[R-SIG-Mac] Rstan compilation hangs misterisouly

Mon Nov 9 21:00:45 CET 2020

Hi,

Not sure if this helps and/or is even related but since about 2 months I have not been able to get rstan to work inside the R-GUI. Like you describe, it hangs and never returns. I don’t use rstan directly but use ulam() in the `rethinking` package to very occasionally check the Stan language program generated by ulam() after running it.

After struggling for a few weeks I decided to try it in vanilla R and found below test script no longer hangs.

Again, not sure this is of any help, but just wanted to chime in.

Rob J Goedman
goedman using icloud.com

```
library(rethinking)
d <- sim_happiness( seed=1977 , N_years=1000 )
precis(d)

## R code 6.22
d2 <- d[ d$age>17 , ] # only adults
d2$A <- ( d2$age - 18 ) / ( 65 - 18 )

## R code 6.23
d2$mid <- d2$married + 1
m6.9 <- quap(
    alist(
        happiness ~ dnorm( mu , sigma ),
        mu <- a[mid] + bA*A,
        a[mid] ~ dnorm( 0 , 1 ),
        bA ~ dnorm( 0 , 2 ),
        sigma ~ dexp(1)
    ) , data=d2 )
precis(m6.9,depth=2)

m6.9u <- ulam(
    alist(
        happiness ~ dnorm( mu , sigma ),
        mu <- a[mid] + bA*A,
        a[mid] ~ dnorm( 0 , 1 ),
        bA ~ dnorm( 0 , 2 ),
        sigma ~ dexp(1)
    ) , data=d2 )
precis(m6.9u,depth=2)
```

> On Nov 9, 2020, at 05:50, Goncalo Ferraz via R-SIG-Mac <r-sig-mac using r-project.org> wrote:
> 
> deleting Makevars didn’t work. The command:
> 
> example(stan_model, package = “rstan”, run.dontrun = TRUE)
> 
> left me hanging with this output:
> 
> stn_md> stancode <- ‘data {real y_mean;} parameters {real y;} model {y ~ normal(y_mean,1);}’
> 
> stn_md> mod <- stan_model(model_code = stancode, verbose = TRUE)
> 
> TRANSLATING MODEL ‘16a540c6086086816528e4524def24d9’ FROM Stan CODE TO C++ CODE NOW.
> successful in parsing the Stan model ‘16a540c6086086816528e4524def24d9’.
> indent preformatted text by 4 spaces
> 
> That’s what’s been happening with any attempt to compile.
> 
> 
> 
>> On Nov 9, 2020, at 7:30 AM, Goncalo Ferraz <gfapple using mac.com> wrote:
>> 
>> Interesting. Thanks! Is it best to delete the line and keep an empty file, or should I just get rid of the file altogether?
>> 
>> 
>>> On Nov 9, 2020, at 6:01 AM, Kasper Daniel Hansen <kasperdanielhansen using gmail.com> wrote:
>>> 
>>> This line will essentially overwrite what RStan does for compilation. So yes, this is potentially a bad thing.
>>> 
>>> On Mon, Nov 9, 2020 at 4:57 AM Goncalo Ferraz via R-SIG-Mac <r-sig-mac using r-project.org> 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
>>>>>>> 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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>>>>>> 
>>>>> 
>>>> 
>>> 
>>> _______________________________________________
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>>> 
>>> -- 
>>> Best,
>>> Kasper
>> 
> 
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