[R-SIG-Mac] adjusting .libPaths

[Kenneth Knoblauch]

Thanks Kevin,

I was thinking after I replied to Duncan that I could just delete the . Renviron file because it doesn’t have anything else in it. 

Ken

Sent from my iPhone

> On 28 Apr 2022, at 19:56, Kevin Ushey <kevinushey using gmail.com> wrote:
> 
> FWIW, you shouldn't need to set R_LIBS_USER in this way -- R will
> choose a sensible default value for you based on your platform + the
> version of R being launched.
> 
> I suspect you would see the "right" behavior if you removed that entry
> from your .Renviron altogether (and you wouldn't need to remember to
> change it in the future)
> 
> See also ?.expand_R_libs_env_var for more information.
> 
> Best,
> Kevin
> 
>> On Thu, Apr 28, 2022 at 7:40 AM Kenneth Knoblauch
>> <ken.knoblauch using inserm.fr> wrote:
>> 
>> That's it! There was a .Renviron file in my home directory with the one
>> line
>> 
>> R_LIBS_USER="/Users/ken/Library/R/4.1/library"
>> 
>> so I changed it to
>> 
>> R_LIBS_USER="/Users/ken/Library/R/x86_64/4.2/library"
>> 
>> and now I get in the Rgui, R terminal and Rstudio
>> 
>> libPaths()
>> [1] "/Users/ken/Library/R/x86_64/4.2/library"
>> [2] "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
>> 
>> which is what I expected to have in the first place.
>> 
>> Thank you, Duncan.
>> 
>> best,
>> 
>> 
>> --
>> Kenneth Knoblauch
>> Inserm U1208
>> Stem-cell and Brain Research Institute
>> 18 avenue du Doyen Lépine
>> 69500 Bron
>> France
>> tel: +33 (0)4 72 91 34 77
>> fax: +33 (0)4 72 91 34 61
>> portable: +33 (0)6 84 10 64 10
>> http://www.sbri.fr/user/1453
>> 
>>> On 2022-04-28 16:26, Duncan Murdoch wrote:
>>> 
>>> On 28/04/2022 9:44 a.m., Kenneth Knoblauch wrote:
>>>> Hi,
>>>> 
>>>> In R 4.2, when I look at .libPaths() from within the standard R gui,
>>>> I
>>>> see:
>>>> 
>>>> .libPaths()
>>>> [1] "/Users/ken/Library/R/x86_64/4.2/library"
>>>> [2] "/Users/ken/Library/R/4.1/library"
>>>> [3] "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
>>>> 
>>>> From a terminal, I get
>>>> 
>>>>> .libPaths()
>>>> [1] "/Users/ken/Library/R/4.1/library"
>>>> [2] "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
>>>> 
>>>> The old 4.1 directory, I suspect, should not be there.  From
>>>> Sys.getenv(), I see
>>>> 
>>>> R_LIBS                       /Users/ken/Library/R/x86_64/4.2/library
>>>> R_LIBS_SITE
>>>> /Library/Frameworks/R.framework/Resources/site-library
>>>> R_LIBS_USER                  /Users/ken/Library/R/4.1/library
>>>> 
>>>> and the system Renviron file contains
>>>> 
>>>> uc7131:Resources ken$ grep R_LIBS etc/Renviron
>>>> R_LIBS_USER=${R_LIBS_USER:-'%U'}
>>>> R_LIBS_SITE=${R_LIBS_SITE:-'%S'}
>>>> 
>>>> but I wouldn't know what to adjust these to, to fix this (if I even
>>>> should).
>>>> 
>>>> In Rstudio (which is not the problem of this list), I also get
>>>> 
>>>>> .libPaths()
>>>> [1] "/Users/ken/Library/R/4.1/library"
>>>> [2] "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
>>>> 
>>>> and I would guess the 4.1 entry is why Rstudio bombs when I try to
>>>> execute any graphics.
>>>> 
>>>> I would be grateful for any suggestions as to how to fix this.
>>> 
>>> I'd guess the 41 isn't coming from the system file, but from a user
>>> file
>>> on your account or in the directory where you start Rgui.  Running
>>> getwd() as the first command might find that dir, as long as some
>>> profile code hasn't changed it.
>>> 
>>> The filename might be ".Renviron" rather than "Renviron"
>>> 
>>> Duncan Murdoch
>> 
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