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
> <roy.mendelss...@noaa.gov> 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 <simon.urba...@r-project.org>
>> 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_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.urba...@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 <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
>>>>>
>>>>> 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 <jer...@berkeley.edu> wrote:
>>>>>>
>>>>>>> On Wed, May 19, 2021 at 11:34 AM Renato Morais
>>>>>>> <renatomoraisara...@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@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@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
>
> **********************
> "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.mendelss...@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.
>
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