The symbolic link is the standard way R is installed on a Mac. It's installed as a "framework", but the symlink in /usr/local/bin/R makes Unix-like tools see it as a standard program, which is what you want from the terminal.

The warnings and errors Fernando was seeing, like

  package ‘datasets’ in options("defaultPackages") was not found

make it look as though the framework is broken. I have no idea how that would happen. Maybe he'll learn more by running

.libPaths()

in R. It should print something like

[1] "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library"

but maybe not identical to that. Running ls on that directory in the terminal should list all the installed packages (including datasets and everything else that is supposed to be installed).

Duncan Murdoch


On 08/06/2023 3:16 p.m., John Helly via R-SIG-Mac wrote:
Not clear why there is a symbolic link.  Maybe try using the fullpath
name to invoke R and see if that works.  It seems to me that
'sometimes', on OSX, some symbolic links behave oddly.  This may be
related to the Privacy/Security settings but I don't have any clear
understanding of what's going on.

J.

On 6/8/23 06:37, DePaolis, Fernando wrote:
This is what I get after the current failure, where neither R.app nor the call 
from the command line work.


fernandodepaolis@MacBook-Pro-2 ~ % ls -l `which R`

lrwxr-xr-x  1 root  admin  47 Jun  5 10:23 /usr/local/bin/R -> 
/Library/Frameworks/R.framework/Resources/bin/R


fernandodepaolis@MacBook-Pro-2 ~ % ls -l 
/Library/Frameworks/R.framework/Resources/bin/R

-rwxrwxr-x  1 root  admin  9196 Apr 21 14:47 
/Library/Frameworks/R.framework/Resources/bin/R



which is identical to what I got when it was working fine a couple of days ago.

Thank you



Fernando DePaolis, Ph.D.
Dean of Academic Operations & Integration
Associate Professor
Middlebury Institute of International 
Studies<https://urldefense.com/v3/__http://www.middlebury.edu/institute__;!!Mih3wA!Fr3HvZOZi4Vn9PoE48tKxAfj3AtOpcj4qLfq1EJ9yNCh3wNtCoPAjKvY7X98gkORFUN5nZHSXmGRARZ26qcicJyf$
 > at Monterey
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From: DePaolis, Fernando <fdepao...@middlebury.edu>
Date: Tuesday, June 6, 2023 at 10:20 AM
To: peter dalgaard <pda...@gmail.com>
Cc: Calboli Federico (LUKE) <federico.calb...@luke.fi>, r-sig-mac@r-project.org 
<r-sig-mac@r-project.org>
Subject: Re: [R-SIG-Mac] Serious problem with R on macOS
Thank you!! I will do that.

PS: No, no additional or different scrubbers/antivirus/etc have been added.



Fernando DePaolis, Ph.D.
Dean of Academic Operations & Integration
Associate Professor
Middlebury Institute of International 
Studies<https://urldefense.com/v3/__http://www.middlebury.edu/institute__;!!Mih3wA!Fr3HvZOZi4Vn9PoE48tKxAfj3AtOpcj4qLfq1EJ9yNCh3wNtCoPAjKvY7X98gkORFUN5nZHSXmGRARZ26qcicJyf$
 > at Monterey
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otherwise indicated.

From: peter dalgaard <pda...@gmail.com>
Date: Tuesday, June 6, 2023 at 9:50 AM
To: DePaolis, Fernando <fdepao...@middlebury.edu>
Cc: Calboli Federico (LUKE) <federico.calb...@luke.fi>, r-sig-mac@r-project.org 
<r-sig-mac@r-project.org>
Subject: Re: [R-SIG-Mac] Serious problem with R on macOS
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  ]

Hum...

Best I can think of is to take the hint (from Simon Urbanek) and move the .pkg 
file from Downloads and into another folder before installing. Some system 
cleaner-upper or virus checker could be moving stuff around. You haven't 
perchance some virus scrubber running which might be restoring your executable 
directories to a previous state?

You might want to make a note of the location and ownership of installed files, 
like in

Peters-Air:R pd$ ls -l `which R`
lrwxr-xr-x  1 root  wheel  47 Jun  6 17:41 /usr/local/bin/R -> 
/Library/Frameworks/R.framework/Resources/bin/R
Peters-Air:R pd$ ls -l /Library/Frameworks/R.framework/Resources/bin/R
-rwxrwxr-x  1 root  admin  9196 Apr 21 23:47 
/Library/Frameworks/R.framework/Resources/bin/R

and then, if/when it stops working, see if files have disappeared or changed 
owner or permissions.

