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

Thu Jun 8 23:14:25 CEST 2023

Yes, this is consistent with the fact that R starts for you. Some other files seem to have gone missing though, notably the datasets and compiler package, so that R does not get very far before givinng up the ghost.

The pattern of recently created files disappearing is worrying, but not likely due to anything that R itself is doing. It is quite possible that you have a disk error, either physical or logical (inconsistent file system state), or it could be the OS error that Sarah was alluding to. You might want to try the First Aid option in the Disc Utility app (possibly enlist a local expert).

- Peter

> On 8 Jun 2023, at 18:37 , DePaolis, Fernando <fdepaolis using middlebury.edu> 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 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 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://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
> >
> > --
> > 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
> 

-- 
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