[R-SIG-Mac] Rstan compilation hangs misterisouly

[Kasper Daniel Hansen]

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

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