detach all packages while working in R
RWorkspaceR Problem Overview
While working to solve another problem I got this problem:
I can remove all R objects by:
rm(list = ls(all = TRUE))
Is there equivalent command that can detach installed packages during 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
> require(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 worked in not 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 am loking for is something global like:
rm(list = ls(all = TRUE))
for objects, expect it would not remove attached base packages
thanks;
R Solutions
Solution 1 - R
So, someone should have simply answered the following.
lapply(paste('package:',names(sessionInfo()$otherPkgs),sep=""),detach,character.only=TRUE,unload=TRUE)
(edit: 6-28-19) In the latest version of R 3.6.0 please use instead.
invisible(lapply(paste0('package:', names(sessionInfo()$otherPkgs)), detach, character.only=TRUE, unload=TRUE))
Note the use of invisible(*) is not necessary but can be useful to prevent the NULL reply from vertically spamming the R window.
(edit: 9/20/2019) In version 3.6.1
It may be helpful to convert loaded only names(sessionInfo()$loadedOnly) to explicitly attached packages first, and then detach the packages, as so.
lapply(names(sessionInfo()$loadedOnly), require, character.only = TRUE)
invisible(lapply(paste0('package:', names(sessionInfo()$otherPkgs)), detach, character.only=TRUE, unload=TRUE, force=TRUE))
One can attempt to unload base packages via $basePkgs and also attempt using unloadNamespace(loadedNamespaces()). However these typically are fraught with errors and could break basic functionality such as causing sessionInfo() to return only errors. This typically occurs because of a lack of reversibility in the original package's design. Currently timeDate can break irreversibly, for example.
(edit: 9/24/20) for version 4.0.2 The following first loads packages to test and then gives a sequence to fully detach all packages except for package "base" and "utils". It is highly recommended that one does not detach those packages.
invisible(suppressMessages(suppressWarnings(lapply(c("gsl","fBasics","stringr","stringi","Rmpfr"), require, character.only = TRUE))))
invisible(suppressMessages(suppressWarnings(lapply(names(sessionInfo()$loadedOnly), require, character.only = TRUE))))
sessionInfo()
#the above is a test
invisible(lapply(paste0('package:', c("stringr","fBasics")), detach, character.only=TRUE,unload=TRUE))
#In the line above, I have inserted by hand what I know the package dependencies to be. A user must know this a priori or have their own automated
#method to discover it. Without removing dependencies first, the user will have to cycle through loading namespaces and then detaching otherPkgs a
#second time through.
invisible(lapply(paste0('package:', names(sessionInfo()$otherPkgs)), detach, character.only=TRUE,unload=TRUE))
bspkgs.nb<-sessionInfo()$basePkgs[sessionInfo()$basePkgs!="base"]
bspkgs.nbu<-bspkgs.nb[bspkgs.nb!="utils"]
names(bspkgs.nbu)<-bspkgs.nbu
suppressMessages(invisible(lapply(paste0('package:', names(bspkgs.nbu)), detach, character.only=TRUE,unload=TRUE)))
#again this thoroughly removes all packages and loaded namespaces except for base packages "base" and "utils" (which is highly not recommended).
Solution 2 - R
Please try this:
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()
Solution 3 - R
You were close. Note what ?detach has to say about the first argument name of 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’.
So we need to repeatedly call detach() once per element of pkg. There are a couple of other arguments we need to specify to get this to work. The first is character.only = TRUE, which allows the function to assume that name is a character string - it won't work without it. Second, we also probably want to unload any associated namespace. This can be achieved by setting unload = TRUE. So the solution is, for example:
pkg <- c("package:vegan","package:permute")
lapply(pkg, detach, character.only = TRUE, unload = TRUE)
Here is a full 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, study the code in sessionInfo() to see how it identifies what it labels as "other attached packages:". Combine that bit of code with the idea above in a single function and you are home and dry. I'll leave that bit up to you though.
Solution 4 - R
nothing
It may be worth to add solution made available by Romain François. When loaded the package nothing, which is currently available on GitHub, will unload all of the loaded 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
With use of the devtools package:
devtools::install_github("romainfrancois/nothing")
pacman
An alternative approach uses pacman package available through CRAN:
pacman::p_unload(pacman::p_loaded(), character.only = TRUE)
Solution 5 - R
Building on Gavin's answer but not quite to a full function would be this sequence:
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)
Solution 6 - R
#Detach all packages
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()
this will make sure all packages gets detached apart from your basic packages
Solution 7 - R
or if you have RStudio, simply uncheck all the checked boxes in Packages Tab to detach
Solution 8 - R
Most of the times its the plyr vs dplyr issue. Use this in the beginning of the code:
detach("package:plyr", unload=TRUE)
So whenever the script runs, its clears the plyr package
Solution 9 - R
Combining bits from various answers gave the most robust solution I could find...
packs <- c(names(sessionInfo()$otherPkgs), names(sessionInfo()$loadedOnly))
if(length(packs) > 0){
message('Unloading packages -- if any problems occur, please try this from a fresh R session')
while(length(packs) > 0){
newpacks <- c()
for(packi in 1:length(packs)){
u=try(unloadNamespace(packs[packi]))
if(class(u) %in% 'try-error') newpacks <- c(newpacks,packs[packi])
}
packs <- newpacks
Sys.sleep(.1)
}
}
Solution 10 - R
Why not the below to remove all attached packages ?
intialPackages = search() # added as 1st line of R script to get list of default packages
# below lines are added when newly attached packages needs to be removed
newPackages = search()[!(search() %in% intialPackages)]
try(sapply(newPackages, detach, character.only=TRUE, unload=TRUE, force=TRUE), silent=TRUE)
Solution 11 - R
if you're having problems with packages that have similarly named functions conflicting with each other, you can always reference the namespace of the package who's function you DO want.
pkg_name::function_i_want()