[R-SIG-Mac] Serious problem with R on macOS

Thu Jun 8 22:23:22 CEST 2023

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 using 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 using 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
>> ----------------------------------------------------------------------
>> [Sent from Outlook for Mac �MacBook Pro]
>> 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 <fdepaolis using middlebury.edu>
>> Date: Tuesday, June 6, 2023 at 10:20 AM
>> To: peter dalgaard <pdalgd using gmail.com>
>> Cc: Calboli Federico (LUKE) <federico.calboli using luke.fi>, r-sig-mac using r-project.org <r-sig-mac using 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
>> ----------------------------------------------------------------------
>> [Sent from Outlook for Mac �MacBook Pro]
>> 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: peter dalgaard <pdalgd using gmail.com>
>> Date: Tuesday, June 6, 2023 at 9:50 AM
>> To: DePaolis, Fernando <fdepaolis using middlebury.edu>
>> Cc: Calboli Federico (LUKE) <federico.calboli using luke.fi>, r-sig-mac using r-project.org <r-sig-mac using r-project.org>
>> Subject: Re: [R-SIG-Mac] Serious problem with R on macOS
>> [You don't often get email from pdalgd using gmail.com. Learn why this is important at https://urldefense.com/v3/__https://aka.ms/LearnAboutSenderIdentification__;!!Mih3wA!Fr3HvZOZi4Vn9PoE48tKxAfj3AtOpcj4qLfq1EJ9yNCh3wNtCoPAjKvY7X98gkORFUN5nZHSXmGRARZ26tXIOdrG$  ]
>>
>> 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 <fdepaolis using 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
>>> ----------------------------------------------------------------------
>>> [Sent from Outlook for Mac �MacBook Pro]
>>> 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: peter dalgaard <pdalgd using gmail.com>
>>> Date: Tuesday, June 6, 2023 at 8:48 AM
>>> To: DePaolis, Fernando <fdepaolis using middlebury.edu>
>>> Cc: Calboli Federico (LUKE) <federico.calboli using luke.fi>, r-sig-mac using r-project.org <r-sig-mac using r-project.org>
>>> Subject: Re: [R-SIG-Mac] Serious problem with R on macOS
>>>
>>> [You don't often get email from pdalgd using gmail.com. Learn why this is important at https://urldefense.com/v3/__https://aka.ms/LearnAboutSenderIdentification__;!!Mih3wA!Fr3HvZOZi4Vn9PoE48tKxAfj3AtOpcj4qLfq1EJ9yNCh3wNtCoPAjKvY7X98gkORFUN5nZHSXmGRARZ26tXIOdrG$  ]
>>>
>>> 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 <fdepaolis using 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
>>>> ----------------------------------------------------------------------
>>>> [Sent from Outlook for Mac �MacBook Pro]
>>>> 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: Calboli Federico (LUKE) <federico.calboli using luke.fi>
>>>> Date: Tuesday, June 6, 2023 at 12:54 AM
>>>> To: DePaolis, Fernando <fdepaolis using middlebury.edu>, r-sig-mac using r-project.org <r-sig-mac using r-project.org>
>>>> Subject: Re: Serious problem with R on macOS
>>>>
>>>> You don't often get email from federico.calboli using 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
>>>> ----------------------------------------------------------------------
>>>> [Sent from Outlook for Mac �MacBook Pro]
>>>> 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 <fdepaolis using middlebury.edu>
>>>> Date: Monday, June 5, 2023 at 10:19 AM
>>>> To: CRAN-sysadmin using R-project.org <CRAN-sysadmin using 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
>>>> ----------------------------------------------------------------------
>>>> [Sent from Outlook for Mac �MacBook Pro]
>>>> 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.
>>>> _______________________________________________
>>>> R-SIG-Mac mailing list
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>>> --
>>> Peter Dalgaard, Professor,
>>> Center for Statistics, Copenhagen Business School
>>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>>> Phone: (+45)38153501
>>> Office: A 4.23
>>> Email: pd.mes using cbs.dk  Priv: PDalgd using gmail.com
>>>
>> --
>> Peter Dalgaard, Professor,
>> Center for Statistics, Copenhagen Business School
>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>> Phone: (+45)38153501
>> Office: A 4.23
>> Email: pd.mes using cbs.dk  Priv: PDalgd using gmail.com
>>
>> 	[[alternative HTML version deleted]]
>>
>>
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>