Re: [Rd] How to understand packages, namespaces, environments
On 5/8/05, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: [Alexander Stoddard] Subject: Re: [Rd] How to understand packages, namespaces, environments Does saying the following load package 'foo' into its own environment ? library(foo) [Duncan Murdoch] This loads some of the (name, object) pairs from the package into two environments: the public one the user can see, and the namespace one that the code in the package can see. They're related, you don't get two copies of the objects. That's interesting-- I thought there really were two copies. In my debug package, I've taken the approach of changing both copies. How does one refer to the two different copies? Thanks. __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
RE: [Rd] How to understand packages, namespaces, environments
On 5/8/05, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: [Alexander Stoddard] Subject: Re: [Rd] How to understand packages, namespaces, environments Does saying the following load package 'foo' into its own environment ? library(foo) [Duncan Murdoch] This loads some of the (name, object) pairs from the package into two environments: the public one the user can see, and the namespace one that the code in the package can see. They're related, you don't get two copies of the objects. [MVB] That's interesting-- I thought there really were two copies. In my debug package, I've taken the approach of changing both copies. [Gabor Grothendieck] How does one refer to the two different copies? Thanks. The help for fun.locator (in the debug package) contains my interpretation of what's going on (which might be wrong, but seems to work). A slightly simplified version of the guts of fun.locator is as follows: # function to check for something called fname is.here - function( env) exists( fname, env=env, inherits=FALSE) # Search path search.envs - lapply( 1:length( search()), pos.to.env) ff - search.envs[ sapply( search.envs, is.here)] # Hidden namespace environments ln - lapply( loadedNamespaces(), asNamespace) ff - c( ff, ln[ sapply( ln, is.here)]) # S3 methods: S3 - lapply( ln, function( x) if( exists( '.__S3MethodsTable__.', x, inherits=FALSE)) get( '.__S3MethodsTable__.', x) else 0) S3 - S3[ !sapply( S3, is.numeric)] ff - c( ff, S3[ sapply( S3, is.here)]) Then ff is a list of environments where a copy (?) of fname exists-- and you can use ff[[i]][[fname]] or get(fname, env=ff[[i]]) assign( fname, ..., env=ff[[i]]) I should point out that the doco for asNamespace says not intended to be called directly-- but I couldn't see an alternative, and anyway it seems to work (for now). Mark __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
RE: [Rd] How to understand packages, namespaces, environments
On Mon, 9 May 2005 [EMAIL PROTECTED] wrote: [Alexander Stoddard] Subject: Re: [Rd] How to understand packages, namespaces, environments Does saying the following load package 'foo' into its own environment ? library(foo) [Duncan Murdoch] This loads some of the (name, object) pairs from the package into two environments: the public one the user can see, and the namespace one that the code in the package can see. They're related, you don't get two copies of the objects. That's interesting-- I thought there really were two copies. In my debug package, I've taken the approach of changing both copies. Is one of the copies a master, and the other one something like an activeBinding? Can I get away with changing just one of them? Duncan is wrong here (or misquoted). Loading a package with a namespace loads all the objects in the package (possibly as promises) into the namespace environment. Then some are copied (using assign) to the package environment. Since like most R copies this is really copy-on-change you do not get a real copy (nor force a promise) until use. See ?fixInNamespace for explicit statements about this. There can be more than two copies, since importing also `copies', as does S3 method registration (the latter does sometimes force promises). -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] How to understand packages, namespaces, environments
Prof Brian Ripley wrote: On Mon, 9 May 2005 [EMAIL PROTECTED] wrote: [Alexander Stoddard] Subject: Re: [Rd] How to understand packages, namespaces, environments Does saying the following load package 'foo' into its own environment ? library(foo) [Duncan Murdoch] This loads some of the (name, object) pairs from the package into two environments: the public one the user can see, and the namespace one that the code in the package can see. They're related, you don't get two copies of the objects. That's interesting-- I thought there really were two copies. In my debug package, I've taken the approach of changing both copies. Is one of the copies a master, and the other one something like an activeBinding? Can I get away with changing just one of them? Duncan is wrong here (or misquoted). Wrong, not misquoted. Sorry about that. Thanks for the correct description. Duncan Murdoch Loading a package with a namespace loads all the objects in the package (possibly as promises) into the namespace environment. Then some are copied (using assign) to the package environment. Since like most R copies this is really copy-on-change you do not get a real copy (nor force a promise) until use. See ?fixInNamespace for explicit statements about this. There can be more than two copies, since importing also `copies', as does S3 method registration (the latter does sometimes force promises). __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] How to understand packages, namespaces, environments
I would be very glad of pointers to information on how the concepts of packages, namespaces and environments are interrelated in R. I am trying to get a handle on this both so I can delve further into understanding other people's code and so I can organize my own in a more coherent manner. From my reading about environments it seems they function as what I would intuitively call namespaces. However, the documentation for the 'library' function implies that namespace has a specific meaning in R that I have so far failed to grasp. What is that meaning (or where should I look to read up on it) ? I can think of the following more specific questions. Perhaps they may most usefully serve to reveal my misconceptions, so corrections would be very helpful. Does saying the following load package 'foo' into its own environment ? library(foo) Do environments have names? Of what does the list returned by search() actually consist? Is it a list of environments, a list that may include environments, or something else? What is actually designated by a character vector of form package:foo? In what ways can I use the character vector package:foo when interacting with R? Many thanks, Alex Stoddard P.S. It took me a long time of flailing about to discover the 'search' function. Perhaps it could be included in the See Also section of the help for 'ls'. __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] How to understand packages, namespaces, environments
