[R-SIG-Mac] Rstan compilation hangs misterisouly

[Ken Beath]

It looks like what used to be suggested for stan. Move it elsewhere and then see what happens.

Ken

> On 9 Nov 2020, at 2:57 pm, Goncalo Ferraz <gfapple using mac.com> wrote:
> 
> 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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>>>>> 
>>>>> **********************
>>>>> "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
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>>>>> ***Note new street address***
>>>>> 110 McAllister Way
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>>>>> Fax: (831) 420-3980
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>>>>> 
>>>>> "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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>>> 
>> 
>