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]: ywhen 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 at 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 at 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 at 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 at 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.
On Thu, 22 Oct 2020 18:13:11 -0700 Henrik Bengtsson <henrik.bengtsson at 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.<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 -- Honorary Research Fellow Department of Statistics University of Auckland Phone: +64-9-373-7599 ext. 88276
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:>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 at 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 at 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 at 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 at 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.
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 at 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 at 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 at 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 at 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 at 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 at 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.