R help - Oct 2016 - Visibility of libraries called from within functions

Hi All,

in my R programs I use different libraries to work with Excel sheets, i. 
e. xlsx, excel.link.

When running chunks of code repeatedly and not always in the order the 
program should run for development purposes I ran into trouble. There were 
conflicts between the methods within these functions causing R to crash.

I thought about defining functions for the different task and calling the 
libraries locally to there functions. Doing this test

-- cut --

f_test <- function() {
    library(xlsx)
    cat("Loaded packages AFTER loading library")
    print(search())
}

cat("Loaded packages BEFORE function call
----------------------------")
search()

f_test()

cat("Loaded packages AFTER function call
-----------------------------")
search()

-- cut --

showed that the library "xlsx" was loaded into the global environment
and
stayed there although I had expected R to unload the library when leaving 
the function. Thus confilics can occur more often.

I had a look into ?library and saw that there is no argument telling R to 
hold the library in the calling environment.

How can I load libraries locally to the calling functions?

Kind regards

Georg

On 13/10/2016 4:18 AM, G.Maubach at weinwolf.de wrote:
> Hi All,
>
> in my R programs I use different libraries to work with Excel sheets, i.
> e. xlsx, excel.link.
>
> When running chunks of code repeatedly and not always in the order the
> program should run for development purposes I ran into trouble. There were
> conflicts between the methods within these functions causing R to crash.
>
> I thought about defining functions for the different task and calling the
> libraries locally to there functions. Doing this test
>
> -- cut --
>
> f_test <- function() {
>     library(xlsx)
>     cat("Loaded packages AFTER loading library")
>     print(search())
> }
>
> cat("Loaded packages BEFORE function call
----------------------------")
> search()
>
> f_test()
>
> cat("Loaded packages AFTER function call
-----------------------------")
> search()
>
> -- cut --
>
> showed that the library "xlsx" was loaded into the global
environment and
> stayed there although I had expected R to unload the library when leaving
> the function. Thus confilics can occur more often.
>
> I had a look into ?library and saw that there is no argument telling R to
> hold the library in the calling environment.
>
> How can I load libraries locally to the calling functions?
You can detach at the end of your function, but that's tricky to get 
right:  the package might have been on the search list before your 
function was called.  It's better not to touch the search list at all.

The best solution is to use :: notation to get functions without putting 
them on the search list.  For example, use

xlsx::write.xlsx(data, file)

If you are not sure if your user has xlsx installed, you can use 
requireNamespace() to check.

Duncan Murdoch

Hi Duncan,

many thanks for your reply.

Your suggestion of using requireNamespace() together with explicit 
namespace calling using the "::" operator is what I was looking for:

-- cut --

f_test <- function() {
    requireNamespace("openxlsx")
    cat("Loaded packages AFTER loading library")
    print(search())
    xlsx::read.xlsx(file = "c:/temp/test.xlsx",
                    sheetName = "test")
}

cat("Loaded packages BEFORE function call
----------------------------")
search()

f_test()

cat("Loaded packages AFTER function call
-----------------------------")
search()

-- cut  --

When reading ?requireNamespace I did not really get how R operates behind 
the scenes.

Using "library" attaches the namespace to the search path. Using 
"requireNamespace" does not do that.

But how does R find the namespace then? What kind of list or directory 
used R to to store the namespace and lookup the correct function or 
methods of this namespace?

Kind regards

Georg




Von:    Duncan Murdoch <murdoch.duncan at gmail.com>
An:     G.Maubach at weinwolf.de, r-help at r-project.org, 
Datum:  13.10.2016 10:43
Betreff:        Re: [R] Visibility of libraries called from within 
functions



On 13/10/2016 4:18 AM, G.Maubach at weinwolf.de wrote:
> Hi All,
>
> in my R programs I use different libraries to work with Excel sheets, i.
> e. xlsx, excel.link.
>
> When running chunks of code repeatedly and not always in the order the
> program should run for development purposes I ran into trouble. There 
were
> conflicts between the methods within these functions causing R to crash.
>
> I thought about defining functions for the different task and calling 
the
> libraries locally to there functions. Doing this test
>
> -- cut --
>
> f_test <- function() {
>     library(xlsx)
>     cat("Loaded packages AFTER loading library")
>     print(search())
> }
>
> cat("Loaded packages BEFORE function call
----------------------------")
> search()
>
> f_test()
>
> cat("Loaded packages AFTER function call
-----------------------------")
> search()
>
> -- cut --
>
> showed that the library "xlsx" was loaded into the global
environment
and
> stayed there although I had expected R to unload the library when 
leaving
> the function. Thus confilics can occur more often.
>
> I had a look into ?library and saw that there is no argument telling R 
to
> hold the library in the calling environment.
>
> How can I load libraries locally to the calling functions?
You can detach at the end of your function, but that's tricky to get 
right:  the package might have been on the search list before your 
function was called.  It's better not to touch the search list at all.

The best solution is to use :: notation to get functions without putting 
them on the search list.  For example, use

xlsx::write.xlsx(data, file)

If you are not sure if your user has xlsx installed, you can use 
requireNamespace() to check.

Duncan Murdoch