-pd


On 6 Jun 2023, at 18:05 , DePaolis, Fernando <fdepao...@middlebury.edu> wrote:

OS: Ventura 13.4 (22F66)
Downloaded R-4.3.0-x86_64.pkg from CRAN
Installation: Successful�everything works fine
Suggestion to move the installer to Trash: Declined (because I know I will need 
the installer again).
CRAN suggests reinstalling Xquartz, which I did a few times on the onset of the 
symptoms (I don�t do that anymore because there sems to be no point to it).
Use: I only use RStudio and everything works fine, until at a random time a few 
days later (or hours in a few instances), RStudio fails to �find R�, which 
doesn�t run on its own or from the console.
Possible emerging conflicts: At the beginning, I thought this could be 
happening because other software were install afterward, but that is not the 
case.
Looked for alternatives: I couldn�t find any reference online, so I suspect 
this is quite specific to my machine and/or environment. About the 
�environment�, I cannot think of anything, as no changes have been made, except 
for routine updates (which is unlikely, but not impossible to have undesirable 
effects).


Thank you



Fernando DePaolis, Ph.D.
Dean of Academic Operations & Integration
Associate Professor
Middlebury Institute of International Studies at Monterey
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From: peter dalgaard <pda...@gmail.com>
Date: Tuesday, June 6, 2023 at 8:48 AM
To: DePaolis, Fernando <fdepao...@middlebury.edu>
Cc: Calboli Federico (LUKE) <federico.calb...@luke.fi>, r-sig-mac@r-project.org 
<r-sig-mac@r-project.org>
Subject: Re: [R-SIG-Mac] Serious problem with R on macOS

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  ]

OK, so

- OS version?
- What do you do to install?
- What happens when you do it?

e.g.:

- Monterey 12.6.5
- Downloaded R-4.3.0-x86_64.pkg from CRAN
- As user with admin privilege, open from Downloads folder and follow 
instructions
- "The installation was succesful"
- Close, move to bin.

I gather that on newer OS, you may need to move the installer out of Downloads 
first.


-pd


On 6 Jun 2023, at 17:07 , DePaolis, Fernando <fdepao...@middlebury.edu> wrote:

Thank you all�it is not an RStudio issue. I cannot run R from its app or the 
command line�It is certainly an R issue.
Next time it �uninstalls itself� I will try to install it on another user and 
see what happens (although I have already tried to install it �just for me� or 
for all users).

Thank you again,


Fernando DePaolis, Ph.D.
Dean of Academic Operations & Integration
Associate Professor
Middlebury Institute of International Studies at Monterey
----------------------------------------------------------------------
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My working hours (US Pacific time zone) may not be your working hours. Please 
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otherwise indicated.

From: Calboli Federico (LUKE) <federico.calb...@luke.fi>
Date: Tuesday, June 6, 2023 at 12:54 AM
To: DePaolis, Fernando <fdepao...@middlebury.edu>, r-sig-mac@r-project.org 
<r-sig-mac@r-project.org>
Subject: Re: Serious problem with R on macOS

You don't often get email from federico.calb...@luke.fi. Learn why this is 
important
If you can use R.app or R on the terminal, it is a R studio bug.  Have you 
tested?  Also, �reinstall� works best after removing all actual files, such as 
the whole ~/.R, all the ~/.R* files, and whatever R studio might add.

BW

F

Federico Calboli
Tutkija
Genomiikka ja jalostus
Luonnonvarakeskus

Uwe Ligges (from CRAN sys admin) recommended that I post this to the list.

Thank you.



Fernando DePaolis, Ph.D.
Dean of Academic Operations & Integration
Associate Professor
Middlebury Institute of International Studies at Monterey
----------------------------------------------------------------------
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My working hours (US Pacific time zone) may not be your working hours. Please 
do not feel obligated to respond outside your normal work hours, unless 
otherwise indicated.

From: DePaolis, Fernando <fdepao...@middlebury.edu>
Date: Monday, June 5, 2023 at 10:19 AM
To: cran-sysad...@r-project.org <cran-sysad...@r-project.org>
Subject: Serious problem with R on macOS

Hello,
For a few months now, I�ve been having an odd and rather annoying problem. I 
use RStudio and it frequently cannot start R, producing the error message 
attached below. This is clearly not the, as I worked on it the night before or 
even just a few hours earlier. What is clear is that R is not available on my 
system, although all the files are still there (in 
/Library/Frameworks/R.framework). It could be that a critical file becomes 
corrupted, or the system can�t find it. I have not been able to determine 
whether that is the case, or which file could be affected. I might have 
re-installed R dozens of times in the last month. This is something that never 
happened in the previous more than 15 years of using R.

I�ve tried everything I can think of, and the problem persists�and haven�t 
found any satisfactory feedback online either.
Have you ever heard of a problem like this? Or do you have any suggestions?

Thank you so much for your support.


<image001.png>



Fernando DePaolis, Ph.D.
Dean of Academic Operations & Integration
Associate Professor
Middlebury Institute of International Studies at Monterey
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[Sent from Outlook for Mac �MacBook Pro]
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do not feel obligated to respond outside your normal work hours, unless 
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Solbjerg Plads 3, 2000 Frederiksberg, Denmark
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