[R] vanilla session in R Gui or RStudio

Fri Oct 23 05:11:37 CEST 2020

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

$ R --quiet --vanilla
> fcn <- Matrix::Matrix
> environment(fcn)
<environment: namespace:Matrix>
> quit("yes")  # saves the workspace in an .RData file

# Loading the .RData file at startup triggers 'Matrix' to be loaded
$ R --quiet --no-init-file -e "loadedNamespaces()"
> 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 using dcn.davis.ca.us> wrote:
>
> 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 using gmail.com> wrote:
> >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:
> >
> >> Save workspace image? [y/n/c]: y
> >
> >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:
> >
> >> startup::startup(debug = TRUE, dryrun = TRUE)
> >
> >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 using dcn.davis.ca.us> wrote:
> >>
> >> 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 using yorku.ca> wrote:
> >> >[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?
> >> >
> >> >> sessionInfo()
> >> >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
> >> >
> >> >______________________________________________
> >> >R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >> >https://stat.ethz.ch/mailman/listinfo/r-help
> >> >PLEASE do read the posting guide
> >> >http://www.R-project.org/posting-guide.html
> >> >and provide commented, minimal, self-contained, reproducible code.
> >>
> >> --
> >> Sent from my phone. Please excuse my brevity.
> >>
> >> ______________________________________________
> >> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide
> >http://www.R-project.org/posting-guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
>
> --
> Sent from my phone. Please excuse my brevity.