subject:"\[R\-SIG\-Mac\] R 4.1 for my Mac M1 crashing on installing packages"

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

2021-05-22 Thread Simon Urbanek



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



> On May 23, 2021, at 10:15 AM, Roy Mendelssohn - NOAA Federal 
>  wrote:
> 
> 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
> 
>> On May 22, 2021, at 2:57 PM, Simon Urbanek  
>> wrote:
>> 
>> 
>> 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  
>>> 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_m4crgn/T/RtmpydK1sm/downloaded_packages’
>>> Warning message:
>>> In install.packages("rgdal") :
>>> installation of package ‘rgdal’ had non-zero exit status
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> On Thu, 20 May 2021 at 11:46, Simon Urbanek  
>>> 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  
 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  
 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  
> wrote:
> 
> Hi Simon,
> 
> I'm happy to, I'm just not sure how to check previous logs...
>

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

2021-05-22 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac

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

> On May 22, 2021, at 2:57 PM, Simon Urbanek  
> wrote:
> 
> 
> 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  
>> 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_m4crgn/T/RtmpydK1sm/downloaded_packages’
>> Warning message:
>> In install.packages("rgdal") :
>>  installation of package ‘rgdal’ had non-zero exit status
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> On Thu, 20 May 2021 at 11:46, Simon Urbanek  
>> 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  
>>> 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  
>>> 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  
 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:

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

2021-05-22 Thread Renato Morais

Ok, thanks for the clarification Simon.

Cheers,
Renato

On Sun, 23 May 2021 at 07:57, Simon Urbanek 
wrote:

> 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 <
> renatomoraisara...@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_m4crgn/T/RtmpydK1sm/downloaded_packages’
> > Warning message:
> > In install.packages("rgdal") :
> >   installation of package ‘rgdal’ had non-zero exit status
> >
> >
> > 
> >
> >
> >
> >
> > On Thu, 20 May 2021 at 11:46, Simon Urbanek 
> 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 <
> renatomoraisara...@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.urba...@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 <
> renatomoraisara...@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
> > > >

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

2021-05-22 Thread Simon Urbanek



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  
> 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_m4crgn/T/RtmpydK1sm/downloaded_packages’
> Warning message:
> In install.packages("rgdal") :
>   installation of package ‘rgdal’ had non-zero exit status
> 
> 
> 
> 
> 
> 
> 
> On Thu, 20 May 2021 at 11:46, Simon Urbanek  
> 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  
> > 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  
> > 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  
> > > 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  
> > > 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,

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

2021-05-19 Thread Simon Urbanek



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  
> 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  
> 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  
> > 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  
> > 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  
> > > 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  wrote:
> > > 
> > >> On Wed, May 19, 2021 at 11:34 AM Renato Morais
> > >>  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@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

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

2021-05-19 Thread Simon Urbanek



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


> On 20/05/2021, at 12:28 PM, Renato Morais  
> 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  
> 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  
> > 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  
> > 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  
> > > 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  wrote:
> > > 
> > >> On Wed, May 19, 2021 at 11:34 AM Renato Morais
> > >>  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

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

2021-05-19 Thread 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 
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 
> 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 
>> 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.urba...@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 <
>> renatomoraisara...@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 
>> wrote:
>> > >
>> > >> On Wed, May 19, 2021 at 11:34 AM Renato Morais
>> > >>  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@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
>> >

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

2021-05-19 Thread Simon Urbanek



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  
> 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  
> 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  
> > 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  wrote:
> > 
> >> On Wed, May 19, 2021 at 11:34 AM Renato Morais
> >>  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@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
>  
> -- 

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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

2021-05-19 Thread Renato Morais

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 
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 
> 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  wrote:
> >
> >> On Wed, May 19, 2021 at 11:34 AM Renato Morais
> >>  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@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



--

[[alternative HTML version deleted]]

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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

2021-05-19 Thread Simon Urbanek



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  
> 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  wrote:
> 
>> On Wed, May 19, 2021 at 11:34 AM Renato Morais
>>  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@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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

2021-05-19 Thread Renato Morais

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  wrote:

> On Wed, May 19, 2021 at 11:34 AM Renato Morais
>  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@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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

2021-05-19 Thread Ken Beath

According to RStudio support for ARM R is only available in the RStudio daily 
builds https://dailies.rstudio.com  which are 
very unstable.

Ken

> On 19 May 2021, at 7:33 pm, Renato Morais  
> 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.
> 
> 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
> 
> -- 
> 
> *Renato Morais*
> 
> 
> 
> --
> 
>   [[alternative HTML version deleted]]
> 
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac


[[alternative HTML version deleted]]

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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

2021-05-19 Thread Jeroen Ooms

On Wed, May 19, 2021 at 11:34 AM Renato Morais
 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.

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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

2021-05-19 Thread 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

-- 

*Renato Morais*



--

[[alternative HTML version deleted]]

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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

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

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

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

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

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

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

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

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

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

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

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

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

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

14 matches

Site Navigation

Mail list logo

Footer information