[Rd] Minor documentation change for assign
Good afternoon,
Today I was reading the documentation
,
| help('<<-');
`
.
The passage (I added the asterisks)
The operators '' are normally only used in functions, and
cause a search *to* made through parent environments for an
existing definition of the variable being assigned. If such
a
looks like it might have wanted to have been phrased as
The operators '' are normally only used in functions, and
cause a search *to be* made through parent environments for
an existing definition of the variable being assigned. If
such a
.
Wanted to share that with the devs, and if that is a wanted change do
people usually submit patches
or what is the preferred mechanism?
,
| sessionInfo()
`
,
| R version 3.1.1 (2014-07-10)
| Platform: x86_64-apple-darwin13.2.0 (64-bit)
|
| locale:
| [1] en_US/en_US/en_US/C/en_US/en_US
|
| attached base packages:
| [1] stats graphics grDevices utils datasets methods base
|
| loaded via a namespace (and not attached):
| [1] compiler_3.1.1 tools_3.1.1
`
Kind regards,
Grant Rettke | ACM, ASA, FSF, IEEE, SIAM
g...@wisdomandwonder.com | http://www.wisdomandwonder.com/
“Wisdom begins in wonder.” --Socrates
((λ (x) (x x)) (λ (x) (x x)))
“Life has become immeasurably better since I have been forced to stop
taking it seriously.” --Thompson
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[Rd] Is it a good idea or even possible to redefine attach?
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
g...@wisdomandwonder.com | http://www.wisdomandwonder.com/
“Wisdom begins in wonder.” --Socrates
((λ (x) (x x)) (λ (x) (x x)))
“Life has become immeasurably better since I have been forced to stop
taking it seriously.” --Thompson
__
R-devel@r-project.org mailing list
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Re: [Rd] Is it a good idea or even possible to redefine attach?
On Tue, Aug 5, 2014 at 2:49 PM, Grant Rettke wrote:
> 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")}
> `
Just masking it with your own function, e.g.,
attach <- function(...) {stop("NEVER USE ATTACH")}
should be enough to discourage you from using it.
>
> 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?
Anything that uses attach.
>
> 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
> g...@wisdomandwonder.com | http://www.wisdomandwonder.com/
> “Wisdom begins in wonder.” --Socrates
> ((λ (x) (x x)) (λ (x) (x x)))
> “Life has become immeasurably better since I have been forced to stop
> taking it seriously.” --Thompson
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
__
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Re: [Rd] Is it a good idea or even possible to redefine attach?
On Tue, Aug 5, 2014 at 1:49 PM, Grant Rettke wrote:
>
> 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?
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$attach <- function(...) {stop("NEVER USE ATTACH")}
base::attach(e, name = "my_stuff", warn.conflicts = FALSE)
# Test it out:
attach()
# You can see that the "my_stuff" env is the parent of global env
search()
-Winston
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Re: [Rd] Is it a good idea or even possible to redefine attach?
That is delightful.
When I run it like this:
• Start R
• Nothing in .Rprofile
• Paste in your code
╭
│ gcrenv <- new.env()
│ gcrenv$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
g...@wisdomandwonder.com | http://www.wisdomandwonder.com/
“Wisdom begins in wonder.” --Socrates
((λ (x) (x x)) (λ (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 wrote:
> On Tue, Aug 5, 2014 at 1:49 PM, Grant Rettke wrote:
>>
>> 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?
>
>
> 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
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[Rd] More than one package document with the same name
Hi, I sent this to the Bioconductor mailing list (q.v.), replies recommended this forum. Here it is: A suggestion. Typically a package provides documentation of two types, one or more vignettes and a reference manual; and they have the same file name, PackageName.pdf. When downloaded some file name manipulation is required, or accept PackageName(1).pdf. I suggest the documents be given different names, for example the reference manual could be named PackageNameRefMan.pdf. Package checking could enforce the rule. Jerry [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] More than one package document with the same name
On Tue, Aug 5, 2014 at 5:47 PM, Davison, Jerry wrote:
> Hi,
>
> I sent this to the Bioconductor mailing list (q.v.), replies recommended this
> forum. Here it is:
> A suggestion. Typically a package provides documentation of two types, one or
> more vignettes and a reference manual; and they have the same file name,
> PackageName.pdf. When downloaded some file name manipulation is required, or
> accept PackageName(1).pdf.
>
> I suggest the documents be given different names, for example the reference
> manual could be named PackageNameRefMan.pdf. Package checking could enforce
> the rule.
> Jerry
>
Sounds like you want to put all the pdf files in a single directory. I
like that too. I cheat. I run Linux. I have a ~/Documents/R-pdfs in
which I keep "symlinks" to all the pdf files. And I do it similar to
the way that you indicate. I make the name of the pdf be
${enclosing_directory}_${original_pdf_name.pdf}. I do something like:
cd ~/Documents/R-pdf
find /usr/lib64/R -name '*.pdf'|\
while read i;do
file=${i##*/};
dir=${i%%/doc/*.pdf};
package=${dir##*/};
ln -s "$i" "${package}_${file}";
done
Above won't work if anything has a blank in it. Windows people tend to
do this. Most UNIX people are better trained.
It would be nice if the packagers did this. But the above works for
me. On Linux and other UNIX like systems. Won't work for the poor,
benighted Windows people. But I think something similar is possible.
But I don't know Windows well enough.
Maranatha! <><
John McKown
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Re: [Rd] Is it a good idea or even possible to redefine attach?
On Tue, Aug 5, 2014 at 4:37 PM, Grant Rettke wrote:
>
> 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.
>
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()
# }
#
# 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 b
