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

[Renato Morais]

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 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
>
>
>
> --
>


-- 

*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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