detach all packages while working in R

Question

While working to solve another problem I got this problem:

I can remove all R objects by:

rm(list = ls(all = TRUE))

Is there equiv

Answer 1

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

Answer 2

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)
  }
}

Answer 3

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.

Answer 4

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()