[R-SIG-Mac] R 4.1 for my Mac M1 crashing on installing packages

Simon Urbanek @|mon@urb@nek @end|ng |rom R-project@org
Sat May 22 23:57:14 CEST 2021 

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



> On May 22, 2021, at 12:31 PM, Renato Morais <renatomoraisaraujo using gmail.com> wrote:
> 
> 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
> 
> > install.packages('rgdal')
> 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.png>
> 
> 
> 
> 
> On Thu, 20 May 2021 at 11:46, Simon Urbanek <simon.urbanek using r-project.org> wrote:
> 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
> 
> 
> 
> 
> 
> > On 20/05/2021, at 12:28 PM, Renato Morais <renatomoraisaraujo using gmail.com> wrote:
> > 
> > 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 using r-project.org> wrote:
> > 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
> > 
> > 
> > 
> > > On 20/05/2021, at 10:27 AM, Renato Morais <renatomoraisaraujo using gmail.com> wrote:
> > > 
> > > 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 using r-project.org> wrote:
> > > 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
> > > 
> > > 
> > > > On 20/05/2021, at 12:07 AM, Renato Morais <renatomoraisaraujo using gmail.com> wrote:
> > > > 
> > > > 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 using berkeley.edu> wrote:
> > > > 
> > > >> On Wed, May 19, 2021 at 11:34 AM Renato Morais
> > > >> <renatomoraisaraujo using gmail.com> wrote:
> > > >>> 
> > > >>> 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.
> > > >> 
> > > >> 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.
> > > >> 
> > > > 
> > > > 
> > > > -- 
> > > > 
> > > > *Renato Morais | **ARC Postdoctoral Research Associate*
> > > > 
> > > > Research Hub for Coral Reef Ecosystem Functions
> > > > 
> > > > College of Science and Engineering
> > > > 
> > > > ARC Centre of Excellence for Coral Reef Studies
> > > > 
> > > > James Cook University
> > > > 
> > > > Townsville, Queensland, Australia
> > > > 
> > > > https://www.reeffunctionhub.org
> > > > 
> > > > http://thebellwoodreeffishlab.com
> > > > 
> > > > 
> > > > 
> > > > --
> > > > 
> > > >       [[alternative HTML version deleted]]
> > > > 
> > > > _______________________________________________
> > > > R-SIG-Mac mailing list
> > > > R-SIG-Mac using r-project.org
> > > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> > > > 
> > > 
> > > 
> > > 
> > > -- 
> > > Renato Morais | ARC Postdoctoral Research Associate
> > > 
> > > Research Hub for Coral Reef Ecosystem Functions
> > > College of Science and Engineering
> > > ARC Centre of Excellence for Coral Reef Studies
> > > James Cook University
> > > Townsville, Queensland, Australia
> > > https://www.reeffunctionhub.org
> > > http://thebellwoodreeffishlab.com
> > >  
> > > -- 
> > 
> > 
> > 
> > -- 
> > Renato Morais | ARC Postdoctoral Research Associate
> > 
> > Research Hub for Coral Reef Ecosystem Functions
> > College of Science and Engineering
> > ARC Centre of Excellence for Coral Reef Studies
> > James Cook University
> > Townsville, Queensland, Australia
> > https://www.reeffunctionhub.org
> > http://thebellwoodreeffishlab.com
> >  
> > -- 
> > <R_2021-05-17-082003_Renatos-MacBook-Pro.crash><X11.bin_2021-05-19-184846_Renatos-MacBook-Pro.crash><rsession_2021-05-19-182539_Renatos-MacBook-Pro.crash><rsession_2021-05-19-193014_Renatos-MacBook-Pro.crash><rsession_2021-05-19-182051_Renatos-MacBook-Pro.crash><R_2021-05-19-181442_Renatos-MacBook-Pro.crash><rsession_2021-05-19-182006_Renatos-MacBook-Pro.crash>_______________________________________________
> > R-SIG-Mac mailing list
> > R-SIG-Mac using r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
> 
> 
> -- 
> Renato Morais | ARC Postdoctoral Research Associate
> 
> Research Hub for Coral Reef Ecosystem Functions
> College of Science and Engineering
> ARC Centre of Excellence for Coral Reef Studies
> James Cook University
> Townsville, Queensland, Australia
> https://www.reeffunctionhub.org
> http://thebellwoodreeffishlab.com
>  
> --

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