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vanilla session in R Gui or RStudio

6 messages · Michael Friendly, Rolf Turner, Jeff Newmiller +1 more

Michael Friendly
# 
[env: Windows, R 3.6.6]

When I start R from the R Gui icon or from RStudio, I get a large number of packages loaded via a namespace. Not entirely clear where these come from.

As a result, I often run into problems updating packages because something is already loaded.  How can start a new gui session with minimal packages loaded?
R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] statmod_1.4.34   xfun_0.18        tidyselect_1.1.0 reshape2_1.4.4   purrr_0.3.4      mitools_2.4     
 [7] splines_3.6.3    lattice_0.20-41  coefplot_1.2.6   carData_3.0-4    colorspace_1.4-1 vctrs_0.3.4     
[13] generics_0.0.2   htmltools_0.5.0  yaml_2.2.1       survival_3.2-7   rlang_0.4.7      pillar_1.4.6    
[19] nloptr_1.2.2.2   glue_1.4.2       DBI_1.1.0        lifecycle_0.2.0  plyr_1.8.6       stringr_1.4.0   
[25] effects_4.2-0    munsell_0.5.0    gtable_0.3.0     evaluate_0.14    knitr_1.30       fansi_0.4.1     
[31] Rcpp_1.0.5       scales_1.1.1     useful_1.2.6     fs_1.4.2         lme4_1.1-23      packrat_0.5.0   
[37] ggplot2_3.3.2    digest_0.6.25    stringi_1.4.6    insight_0.9.6    dplyr_1.0.2      survey_4.0      
[43] grid_3.6.3       cli_2.1.0        tools_3.6.3      magrittr_1.5     tibble_3.0.4     crayon_1.3.4    
[49] pkgconfig_2.0.3  ellipsis_0.3.1   MASS_7.3-53      Matrix_1.2-18    reprex_0.3.0     assertthat_0.2.1
[55] minqa_1.2.4      rmarkdown_2.4    rstudioapi_0.11  R6_2.4.1         boot_1.3-25      nnet_7.3-14     
[61] nlme_3.1-149     compiler_3.6.3
Michael Friendly     Email: friendly AT yorku DOT ca 
Professor, Psychology Dept. & Former Chair, ASA Statistical Graphics Section
York University      Voice: 416 736-2100 x66249 
4700 Keele Street    Web: http://www.datavis.ca | @datavisFriendly
Toronto, ONT  M3J 1P3 CANADA
Jeff Newmiller
# 
Have you looked into your .Rprofile file? Loading packages is not something R normally does without your telling it to do so, but many people forget that they have done so.
On October 22, 2020 3:47:04 PM PDT, Michael L Friendly <friendly at yorku.ca> wrote:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Henrik Bengtsson
    

    

      
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As Jeff says, it might be that you have a ~/.Rprofile file with
instructions to load packages when R starts.  It could also be that
you have a .RData file, which is saved if you answer yes to:

            

      
      
      
    

        
when you quit R.   If this file exists, then R loads it and all the
objects you had when you saved it. If there are objects associated
with packages, then that will cause those packages to be loaded when R
starts.  To avoid this, you need to move or delete the .RData file.

You can use:

            

      
      
      
    

        
to get detailed information on what happens when R starts, e.g. if you
have a .Rprofile file and an .RData file.  That might help you to
track down what's going on.  The 'startup' package is on CRAN.

I don't know of an easy way to restart RGui or RStudio Console in
vanilla mode, similarly how you can start R at the terminal with 'R
--vanilla'.

/Henrik

        
On Thu, Oct 22, 2020 at 4:14 PM Jeff Newmiller <jdnewmil at dcn.davis.ca.us> wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Rolf Turner
    

    

      
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On Thu, 22 Oct 2020 18:13:11 -0700

        
Henrik Bengtsson <henrik.bengtsson at gmail.com> wrote:

        

            

      
      
      
    

        
<SNIP>

I don't believe that the forgoing is *exactly* correct.  Perhaps it
depends on what is meant by "objects associated with packages".
I have vague recollections that funny things can happen if objects
in the saved .RData file have complicated environments, but I can't
remember details.

cheers,

Rolf Turner

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Jeff Newmiller
    

    

      
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Can you be more specific about what conditions cause R to automatically load a package when a .RData file is loaded? My experience has actually been the opposite.

        
On October 22, 2020 6:13:11 PM PDT, Henrik Bengtsson <henrik.bengtsson at gmail.com> wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Henrik Bengtsson
    

    

      
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This can happens if save an object with an environment part of a package, e.g.

$ R --quiet --vanilla

            

      
      
      
    

        
<environment: namespace:Matrix>

            

      
      
      
    

        
# Loading the .RData file at startup triggers 'Matrix' to be loaded
$ R --quiet --no-init-file -e "loadedNamespaces()"

            

      
      
      
    

        
[1] "compiler"  "Matrix"    "graphics"  "utils"     "grDevices" "stats"
 [7] "datasets"  "grid"      "methods"   "base"      "lattice"

            

      
      
      
    

        
Also, if you have saved S4 objects (e.g. x <- Matrix::Matrix(0, 3,
2)), they will trigger their corresponding packages to be loaded when
"used" (e.g. print():ed) but not before.

Not saying it explains all of OPs packages - just wanted to say the
content of .RData may trigger packages being loaded.

/Henrik

        
On Thu, Oct 22, 2020 at 7:54 PM Jeff Newmiller <jdnewmil at dcn.davis.ca.us> wrote: