Disconnect all packages while running in R

Question

While working on a solution to another problem, I had this problem:

I can delete all R objects with:

rm(list = ls(all = TRUE)) 

Is there an equivalent command that can disable installed packages during a working session?

 > sessionInfo() R version 2.12.2 (2011-02-25) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base 

required (ggplot2)

 Loading required package: ggplot2 Loading required package: reshape Loading required package: plyr Attaching package: 'reshape' The following object(s) are masked from 'package:plyr': round_any Loading required package: grid Loading required package: proto 

sessionInfo ()

 R version 2.12.2 (2011-02-25) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] ggplot2_0.8.9 proto_0.3-9.1 reshape_0.8.4 plyr_1.4 

I tried this way, although even it did not work in a global solution:

 pkg <- c("package:ggplot2_0.8.9", "package:proto_0.3-9.1", "package:reshape_0.8.4", "package:plyr_1.4") detach(pkg, character.only = TRUE) Error in detach(pkg, character.only = TRUE) : invalid 'name' argument In addition: Warning message: In if (is.na(pos)) stop("invalid 'name' argument") : the condition has length > 1 and only the first element will be used 

What I'm looking for is something global:

  rm(list = ls(all = TRUE)) 

for objects, expect it to not remove attached base packages

thank;

Answer 1

So, someone just had to answer the following.

 lapply(paste('package:',names(sessionInfo()$otherPkgs),sep=""),detach,character.only=TRUE,unload=TRUE) 

(edit: 6-28-19) In the latest version of R 3.6.0, use instead.

 invisible(lapply(paste0('package:', names(sessionInfo()$otherPkgs)), detach, character.only=TRUE, unload=TRUE)) 

Note that using invisible (*) is optional, but may be useful to prevent vertical spam in the NULL response message.

Answer 2

Please try the following:

 detachAllPackages <- function() { basic.packages <- c("package:stats","package:graphics","package:grDevices","package:utils","package:datasets","package:methods","package:base") package.list <- search()[ifelse(unlist(gregexpr("package:",search()))==1,TRUE,FALSE)] package.list <- setdiff(package.list,basic.packages) if (length(package.list)>0) for (package in package.list) detach(package, character.only=TRUE) } detachAllPackages() 

Answer 3

You were close. Note that ?detach should say about the first argument to name detach() :

Arguments:

 name: The object to detach. Defaults to 'search()[pos]'. This can be an unquoted name or a character string but _not_ a character vector. If a number is supplied this is taken as 'pos'. 

Therefore, we need to repeatedly call detach() once per item from pkg . There are several other arguments that we need to specify in order to make this work. The first character.only = TRUE , which allows the function to assume that name is a character string - without it, it will not work. Secondly, we also probably want to unload any associated namespace. This can be achieved by setting unload = TRUE . Thus, there is a solution, for example:

 pkg <- c("package:vegan","package:permute") lapply(pkg, detach, character.only = TRUE, unload = TRUE) 

Here is a complete example:

 > require(vegan) Loading required package: vegan Loading required package: permute This is vegan 2.0-0 > sessionInfo() R version 2.13.1 Patched (2011-09-13 r57007) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C [3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8 [7] LC_PAPER=en_GB.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods [7] base other attached packages: [1] vegan_2.0-0 permute_0.7-0 loaded via a namespace (and not attached): [1] grid_2.13.1 lattice_0.19-33 tools_2.13.1 > pkg <- c("package:vegan","package:permute") > lapply(pkg, detach, character.only = TRUE, unload = TRUE) [[1]] NULL [[2]] NULL > sessionInfo() R version 2.13.1 Patched (2011-09-13 r57007) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C [3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8 [7] LC_PAPER=en_GB.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods [7] base loaded via a namespace (and not attached): [1] grid_2.13.1 lattice_0.19-33 tools_2.13.1 

If you want to turn this into a function, examine the code in sessionInfo() to find out how it identifies what it means as "other attached packages:". Combine this bit of code with the idea above in one function and you are at home and dry. I will leave it to you, though.

Answer 4

nothing

It might be worth adding a solution made by Romain François . When you download the nothing package, which is currently available on GitHub , it will unload all downloaded packages; as in the example that Romain provides:

 loadedNamespaces() [1] "base" "datasets" "grDevices" "graphics" "methods" "stats" [7] "utils" require(nothing, quietly = TRUE) loadedNamespaces() [1] "base" 

Installation

Using the devtools package:

 devtools::install_github("romainfrancois/nothing") 

pacman

An alternative approach uses the pacman package available through CRAN:

 pacman::p_unload(pacman::p_loaded(), character.only = TRUE) 

Answer 5

Building Gavin's answer, but not a complete function, would be as follows:

 sess.pkgs <- function (package = NULL) { z <- list() if (is.null(package)) { package <- grep("^package:", search(), value = TRUE) keep <- sapply(package, function(x) x == "package:base" || !is.null(attr(as.environment(x), "path"))) package <- sub("^package:", "", package[keep]) } pkgDesc <- lapply(package, packageDescription) if (length(package) == 0) stop("no valid packages were specified") basePkgs <- sapply(pkgDesc, function(x) !is.null(x$Priority) && x$Priority == "base") z$basePkgs <- package[basePkgs] if (any(!basePkgs)) { z$otherPkgs <- package[!basePkgs] } z } lapply(paste("package:",sess.pkgs()$otherPkgs, sep=""), detach, character.only = TRUE, unload = TRUE) 

Answer 6

or if you have RStudio, just uncheck all the boxes in the Packages tab to disconnect

Answer 7

In most cases, the problem is with plyr vs dplyr . Use this at the beginning of the code:

 detach("package:plyr", unload=TRUE) 

Therefore, whenever a script is executed, it clears the plyr package

Answer 8

If you have problems with packages whose functions with the same name conflict with each other, you can always refer to the namespace of the package whose function you want.

 pkg_name::function_i_want()