rm(list=ls()) doesn't completely clear the workspace

Question

This is a very minor issue, but I would like to understand exactly what is going on here.

Say I do the following:

library(RMySQL) con <- dbConnect(MySQL(), host="some.server.us-east-1.rds.amazonaws.com",user="aUser", password="password", dbname="mydb")  values1 <- dbGetQuery(con,"select x,y from table1") attach(values1) 

At this point, I can do

rm(list=ls())  values2 <- dbGetQuery("select x,y from table1") attach(values2) 

but the attach gives me a warning about masking an x and y. I thought I had already clobbered those. What is going on? How do I completely clear a workspace?

Answer 1

attach() does not make copies of x and y in your global environment, it attaches a dataframe to the search path.

From ?attach:

The database is not actually attached.  Rather, a new environment  is created on the search path and the elements of a list  (including columns of a data frame) or objects in a save file or  an environment are _copied_ into the new environment.  If you use  ‘<<-’ or ‘assign’ to assign to an attached database, you only  alter the attached copy, not the original object.  (Normal  assignment will place a modified version in the user's workspace:  see the examples.)  For this reason ‘attach’ can lead to  confusion. 

For example:

> search() [1] ".GlobalEnv"        "package:stats"     "package:graphics"  [4] "package:grDevices" "package:utils"     "package:datasets"  [7] "package:methods"   "Autoloads"         "package:base"      > a <- data.frame(stuff=rnorm(100)) > search() [1] ".GlobalEnv"        "package:stats"     "package:graphics"  [4] "package:grDevices" "package:utils"     "package:datasets"  [7] "package:methods"   "Autoloads"         "package:base"      > attach(a) > search()  [1] ".GlobalEnv"        "a"                 "package:stats"      [4] "package:graphics"  "package:grDevices" "package:utils"      [7] "package:datasets"  "package:methods"   "Autoloads"         [10] "package:base"      > rm(list=ls()) > search()  [1] ".GlobalEnv"        "a"                 "package:stats"      [4] "package:graphics"  "package:grDevices" "package:utils"      [7] "package:datasets"  "package:methods"   "Autoloads"         [10] "package:base"      > stuff   [1] -0.91436377  0.67397624  0.62891651 -0.99669584  2.07692590 -0.62702302   [...] > detach(a) > search() [1] ".GlobalEnv"        "package:stats"     "package:graphics"  [4] "package:grDevices" "package:utils"     "package:datasets"  [7] "package:methods"   "Autoloads"         "package:base"     

Answer 2

Just to mention... if you, perhaps, have hidden objects in your environment, like .First and .Last functions, you can remove them with rm(list = ls(all.names = TRUE)). But in your case, use detach(objectname) to remove object from search path. detach() will remove any object in position #2, since .GlobalEnv cannot be removed (and base too). With detach() you can unload previously loaded packages, so be careful (though you can always load them with library(packagename)).