R help - Nov 2012 - save/load and package namespaces

Could someone explain to me what namespaces are loaded/saved when objects
are saved?

Specifically, I'm using this:
 save(list = ls(all.names = TRUE, envir = envir), file = name, envir envir)
to save out everything from an environment.

Later, loading it on another machine, I'm surprised to see the load failing
for being unable to load certain packages.  Could anyone help me understand
why this happens?

Jamie Olson

	[[alternative HTML version deleted]]

Could someone explain to me what namespaces are loaded/saved when objects
are saved?

Specifically, I'm using this:
 save(list = ls(all.names = TRUE, envir = envir), file = name, envir envir)
to save out everything from an environment.

Later, loading it on another machine, I'm surprised to see the load failing
for being unable to load certain packages.  Could anyone help me understand
why this happens?
Jamie Olson

	[[alternative HTML version deleted]]

Stop being surprised. Loaded packages are not part of "envir"
(whatever that is), nor are they part of the global environment.  You have to
reload any packages needed separately from the load call.
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Jamie Olson <inspired2apathy at gmail.com> wrote:
>Could someone explain to me what namespaces are loaded/saved when
>objects
>are saved?
>
>Specifically, I'm using this:
> save(list = ls(all.names = TRUE, envir = envir), file = name, envir
>envir)
>to save out everything from an environment.
>
>Later, loading it on another machine, I'm surprised to see the load
>failing
>for being unable to load certain packages.  Could anyone help me
>understand
>why this happens?
>Jamie Olson
>
>	[[alternative HTML version deleted]]
>
>______________________________________________
>R-help at r-project.org mailing list
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.

On Nov 7, 2012, at 9:50 AM, Jamie Olson wrote:
> Could someone explain to me what namespaces are loaded/saved when objects
> are saved?
None. That's what require() or library() or source() are for.
> 
> Specifically, I'm using this:
> save(list = ls(all.names = TRUE, envir = envir), file = name, envir >
envir)
> to save out everything from an environment.
You need to read more carefully:

?ls
?objects
?search
> 
> Later, loading it on another machine, I'm surprised to see the load
failing
> for being unable to load certain packages.  Could anyone help me understand
> why this happens?
`ls` with default settings only lists data and function objects that the user
has defined. The history mechanism could be used to restore packages that were
loaded during a session.

?history

You should be able to see this by looking at what ls() produces. It does not
generally return a listing of items in loaded packages.

-- 

David Winsemius, MD
Alameda, CA, USA

On 07/11/2012 12:50 PM, Jamie Olson wrote:
> Could someone explain to me what namespaces are loaded/saved when objects
> are saved?
None are loaded or saved when you save the object, but the names of some 
are saved.  For example,

library(Hmisc)  # not normally loaded/attached
x <- zoom # copy a function from Hmisc
save(x, file="x.RData")

This will save a copy of a function from Hmisc to the file, but the 
function's environment is the Hmisc namespace.  To properly load that 
function via

load("x.RData")

R will load the referenced namespace.  You will see it appear in 
loadedNamespaces() after the load (assuming you still have Hmisc available).

I believe this will also happen if you try to load an S4 object; you'll 
need to be able to load the namespace of its class.

Duncan Murdoch

>
> Specifically, I'm using this:
>   save(list = ls(all.names = TRUE, envir = envir), file = name, envir >
envir)
> to save out everything from an environment.
>
> Later, loading it on another machine, I'm surprised to see the load
failing
> for being unable to load certain packages.  Could anyone help me understand
> why this happens?
> Jamie Olson
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.