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R 4.1 for my Mac M1 crashing on installing packages

16 messages · Renato Morais, Jeroen Ooms, Ken Beath +2 more

Original
Renato Morais
# 
Hi all,

I'm new here, so please forgive my clumsy error reporting.

I have just downloaded *R-4.1-branch.pkg* for my Mac M1, as I wanted to
finally enjoy a native normal-speed R (for some reason running v 4.0.5 on
Rosetta was extremely slow on my machine). I also installed the latest
XQuartz, as indicated (v 2.8.1).

Sad story is, when I try a simple install.packages command, it first
appears to ignore me, after returning 'Please select a CRAN mirror for use
in this session'. if I insist, it crashes. No useful error messages. Trying
via the Package Installer tab didn't work either. It doesn't find any
packages, indeed it crashes if I ask it to load the list.

Trying to open via R.Studio 1.4.1106 was as unsuccessful. In fact, I get a
nice 'Error starting R' rendered window saying it cannot load my library:

dyld: could not load inserted library
'/Library/Frameworks/R.framework/Resources/lib/libR.dylib' because no
suitable image found. Did find:
/Library/Frameworks/R.framework/Resources/lib/libR.dylib: mach-o, but wrong
architecture /Library/Frameworks/R.framework/Resources/lib/libR.dylib:
stat() failed with errno=1

In summary, can anybody give me an insight on what might be going on?

Cheers and thanks in advance,
Renato
Jeroen Ooms
# 
On Wed, May 19, 2021 at 11:34 AM Renato Morais
<renatomoraisaraujo at gmail.com> wrote:
This indeed sounds like an xQuartz issue, failing to popup the mirror
selection menu. Does everything work if you manually set your CRAN
mirror first, e.g:

  options(repos=c(CRAN="https://cloud.r-project.org"))

Alternatively you can disable the popup menus all-together using:

  options(menu.graphics=FALSE)

Which should probably be the default.
Ken Beath
# 
According to RStudio support for ARM R is only available in the RStudio daily builds https://dailies.rstudio.com <https://dailies.rstudio.com/> which are very unstable.

Ken

  
  


  


      

    

    

      
      

        


  

        

      Renato Morais
    

    

      
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Thanks Jeroen, fixing the repo connected me with CRAN (it was defaulted to
'@CRAN@' I think)!

Cheers,
Renato

        
On Wed, 19 May 2021 at 21:00, Jeroen Ooms <jeroen at berkeley.edu> wrote:

        

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
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Renato,

I'm glad you have work-around, but I'd still like to get to the core of the issue, we don't want R to crash ;).
Can you, please, check your Console log to see if there is a trace of the crash and if so, send it to me?
Also are you using R in the Terminal or the R.app GUI?

Thanks,
Simon

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Renato Morais
    

    

      
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Hi Simon,

I'm happy to, I'm just not sure how to check previous logs...

On another note, and I'm sure this is a problem with the compiler, now that
my packages are installed, the ones I had to compile from the source cannot
be loaded.

Error: package or namespace load failed for ?nlme? in dyn.load(file,
DLLpath = DLLpath, ...):

 unable to load shared object
'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/nlme/libs/nlme.so':

  dlopen(/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/nlme/libs/nlme.so,
6): Library not loaded: /opt/R/arm64/gfortran/lib/libgfortran.5.dylib

  Referenced from:
/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/nlme/libs/nlme.so

  Reason: image not found


Any insights on how that could be solved?


Thanks again for your help,

Renato

On Thu, 20 May 2021 at 07:00, Simon Urbanek <simon.urbanek at r-project.org>
wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
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Renato,

just open the Console application (under Utilities) - it has all logs from your machine - there will be either an R crash log or some entries in the system log.

As for packages, it will be solved once the R 4.1.0 binaries for arm64 are released (as soon as all builds finish), but you will have to make sure you re-install all packages to remove the pre-releases.

Thanks,
Simon

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Renato Morais
    

    

      
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Hi Simon,

I'll attach the crash reports available, I hope that helps and sorry
there's probably repeated crash reports, as I repeatedly tried the same
things.

So, relative to the source packages there's actually nothing I can do for
now?

Thanks for the attention,
Renato

On Thu, 20 May 2021 at 08:52, Simon Urbanek <simon.urbanek at r-project.org>
wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Renato Morais
    

    

      
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I'd just like to add that Jeroen's workaround is only temporary: whenever I
start a new session, options('repos') becomes @CRAN@ again and I have to
manually set it, otherwise, a new crash...

