[R-SIG-Mac] Rstan compilation hangs misterisouly

Mon Nov 9 11:30:22 CET 2020

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

	[[alternative HTML version deleted]]