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 <[email protected]> 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
>> <[email protected]> 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
>> <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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
>> >>>> <[email protected]> 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
>> >>>>> <[email protected]> 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
>> >>>>> [email protected]
>> >>>>> 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: [email protected] 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
>> >>>> [email protected]
>> >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> >>>
>> >>
>> >
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> [email protected]
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>>
>> --
>> Best,
>> Kasper
>
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