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

Thu Jun 8 21:16:30 CEST 2023

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
>>> R-SIG-Mac using r-project.org
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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
>
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-- 
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