[R-SIG-Mac] adjusting .libPaths

[Kevin Ushey]

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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