[R-SIG-Mac] Rstan compilation hangs misterisouly

Mon Nov 9 11:50:14 CET 2020

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
> 