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

[Simon Urbanek]

Fernando,

that looks like something is deleting files on your disk - that sounds pretty 
bad. I would probably recommend re-installing a fresh macOS as you may have 
some malware (or over-eager anti-virus or corporate software?) on your machine. 
Given that R works after installation it really seems like some issue on your 
OS and not with R itself.

Cheers,
Simon


> On 9/06/2023, at 4:33 AM, DePaolis, Fernando  wrote:
> 
> …well…here it goes again…it failed just now. This is the message I get when I 
> try to run R from the command line on my mac
> 
>  
> 
> fernandodepaolis@MacBook-Pro-2 ~ % R
> 
>  
> 
> R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
> 
> Copyright (C) 2023 The R Foundation for Statistical Computing
> 
> Platform: x86_64-apple-darwin20 (64-bit)
> 
>  
> 
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> 
> You are welcome to redistribute it under certain conditions.
> 
> Type 'license()' or 'licence()' for distribution details.
> 
>  
> 
>   Natural language support but running in an English locale
> 
>  
> 
> R is a collaborative project with many contributors.
> 
> Type 'contributors()' for more information and
> 
> 'citation()' on how to cite R or R packages in publications.
> 
>  
> 
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 
> 'help.start()' for an HTML browser interface to help.
> 
> Type 'q()' to quit R.
> 
>  
> 
> During startup - Warning message:
> 
> package ‘datasets’ in options("defaultPackages") was not found 
> 
> Error in loadNamespace(name) : object 'pkgInfo' not found
> 
> In addition: Warning message:
> 
> In loadNamespace(name) : package ‘compiler’ has no 'package.rds' in Meta/
> 
> Fatal error: unable to initialize the JIT
> 
>  
> 
>  
> 
>  
> 
> There was no ‘message’ of any sort when trying to run R.app. There was a 
> brief flickering (like quick blinking) but nothing else.
> 
>  
> 
> 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 
> Date: Wednesday, June 7, 2023 at 9:13 PM
> To: Simon Urbanek 
> Cc: r-sig-mac@r-project.org 
> Subject: Re: [R-SIG-Mac] Serious problem with R on macOS
> 
> Hi Simon,
> 
> You're right, I didn't post it...I'll make sure I do next time it 
> happens...it's working fine for now...
> 
>  
> 
> Thank you.
> 
>  
> 
>  
> 
>  
> 
> Fernando DePaolis
> 
> Dean Of Academic Operations & Integration 
> 
> Middlebury Institute of International Studies
> 
>  
> 
> Sent from Outlook for iOS. Apologies for any typos.
> 
>  

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

[David Winsemius]

On 6/8/23 09:33, DePaolis, Fernando wrote:

�well�here it goes again�it failed just now. This is the message I get when I 
try to run R from the command line on my mac



You were advised to try using Disk Utility / First Aid. Have you done so 
yet?


 (You are getting intermittent errors accessing base packages. So this 
may just be a flakey disk sector.)



--

David.




fernandodepaolis@MacBook-Pro-2 ~ % R



R version 4.3.0 (2023-04-21) -- "Already Tomorrow"

Copyright (C) 2023 The R Foundation for Statistical Computing

Platform: x86_64-apple-darwin20 (64-bit)



R is free software and comes with ABSOLUTELY NO WARRANTY.

You are welcome to redistribute it under certain conditions.

Type 'license()' or 'licence()' for distribution details.



   Natural language support but running in an English locale



R is a collaborative project with many contributors.

Type 'contributors()' for more information and

'citation()' on how to cite R or R packages in publications.



Type 'demo()' for some demos, 'help()' for on-line help, or

'help.start()' for an HTML browser interface to help.

Type 'q()' to quit R.



During startup - Warning message:

package �datasets� in options("defaultPackages") was not found

Error in loadNamespace(name) : object 'pkgInfo' not found

In addition: Warning message:

In loadNamespace(name) : package �compiler� has no 'package.rds' in Meta/

Fatal error: unable to initialize the JIT



There was no �message� of any sort when trying to run R.app. There was a brief 
flickering (like quick blinking) but nothing else.

