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Is it a good idea or even possible to redefine attach?

7 messages · Ista Zahn, Winston Chang, Grant Rettke

Original
Grant Rettke
# 
Hi,

Today I got curious about whether or not I /could/ remove `attach' from
my system so:
- Backed it up
- Implemented a new one
- Like this

,----
| attach.old <<- attach
| attach <<- function(...) {stop("NEVER USE ATTACH")}
`----

I got the error:

,----
| Error: cannot change value of locked binding for 'attach'
`----

If I unlock `attach' I assume that I could stomp on it... however is
that even a good idea?

What will I break?

My goal was never to allow `attach' in my system, but it was just an
idea.

Kind regards,

Grant Rettke | ACM, ASA, FSF, IEEE, SIAM
gcr at wisdomandwonder.com | http://www.wisdomandwonder.com/
?Wisdom begins in wonder.? --Socrates
((? (x) (x x)) (? (x) (x x)))
?Life has become immeasurably better since I have been forced to stop
taking it seriously.? --Thompson
Ista Zahn
#
On Tue, Aug 5, 2014 at 2:49 PM, Grant Rettke <gcr at wisdomandwonder.com> wrote:
Just masking it with your own function, e.g.,

attach <- function(...) {stop("NEVER USE ATTACH")}

should be enough to discourage you from using it.
Anything that uses attach.
Winston Chang
#
On Tue, Aug 5, 2014 at 1:49 PM, Grant Rettke <gcr at wisdomandwonder.com> wrote:
If you change the base package environment's copy of `attach` (via
`as.environment('package:base')`) , probably not much will break,
except for your own code. If, on the other hand, you change the base
namespace's copy of `attach` (via `asNamespace('base')`, any package
that's subsequently loaded and uses `attach` would run into problems.
Still, either way is probably not a good idea.

I agree with Ista: assigning it yourself in the the global environment
is a better idea. If you want to keep your global env clear of stuff
like this, you can put it in an environment and attach that
environment as a parent of global:

e <- new.env()
e$attach <-  function(...) {stop("NEVER USE ATTACH")}
base::attach(e, name = "my_stuff", warn.conflicts = FALSE)

# Test it out:
attach()

# You can see that the "my_stuff" env is the parent of global env
search()


-Winston
Grant Rettke
# 
That is delightful.

When I run it like this:
? Start R
? Nothing in .Rprofile
? Paste in your code
?????
? gcrenv <- new.env()
? gcrenv$attach.old <- attach
? gcrenv$attach <- function(...){stop("NEVER USE ATTACH")}
? base::attach(gcrenv, name="gcr", warn.conflicts = FALSE)
?????
? I get exactly what is expected, I think
?????
? search()
?????
?????
?  [1] ".GlobalEnv"        "gcr"               "ESSR"
?  [4] "package:stats"     "package:graphics"  "package:grDevices"
?  [7] "package:utils"     "package:datasets"  "package:methods"
? [10] "Autoloads"         "package:base"
?????

Just to be sure:
? Is that what is expected?
? I am surprised because I thought that `gcr' would come first before
  `.GlobalEnv'
  ? Perhaps I mis understand, as `.GlobalEnv' is actually the "REPL"?

My goal is to move that to my .Rprofile so that it is "always run" and I
can forget about it more or less.

Reading [this] I felt like `.First' would be the right place to put it,
but then read further to find that packages are only loaded /after/
`.First' has completed.  Curious, I tried it just to be sure. I am now
:).

This is the .Rprofile file:

?????
? cat(".Rprofile: Setting CMU repository\n")
? r = getOption("repos")
? r["CRAN"] = "http://lib.stat.cmu.edu/R/CRAN/"
? options(repos = r)
? rm(r)
?
? .First <- function() {
?    ?same code as above?
? }
?????

(I included the repository load, and understand it should not impact
things here)

This is run after normal startup of R:

?????
? search()
?????
?????
?  [1] ".GlobalEnv"        "package:stats"     "package:graphics"
?  [4] "package:grDevices" "package:utils"     "package:datasets"
?  [7] "gcr"               "package:methods"   "Autoloads"
? [10] "package:base"
?????

When I read this, I read it as:
? My rebind of `attach' occurs
? Then all of the packages are loaded and they are referring to
  my-rebound `attach'
? That is a problem because it *will* break package code
? Clearly me putting that code in `.Rprofile' is the wrong place.

What I am looking for now is the "right way" to achieve what is
demonstarted but automatically via a startup file.

