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-3.21-bioc/meat/rexposome.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘rexposome’ ...
** this is package ‘rexposome’ version ‘1.30.0’
** 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)