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 
Date: Wednesday, June 7, 2023 at 9:13 PM
To: Simon Urbanek 
Cc: r-sig-mac@r-project.org 
Subject: Re: [R-SIG-Mac] Serious problem with R on macOS
Hi Simon,
You're right, I didn't post it...I'll make sure I do next time it 
happens...it's working fine for now...

Thank you.



Fernando DePaolis
Dean Of Academic Operations & Integration
Middlebury Institute of International Studies

Sent from Outlook for iOS. Apologies for any typos.


From: Simon Urbanek 
Sent: Wednesday, June 7, 2023 6:08:12 PM
To: DePaolis, Fernando 
Cc: r-sig-mac@r-project.org 
Subject: Re: [R-SIG-Mac] Serious problem with R on macOS

[You don't often get email from simon.urba...@r-project.org. Learn why this is 
important at https://aka.ms/LearnAboutSenderIdentification ]

Fernando,

I don't think you posted the error you get when running R on the command line - 
can you copy/paste what you get when running R in the Terminal? Similarly, do 
you also get an error when running the R app (in Applications)?

Cheers,
Simon




On 6/06/2023, at 6:32 AM, DePaolis, Fernando  wrote:

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 
Date: Monday, June 5, 2023 at 10:19 AM
To: 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.












Fernando DePaolis, Ph.D.
Dean of Academic Operations & Integration

Associate Professor

Middlebury Institute of International Studies at 

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

[peter dalgaard]

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  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 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 
> Date: Tuesday, June 6, 2023 at 10:20 AM
> To: peter dalgaard 
> Cc: Calboli Federico (LUKE) , 
> 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 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 
> Date: Tuesday, June 6, 2023 at 9:50 AM
> To: DePaolis, Fernando 
> Cc: Calboli Federico (LUKE) , 
> r-sig-mac@r-project.org 
> Subject: Re: [R-SIG-Mac] Serious problem with R on macOS
> 
> [You don't often get email from pda...@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  
> > 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
> >
> >
> 

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

[Duncan Murdoch]

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 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 
Date: Tuesday, June 6, 2023 at 10:20 AM
To: peter dalgaard 
Cc: Calboli Federico (LUKE) , 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 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 
Date: Tuesday, June 6, 2023 at 9:50 AM
To: DePaolis, Fernando 
Cc: Calboli Federico (LUKE) , r-sig-mac@r-project.org 

Subject: Re: [R-SIG-Mac] Serious problem with R on macOS
[You don't often get email from pda...@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  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 

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

[John Helly via R-SIG-Mac]

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 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 
Date: Tuesday, June 6, 2023 at 10:20 AM
To: peter dalgaard 
Cc: Calboli Federico (LUKE) , 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 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 
Date: Tuesday, June 6, 2023 at 9:50 AM
To: DePaolis, Fernando 
Cc: Calboli Federico (LUKE) , r-sig-mac@r-project.org 

Subject: Re: [R-SIG-Mac] Serious problem with R on macOS
[You don't often get email from pda...@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  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 

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

[DePaolis, Fernando]

This is what I got when trying to run R from the console




R version 4.3.0 (2023-04-21) -- "Already Tomorrow"

Copyright (C) 2023 The R Foundation for Statistical Computing

Platform: x86_64-apple-darwin20 (64-bit)



R is free software and comes with ABSOLUTELY NO WARRANTY.

You are welcome to redistribute it under certain conditions.

Type 'license()' or 'licence()' for distribution details.



  Natural language support but running in an English locale



R is a collaborative project with many contributors.

Type 'contributors()' for more information and

'citation()' on how to cite R or R packages in publications.



Type 'demo()' for some demos, 'help()' for on-line help, or

'help.start()' for an HTML browser interface to help.

Type 'q()' to quit R.



During startup - Warning message:

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

Error in loadNamespace(name) : object 'pkgInfo' not found

In addition: Warning message:

In loadNamespace(name) : package ‘compiler’ has no 'package.rds' in Meta/

Fatal error: unable to initialize the JIT





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: Keith Bierman 
Date: Thursday, June 8, 2023 at 9:51 AM
To: DePaolis, Fernando 
Cc: peter dalgaard , r-sig-mac@r-project.org 

Subject: Re: [R-SIG-Mac] Serious problem with R on macOS
You don't often get email from khb...@gmail.com. Learn why this is 
important

On Thu, Jun 8, 2023 at 10:43 AM DePaolis, Fernando 
mailto:fdepao...@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@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

If you open up the "Console" app you should have access to the system logs, 
which might have some useful hints about what is actually failing, or leading 
up to the failure.

