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
```
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> 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> 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> 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> 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> 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> 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> 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> 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@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]]
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> R-SIG-Mac mailing list
>>>>>>>> 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 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.
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> R-SIG-Mac mailing list
>>>>>>> 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
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>
>>>
>>> --
>>> Best,
>>> Kasper
>>
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
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