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

[Renato Morais]

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: 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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