[[alternative HTML version deleted]]

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

[Keith Bierman]

On Thu, Jun 8, 2023 at 10:43 AM 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
> 
>
> If you open up the "Console" app you should have access to the system
logs, which might have some useful hints about what is actually failing, or
leading up to the failure.

[[alternative HTML version deleted]]

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

[DePaolis, Fernando]

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 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 
Date: Tuesday, June 6, 2023 at 10:20 AM
To: peter dalgaard 
Cc: Calboli Federico (LUKE) , 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 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 
Date: Tuesday, June 6, 2023 at 9:50 AM
To: DePaolis, Fernando 
Cc: Calboli Federico (LUKE) , r-sig-mac@r-project.org 

Subject: Re: [R-SIG-Mac] Serious problem with R on macOS
[You don't often get email from pda...@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  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 
> Date: Tuesday, June 6, 2023 at 8:48 AM
> To: DePaolis, Fernando 
> Cc: Calboli Federico (LUKE) , 
> r-sig-mac@r-project.org 
> Subject: Re: [R-SIG-Mac] Serious problem with R on macOS
>
> [You don't often get email from pda...@gmail.com. Learn why this is important 
> at https://aka.ms/LearnAboutSenderIdentification ]
>
> OK, so
>
> - OS version?
> - What do you do 

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

[DePaolis, Fernando]

�well�here it goes again�it failed just now. This is the message I get when I 
try to run R from the command line on my mac


fernandodepaolis@MacBook-Pro-2 ~ % R



R version 4.3.0 (2023-04-21) -- "Already Tomorrow"

Copyright (C) 2023 The R Foundation for Statistical Computing

Platform: x86_64-apple-darwin20 (64-bit)



R is free software and comes with ABSOLUTELY NO WARRANTY.

You are welcome to redistribute it under certain conditions.

Type 'license()' or 'licence()' for distribution details.



  Natural language support but running in an English locale



R is a collaborative project with many contributors.

Type 'contributors()' for more information and

'citation()' on how to cite R or R packages in publications.



Type 'demo()' for some demos, 'help()' for on-line help, or

'help.start()' for an HTML browser interface to help.

Type 'q()' to quit R.



During startup - Warning message:

package �datasets� in options("defaultPackages") was not found

Error in loadNamespace(name) : object 'pkgInfo' not found

In addition: Warning message:

In loadNamespace(name) : package �compiler� has no 'package.rds' in Meta/

Fatal error: unable to initialize the JIT



There was no �message� of any sort when trying to run R.app. There was a brief 
flickering (like quick blinking) but nothing else.

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 
Date: Wednesday, June 7, 2023 at 9:13 PM
To: Simon Urbanek 
Cc: r-sig-mac@r-project.org 
Subject: Re: [R-SIG-Mac] Serious problem with R on macOS
Hi Simon,
You're right, I didn't post it...I'll make sure I do next time it 
happens...it's working fine for now...

Thank you.



Fernando DePaolis
Dean Of Academic Operations & Integration
Middlebury Institute of International Studies

Sent from Outlook for iOS. Apologies for any typos.


From: Simon Urbanek 
Sent: Wednesday, June 7, 2023 6:08:12 PM
To: DePaolis, Fernando 
Cc: r-sig-mac@r-project.org 
Subject: Re: [R-SIG-Mac] Serious problem with R on macOS

[You don't often get email from simon.urba...@r-project.org. Learn why this is 
important at https://aka.ms/LearnAboutSenderIdentification ]

Fernando,

I don't think you posted the error you get when running R on the command line - 
can you copy/paste what you get when running R in the Terminal? Similarly, do 
you also get an error when running the R app (in Applications)?

Cheers,
Simon



> On 6/06/2023, at 6:32 AM, DePaolis, Fernando  wrote:
>
> 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 
> Date: Monday, June 5, 2023 at 10:19 AM
> To: 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.
>
>
>
>
>
> 
>
>
>
>
>
>
> 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