Hi, This is helpful information. Thank you. Meanwhile, I tried reverting to version 2.19.3 of rstan and it does not hang on me. I couldn’t yet understand what is going on with the most recent version, but at least for now I can work.
Gonçalo > On Nov 9, 2020, at 5:00 PM, Robert Goedman <goed...@icloud.com> wrote: > > 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 > goed...@icloud.com <mailto:goed...@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@r-project.org <mailto:r-sig-mac@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 <gfap...@mac.com >>> <mailto:gfap...@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 >>>> <kasperdanielhan...@gmail.com <mailto:kasperdanielhan...@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@r-project.org <mailto:r-sig-mac@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 <k...@kjbeath.com.au >>>>> <mailto:k...@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 <gfap...@mac.com >>>>>> <mailto:gfap...@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 <k...@kjbeath.com.au >>>>>>> <mailto:k...@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@r-project.org <mailto:r-sig-mac@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 <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@r-project.org <mailto:r-sig-mac@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> >>>>>>>>> >>>>>>>>> <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]] >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> R-SIG-Mac mailing list >>>>>>>>> R-SIG-Mac@r-project.org <mailto: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 <mailto:roy.mendelss...@noaa.gov> >>>>>>>> www: https://www.pfeg.noaa.gov/ <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. >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> R-SIG-Mac mailing list >>>>>>>> R-SIG-Mac@r-project.org <mailto:R-SIG-Mac@r-project.org> >>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>>>>>> >>>>>> >>>>> >>>> >>>> _______________________________________________ >>>> R-SIG-Mac mailing list >>>> R-SIG-Mac@r-project.org <mailto:R-SIG-Mac@r-project.org> >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>>> >>>> >>>> -- >>>> Best, >>>> Kasper >>> >> >> _______________________________________________ >> R-SIG-Mac mailing list >> R-SIG-Mac@r-project.org <mailto:R-SIG-Mac@r-project.org> >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > [[alternative HTML version deleted]] _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