On Thu, 20 May 2021 at 10:28, Renato Morais <renatomoraisaraujo at gmail.com>
wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
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Thanks for the logs. Unfortunately, there is no obvious reason for the R crash so I'll need to see if I can replicate it.

As for packages, well, there is if you are really that impatient you can either change the path to the R framework in the package instead of /opt/R or you can install the Fortran compiler from
https://mac.r-project.org/libs-arm64/gfortran-f51f1da0-darwin20.0-arm64.tar.gz
but I don't quite see why you would go into all the trouble just to run the old experimental binaries instead of the release.

Cheers,
Simon

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
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I was able to replicate the problem - it is a bug in select.list() in the R.app GUI and it is present in both the Intel and the arm64 version of R 4.1.0 so it is not M1-specific.

The work-around is as Jeroen said to set
options(menu.graphics=FALSE)

Cheers,
Simon

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    
1 day later

    

      
      

        


  

        

      Renato Morais
    

    

      
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Hi Simon and all,

After reinstalling the official binary and reinstalling all packages,
almost everything is working fine. The only exception is rgdal, which is
not available as a binary and, when I try to compile it, I get the error
below. I did extract gFortran from the link you provided and moved it to
the folder /opt/R/arm64 as indicated on CRAN (print screen below).

Anything I'm clearly doing wrong? I appreciate the help.

Cheers and thanks again,
Renato

            

      
      
      
    

        
Package which is only available in source form, and may need compilation of
C/C++/Fortran: ?rgdal?
Do you want to attempt to install these from sources? (Yes/no/cancel) yes
installing the source package ?rgdal?

trying URL 'https://cran.csiro.au/src/contrib/rgdal_1.5-23.tar.gz'
Content type 'application/x-gzip' length 4393536 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

configure: R_HOME: /Library/Frameworks/R.framework/Resources
configure: CC: clang -arch arm64
configure: CXX: clang++ -arch arm64 -std=gnu++14
configure: CFLAGS: -falign-functions=64 -Wall -g -O2
configure: CPPFLAGS: -I/opt/R/arm64/include
configure: CXXFLAGS: -falign-functions=64 -Wall -g -O2
configure: LDFLAGS: -L/opt/R/arm64/lib
configure: LDFLAGS: -L/opt/R/arm64/lib
configure: CXX11 is: clang++ -arch arm64, CXX11STD is: -std=gnu++11
configure: CXX is: clang++ -arch arm64 -std=gnu++11
configure: C++11 support available
configure: rgdal: 1.5-23
checking for /usr/bin/svnversion... no
configure: svn revision: 1121
checking for gdal-config... no
no

The downloaded source packages are in
?/private/var/folders/g0/k2tmg4q931s1x3cy_vm_m4cr0000gn/T/RtmpydK1sm/downloaded_packages?
Warning message:
In install.packages("rgdal") :
  installation of package ?rgdal? had non-zero exit status


[image: image.png]




On Thu, 20 May 2021 at 11:46, Simon Urbanek <simon.urbanek at r-project.org>
wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
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Renato,

rgdal didn't pass checks in the big-sur build, that's why it was not available. rgdal has a very long list of dependencies that are very fragile, so it is quite hard to build yourself (you'd need to build and compile quite a few libraries).
For now I have temporarily disabled the checks for some of the spatial libraries like sf and rdgal since they don't pass them, but it would be good if the issues could be sorted out upstream.

Cheers,
Simon

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Renato Morais
    

    

      
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Ok, thanks for the clarification Simon.

Cheers,
Renato

On Sun, 23 May 2021 at 07:57, Simon Urbanek <simon.urbanek at r-project.org>
wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Roy Mendelssohn - NOAA Federal
    

    

      
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Hi Simon:

So perhaps the take-home message is that if you depend on that suite of packages,  perhaps the time is not ripe to update to R4.1?

Also wondering how this will affect CRAN checks for packages that have on of those packages as "Suggest" or "Depend"?

Thanks,
-Roy

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        
**********************
"The contents of this message do not reflect any position of the U.S. Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: Roy.Mendelssohn at noaa.gov www: https://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected" 
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

  
  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
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Roy,

yes, note that we are talking about the the Big Sur arm64 build. I would still recommend using the "stable" High Sierra Intel build if you prefer stability over speed.

And, yes, if you depend on/import a package that doesn't pass tests, your package won't be available, either. If you have a package in Suggests, then you hopefully wrote your examples/test such that it works even when that package is not available.

Cheers,
Simon