[R] Help trying to understand R documentation on libraries paths

[Iago Giné Vázquez]

Thanks,

Regarding .libPaths, I am asking for the call to `.libPaths()`, so I understand there is no `new` in the call, as in the documentation I cited.

Iago

________________________________
De: peter dalgaard <pdalgd using gmail.com>
Enviat el: dilluns, 17 de juny de 2024 13:26
Per a: Iago Gin� V�zquez <iago.gine using sjd.es>
A/c: r-help using r-project.org <r-help using r-project.org>
Tema: Re: [R] Help trying to understand R documentation on libraries paths

(Inline)

> On 17 Jun 2024, at 09:51 , Iago Gin� V�zquez <iago.gine using sjd.es> wrote:
>
> Hi,
>
> 1 - On help(".libPaths", help_type = "text") one can read:
>
> First, '.Library.site' is initialized from 'R_LIBS_SITE'.
>
> However, I have
>
>> Sys.getenv("R_LIBS_SITE")
> [1] "c:/Users/i.gine/AppData/Local/Programs/R/R-4.4.1/site-library"
>> .Library.site
> character(0)
>
> Is this consistent?

It is implied that R_LIBS_SITE should point to an existing directory. I see the same thing on Mac:

> .Library.site
character(0)
> Sys.getenv("R_LIBS_SITE")
[1] "/Library/Frameworks/R.framework/Resources/site-library"
> list.files(Sys.getenv("R_LIBS_SITE"))
character(0)

I.e., R_LIBS_SITE is where a site library _if any_ should live. If it is not there, there is no poin in searching it. Unless you actually have a site-library, I don't think there is a problem.

>
> 2 - Next, on the same help document, one can read:
>
> Then, '.libPaths()' is called with the combination
>     of the directories given by 'R_LIBS' and 'R_LIBS_USER'.
>
>
> This time, I get
>> Sys.getenv("R_LIBS")
> [1] ""
>> Sys.getenv("R_LIBS_USER")
> [1] "c:/Users/i.gine/AppData/Local/Programs/R/R-4.4.0/library"
>> .libPaths()
> [1] "C:/Users/i.gine/AppData/Local/Programs/R/R-4.4.0/library" "C:/Users/i.gine/AppData/Local/Programs/R/R-4.4.1/library"
>
>
> Later is written:
>
> Function '.libPaths' always uses the values of '.Library' and
>     '.Library.site' in the base namespace.
>
> and indeed
>
>> .Library
> [1] "c:/Users/i.gine/AppData/Local/Programs/R/R-4.4.1/library"
>
>
> Then, shouldn't be this specified above together with "directories given by 'R_LIBS' and 'R_LIBS_USER'"?
>

The logic of .libPath() is

> .libPaths
function (new, include.site = TRUE)
{
    if (!missing(new)) {
        new <- Sys.glob(path.expand(new))
        paths <- c(new, if (include.site) .Library.site, .Library)
        paths <- paths[dir.exists(paths)]
        .lib.loc <<- unique(normalizePath(paths, "/"))
    }
    else .lib.loc
}

so if you "call it with" new=something, then (.Library.site, .Library) is automagically appended, unless you expressly tell it not to.

-pd

>
> Am I understanding it wrongly? Otherwise, what do you think on the current way this help page is explained?
>
> Thank you for your help and time.
>
> Best regards,
>
> Iago
>
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>
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--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
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Email: pd.mes using cbs.dk  Priv: PDalgd using gmail.com


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