On Fri, 6 May 2005, Alexander Stoddard wrote: I would be very glad of pointers to information on how the concepts of packages, namespaces and environments are interrelated in R. I am trying to get a handle on this both so I can delve further into understanding other people's code and so I can organize my own in a more coherent manner. From my reading about environments it seems they function as what I would intuitively call namespaces. However, the documentation for the 'library' function implies that namespace has a specific meaning in R that I have so far failed to grasp. What is that meaning (or where should I look to read up on it) ? Look in `Writing R Extensions' and on developer.r-project.org. I don't know about `intuitively' but they are similar to other systems (e.g. Perl's) namespaces. More user-level documentation of namespaces (e.g. in R-lang) is on the WOULD-BE-NICE list, but there is enough in `Writing R Extensions' for many package writers and we are talking about more details of what happens under the skin. I can think of the following more specific questions. Perhaps they may most usefully serve to reveal my misconceptions, so corrections would be very helpful. It seems you have revealed that you have not studied the manuals nor the help pages. Please do so before posting (see the posting guide). Does saying the following load package 'foo' into its own environment ? library(foo) Do environments have names? Not in general. You will see environment: some-hex-address printed quite often. I am not at all sure you have grasped what an environment is in R: see the R-lang manual. (Look it up in the index, as at present the term is used before it is defined.) Of what does the list returned by search() actually consist? Is it a list of environments, a list that may include environments, or something else? search() does not return a list: it returns a character vector. It seems you have not read its help page, which tells you that quite explicitly. What is actually designated by a character vector of form package:foo? That is actually a character string, not a character vector. It is a name that can be used to refer to attach'ed objects, as the search() help page says. In what ways can I use the character vector package:foo when interacting with R? I am aware of attach(), detach() and as.environment() (which is used by quite a few functions, e.g. get()). (Asking what you can do it an extensible system such as R is not very helpful.) Generally it is a name used when a package or another attach'ed object might be meant: it is not used if a package is all that can be specified. Many thanks, Alex Stoddard P.S. It took me a long time of flailing about to discover the 'search' function. Perhaps it could be included in the See Also section of the help for 'ls'. This *is* in `An Introduction to R', something we ask all R users to read. I (and I am biased) suggest the right way to get to grips with things like this is to read a good book on the S/R language. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] How to understand packages, namespaces, environments
Alexander Stoddard wrote:
I would be very glad of pointers to information on how the concepts of
packages, namespaces and environments are interrelated in R.
I don't think that documentation exists yet, but I did update the
documentation on environments for 2.1.0. Look in the section (2.1.10 I
think) on Environment Objects in the R language definition manual.
Basically environments are things where you can ask to look up names and
R will return R objects to you. They're a bit more complicated than
just a list of (name, object) pairs, but can (almost) be used as that
(and I'm hoping will be able to be used that way in 2.2.0, but that
remains to be seen).
I am trying to get a handle on this both so I can delve further into
understanding other people's code and so I can organize my own in a more
coherent manner.
From my reading about environments it seems they function as what I
would intuitively call namespaces. However, the documentation for the
'library' function implies that namespace has a specific meaning in R
that I have so far failed to grasp. What is that meaning (or where
should I look to read up on it) ?
A namespace is a more abstract concept, which happens to be implemented
in R using environments. Exactly how is a bit of a mystery to me, I'm
afraid! However, the basic idea is that a namespace defines a fixed set
of meanings for names, which the code in a package can assume won't
change. It may also hide some names from outsiders.
I can think of the following more specific questions. Perhaps they may
most usefully serve to reveal my misconceptions, so corrections would be
very helpful.
Does saying the following load package 'foo' into its own environment ?
library(foo)
This loads some of the (name, object) pairs from the package into two
environments: the public one the user can see, and the namespace one
that the code in the package can see. They're related, you don't get
two copies of the objects.
Do environments have names?
They are R objects, so some of them have names, and some of them are
anonymous parts of other objects.
Of what does the list returned by search() actually consist? Is it a
list of environments, a list that may include environments, or something
else?
It's a list of strings that can be used to get corresponding
environments. You don't get the actual environments.
What is actually designated by a character vector of form package:foo?
That string is used by the as.environment() function to go through the
search list and obtain the environment. For instance, you can do
x - as.environment(package:foo)
and x will be a reference to the environment. Then
ls(x)
will list all the objects there, get('bar', envir=x) will extract the
object named 'bar' from it, etc.
In what ways can I use the character vector package:foo when
interacting with R?
I can't think of any other uses than in as.environment(), but there
might be some, or some automatic calls to it. I'd have to check the man
pages to be sure, but perhaps some functions that accept envir=x type
arguments would automatically call as.environment on x first.
Many thanks,
Alex Stoddard
P.S. It took me a long time of flailing about to discover the 'search'
function. Perhaps it could be included in the See Also section of the
help for 'ls'.
That's a good suggestion. Could you do me a favour, and as you're
reading up on this stuff identify a whole list of deficiencies in the
documentation and suggested fixes for them? Making a change to a man
page has a certain fixed overhead (making sure there are no syntax
errors, committing, possibly porting the change to the patch branch), so
batching them is efficient.
Duncan Murdoch
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