rm(list=ls()) doesn't completely clear the workspace
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?
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"
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) ).
R itself says, in the help for rm :
## remove (almost) everything in the working environment.
## You will get no warning, so don't do this unless you are really sure.
rm(list = ls())
Note the 'almost'. There are different environments.
Did you try detach(values1) ?
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