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

Thu Jun 8 18:37:56 CEST 2023

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<http://www.middlebury.edu/institute> at Monterey
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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<http://www.middlebury.edu/institute> 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: 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://aka.ms/LearnAboutSenderIdentification ]

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://aka.ms/LearnAboutSenderIdentification ]
>
> 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
> > https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-mac&data=05%7C01%7Cfdepaolis%40middlebury.edu%7Cdb2e32f6b6354231b5ff08db66ae2825%7Ca1bb0a191576421dbe93b3a7d4b6dcaa%7C1%7C0%7C638216670441495509%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=MADUiUqcBqTzwqoAW6%2FNlk8M1hZ9dWKkxolDZPqLjIE%3D&reserved=0<https://stat.ethz.ch/mailman/listinfo/r-sig-mac>
>
> --
> 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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