[R-SIG-Mac] Rstan compilation hangs misterisouly

[Goncalo Ferraz]

ok, found it! Makevars is where you said it would be and it contains only this line:

CXX14FLAGS += -O3 -mtune=native -arch x86_64 -ftemplate-depth-256

Does it seem to mean anything relevant?

> On Nov 8, 2020, at 11:24 PM, Ken Beath <ken using kjbeath.com.au> wrote:
> 
> It is actually Makevars. If it is there it will be in the .R directory of your home folder.
> 
> Unless it has been set up for something else, like Rcpp, then it can probably be deleted. 
> 
> Ken
> 
>> On 9 Nov 2020, at 12:43 pm, Goncalo Ferraz <gfapple using mac.com> wrote:
>> 
>> Hi,
>> 
>> Yes, at some point there was a problem with schools.stan, it needed an extra (empty) line added to the end. But that didn’t solve the problem. I tried at least three different tests, with different models, and the same thing happens.
>> 
>> Tried to get rid of .MakeVars and as I remember it didn’t change anything. I wanted to try it again now, but I am not finding a .MakeVars file anywhere on my computer. Where should it be?
>> 
>> Thanks,
>> 
>> Gonçalo
>> 
>>> On Nov 8, 2020, at 8:04 PM, Ken Beath <ken using kjbeath.com.au> wrote:
>>> 
>>> Guessing here. Possibly schools.stan has a problem, that is what teh first error is suggesting. The remaining is a possible problem with .MakeVars which is no longer needed with R. I would also check that files aren’t being saved with a strange encoding.
>>> 
>>> Ken
>>> 
>>>> On 9 Nov 2020, at 7:25 am, Roy Mendelssohn - NOAA Federal via R-SIG-Mac <r-sig-mac using r-project.org> wrote:
>>>> 
>>>> Hi:
>>>> 
>>>> While it is possible you will get the help you seek here,  I think you would likely to get more help,  and more knowledgeable help, on this more specialized issue,  at the Stan Forum.  https://discourse.mc-stan.org.  I remember seeing in the summaries I get some issues with different combinations of versions of R,  Stan and compilers.
>>>> 
>>>> HTH,
>>>> 
>>>> -Roy
>>>> 
>>>>> On Nov 8, 2020, at 12:16 PM, Goncalo Ferraz via R-SIG-Mac <r-sig-mac using r-project.org> wrote:
>>>>> 
>>>>> Hi, 
>>>>> 
>>>>> I’ve been struggling with an rstan problem for weeks. I installed R stan following instructions in https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started#how-to-use-rstan <https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started#how-to-use-rstan> to the letter, but when I try to compile any model R leaves me hanging indefinitely (I’ve waited up to 30 minutes with ridiculously short models). When I press esc R says:
>>>>> 
>>>>> Warning messages:
>>>>> 1: In readLines(file, warn = TRUE) :
>>>>> incomplete final line found on '/Users/gferraz/Documents/MAF/R/schools.stan'
>>>>> 2: In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
>>>>> system call failed: Result too large
>>>>> 3: In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
>>>>> error in running command
>>>>> 
>>>>> And then, R won’t quit. I can only close it by force quitting the software itself and some R process that is set in motion and appears in the Activity Monitor.
>>>>> 
>>>>> I have tried everything that was suggested in the stan forum, including deleting all the contents of /usr/local, removing xcode, R and re-installing everything again.
>>>>> 
>>>>> The only thing that I can think of now is to do a clean install of Mac OS on my machine and really start from scratch.
>>>>> 
>>>>> Anyone has a less radical recommendation?
>>>>> 
>>>>> Thank you,
>>>>> 
>>>>> Gonçalo
>>>>> 	[[alternative HTML version deleted]]
>>>>> 
>>>>> _______________________________________________
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>>>>> R-SIG-Mac using r-project.org
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>>>> 
>>>> **********************
>>>> "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.Mendelssohn using 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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>> 
>