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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:rexposome.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings rexposome_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/rexposome.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘rexposome/DESCRIPTION’ ... OK
* this is package ‘rexposome’ version ‘1.22.0’
* 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  5.3Mb
  sub-directories of 1Mb or more:
    data      2.8Mb
    extdata   1.8Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
  ‘ggridges’ ‘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 ... OK
* 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 documentation object 'ExWAS':
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 documentation object 'ExposomeSet'
  ‘robust’

Undocumented arguments in documentation object 'exwas'
  ‘robust’

Undocumented arguments in documentation object 'imExposomeSet'
  ‘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 ... ERROR
Running examples in ‘rexposome-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotHistogram
> ### Title: It draws a histogram for each exposure in an ExposomeSet
> ### Aliases: plotHistogram
> 
> ### ** Examples
> 
> data("exposome")
> plotHistogram(expo[1:3, ], select = "ldde_lip")
Error in loadNamespace(x) : there is no package called ‘ggridges’
Calls: plotHistogram ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘exposome_data_analysis.Rmd’ using ‘UTF-8’... OK
  ‘mutiple_imputation_data_analysis.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘exposome_data_analysis.Rmd’ using rmarkdown
Warning in eng_r(options) :
  Failed to tidy R code in chunk 'github'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'library'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'files_path'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'ags_read_exposome'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'read_exposome'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'show_es_1'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'ags_load_exposome'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'read_csv_files'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'set_dd_rownames'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'set_ee_rownames'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'set_pp, rownames'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'load_exposome'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'individuals_names'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'exposures_names'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'families_names'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'phenotype_names'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'feature'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'phenotype'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'exposures'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'misssing_data_table'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'missing_exposures_plot'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/rexposome.Rcheck/vign_test/rexposome/vignettes/exposome_data_analysis_files/figure-html/missing_exposures_plot-1.png" but not available.
Warning in eng_r(options) :
  Failed to tidy R code in chunk 'normality'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'no_normality'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'histogram_cleaning'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/rexposome.Rcheck/vign_test/rexposome/vignettes/exposome_data_analysis_files/figure-html/histogram_cleaning-1.png" but not available.
Warning in eng_r(options) :
  Failed to tidy R code in chunk 'histogram_no_normal'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.


Quitting from lines 334-336 [histogram_no_normal] (exposome_data_analysis.Rmd)
Error: processing vignette 'exposome_data_analysis.Rmd' failed with diagnostics:
there is no package called 'ggridges'
--- failed re-building ‘exposome_data_analysis.Rmd’

--- re-building ‘mutiple_imputation_data_analysis.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/rexposome.Rcheck/vign_test/rexposome/vignettes/mutiple_imputation_data_analysis_files/figure-html/plot_family_continuous-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/rexposome.Rcheck/vign_test/rexposome/vignettes/mutiple_imputation_data_analysis_files/figure-html/plot_family_categorical-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/rexposome.Rcheck/vign_test/rexposome/vignettes/mutiple_imputation_data_analysis_files/figure-html/plot_exwas-1.png" but not available.
--- finished re-building ‘mutiple_imputation_data_analysis.Rmd’

SUMMARY: processing the following file failed:
  ‘exposome_data_analysis.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 5 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/rexposome.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL rexposome
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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)