My ideas:
? Manually paste the step each time
? Always use Emacs and ESS to run R and add a hook so that the code will
  be run after ESS loads
? Something I am missing


[this]
http://stat.ethz.ch/R-manual/R-devel/library/base/html/Startup.html
Grant Rettke | ACM, ASA, FSF, IEEE, SIAM
gcr at wisdomandwonder.com | http://www.wisdomandwonder.com/
?Wisdom begins in wonder.? --Socrates
((? (x) (x x)) (? (x) (x x)))
?Life has become immeasurably better since I have been forced to stop
taking it seriously.? --Thompson
On Tue, Aug 5, 2014 at 2:47 PM, Winston Chang <winstonchang1 at gmail.com> wrote:
Winston Chang
#
On Tue, Aug 5, 2014 at 4:37 PM, Grant Rettke <gcr at wisdomandwonder.com> wrote:
That order for search path should actually be fine. To understand why,
you first have to know the difference between the _binding_
environment for an object, and the _enclosing_ environment for a
function.

The binding environment is where you can find an object. For example,
in the global env, you have a bunch bindings (we often call them
variables), that point to various objects - vectors, data frames,
other environments, etc.

The enclosing environment for a function is where the function "runs
in" when it's called.

Most R objects have just a binding environment (a variable or
reference that points to the object); functions also have an enclosing
environment. These two environments aren't necessarily the same.

When you run search(), it shows the set of environments where R will
look for an object of a given name, when you run stuff at the console
(and are in the global env). The trick is that, although you can find
a function (they are bound bound) in one of these _package_
environments, those functions run in (are enclosed by) a different
environment: the a corresponding _namespace_ environment.

The way that a namespace environment is set up with the arrangement of
its ancestor environments, it will find the base namespace version of
`attach` before it finds yours, even if your personal gcr environment
comes early in the search path.

=========================
# Here's an example to illustrate. The `utils::alarm` function calls
`cat`, which is in base.

alarm
# function ()
# {
#     cat("\a")
#     flush.console()
# }
# <environment: namespace:utils>


# Running it makes the screen flash or beep
alarm()
# [screen flashes]


# We'll put a replacement version of cat early in the search path,
between utils and base
my_stuff <- new.env()
my_stuff$cat <- function(...) stop("Tried to call cat")
base::attach(my_stuff, pos=length(search()) - 1, name="my_stuff")

search()
#  [1] ".GlobalEnv"        "tools:rstudio"     "package:stats"
"package:graphics"
#  [5] "package:grDevices" "package:utils"     "package:datasets"
"package:methods"
#  [9] "my_stuff"          "Autoloads"         "package:base"

# Calling cat from the console gives the error, as expected
cat()
# Error in cat() : Tried to call cat

# But when we run alarm(), it still gets the real version of `cat()`,
# because it finds the the original base namespace version of cat
# before it finds yours.
alarm()
# [screen flashes]

==========================

You can even alter package environments without affecting the
corresponding namespace environment. The exception to the package and
namespace environments being distinct is the base environment; change
one and you change the other. (I just realized this and have to
retract my earlier statement about the behavior being different if
change attach in the base package env vs. the base namespace env.)

-Winston
4 days later
Grant Rettke
# 
Thank you for that pleasant and concise explanation!

I will keep at it.
Grant Rettke | ACM, ASA, FSF, IEEE, SIAM
gcr at wisdomandwonder.com | http://www.wisdomandwonder.com/
?Wisdom begins in wonder.? --Socrates
((? (x) (x x)) (? (x) (x x)))
?Life has become immeasurably better since I have been forced to stop
taking it seriously.? --Thompson
On Tue, Aug 5, 2014 at 7:54 PM, Winston Chang <winstonchang1 at gmail.com> wrote:
Grant Rettke
# 
As it turns out, my approach was a bit aggressive. A critical package
was using it and could see my new attach!

I will just warn, and encourage:

.First <- function() {
    gcr <- new.env()
    gcr$unsafe.attach <- attach
    gcr$attach <- function(...) {
        warning("NEVER USE ATTACH! Use `unsafe.attach` if you must.")
        unsafe.attach(...)
    }
    base::attach(gcr, name="gcr", warn.conflicts = FALSE)
}
Grant Rettke | ACM, ASA, FSF, IEEE, SIAM
gcr at wisdomandwonder.com | http://www.wisdomandwonder.com/
?Wisdom begins in wonder.? --Socrates
((? (x) (x x)) (? (x) (x x)))
?Life has become immeasurably better since I have been forced to stop
taking it seriously.? --Thompson
On Sun, Aug 10, 2014 at 9:13 AM, Grant Rettke <gcr at wisdomandwonder.com> wrote: