Re: [R-SIG-Mac] Rstan compilation hangs misterisouly

2020-11-12 Thread Gonçalo Ferraz 
Hello Milani,

Thank you very much for your e-mail. I was not aware of CmdStan and cmdstanr 
and will look into them. Meanwhile, I will continue using rstan 2.19.3.

Regarding Makevars, I am puzzled that now I have two Makevars files, both 
within the folder 
~/Library/Frameworks/R.framework/Versions/4.0/Resources/library 

one sits in the folder RcppArmadillo/Skeleton and contains:

## With R 3.1.0 or later, you can uncomment the following line to tell R to 
## enable compilation with C++11 (where available)
##
## Also, OpenMP support in Armadillo prefers C++11 support. However, for wider
## availability of the package we do not yet enforce this here.  It is however
## recommended for client packages to set it.
##
## And with R 3.4.0, and RcppArmadillo 0.7.960.*, we turn C++11 on as OpenMP
## support within Armadillo prefers / requires it
CXX_STD = CXX11

PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) 
PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

the other, in folder RcppEigen/skeleton, has every line commented out:

## With Rcpp 0.11.0 and later, we no longer need to set PKG_LIBS as there is
## no user-facing library. The include path to headers is already set by R.
#PKG_LIBS =

## With R 3.1.0 or later, you can uncomment the following line to tell R to
## enable compilation with C++11 (or even C++14) where available
## CXX_STD = CXX11

The Renviron file has a lot mor information.

Since you tell me that none of these files are relevant for my problem now, I 
am inclined to forget abou them, but I am still curious as to what is their 
purpose.

Best wishes,

Gonçalo




Gonçalo Ferraz
Departamento de Ecologia, Instituto de Biociências
Universidade Federal do Rio Grande do Sul
http://ferrazlab.org/ 




> On Nov 9, 2020, at 7:05 PM, Milani Chaloupka  wrote:
> 
> Hi Goncalo
> 
> The issue, as I pointed out to you yesterday on Stan Discourse, is rstan (the 
> interface to Stan via R).
> 
> And hence my advice to you there was to downgrade to Stan 2.19.3
> 
> It was not your Makevars file - although that was an incomplete Makevars you 
> had if there were in fact no typos in your previous email.
> 
> As others have pointed out, a Makevars file is no longer necessary to run 
> Stan if using MACOS X Catalina onwards. 
> 
> Nor is the Renviron file.
> 
> Do not upgrade to any rstan higher than 2.19.3 until the rstan issues on 
> various platforms are resolved.
> 
> Meanwhile, you can use, as is my preference, the CmdStan and cmdstanr 
> interface to Stan instead of rstan, which …
> 
> (1) samples quite a bit faster than rstan
> 
> (2) is more up-to-date with Stan although with a few less features than rstan
> 
> http://mc-stan.org/cmdstanr/articles/cmdstanr.html 
> 
> 
> And if you are using the brms interface to Stan then it also has an option in 
> the brm() function to use cmdstanr as the backend rather than rstan.
> 
> regards
> 
> Milani
> 
> 
> 
> Dr Milani Chaloupka
> Ecological Modelling Services P/L
> PO Box 6150, University of Queensland
> St Lucia, Queensland, 4067, Australia
> 
> Honorary Associate Professor
> School of Biological Sciences, University of Queensland
> Brisbane, Queensland, 4072, Australia
> 
> Scientific Advisory Committee (Member)
> Caribbean Conservation Corporation
> Gainesville, Florida, USA
> 
> Science and Statistics Committee (Member)
> Western Pacific Regional Fisheries Management Council
> NOAA, US Dept of Commerce, Honolulu, Hawaii, USA
> 
> [email protected] 
> mobile: (local) 0419180554  (international) + 61 419180554
> skype: milani2005
> 
> 
> 
>> On 10 Nov 2020, at 6:03 am, Goncalo Ferraz via R-SIG-Mac 
>> mailto:[email protected]>> wrote:
>> 
>> 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 >> > 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.
>>> 
> 


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Re: [R-SIG-Mac] Rstan compilation hangs misterisouly

2020-11-09 Thread Milani Chaloupka 
Hi Goncalo

The issue, as I pointed out to you yesterday on Stan Discourse, is rstan (the 
interface to Stan via R).

And hence my advice to you there was to downgrade to Stan 2.19.3

It was not your Makevars file - although that was an incomplete Makevars you 
had if there were in fact no typos in your previous email.

As others have pointed out, a Makevars file is no longer necessary to run Stan 
if using MACOS X Catalina onwards.

Nor is the Renviron file.

Do not upgrade to any rstan higher than 2.19.3 until the rstan issues on 
various platforms are resolved.

Meanwhile, you can use, as is my preference, the CmdStan and cmdstanr interface 
to Stan instead of rstan, which …

(1) samples quite a bit faster than rstan

(2) is more up-to-date with Stan although with a few less features than rstan

http://mc-stan.org/cmdstanr/articles/cmdstanr.html

And if you are using the brms interface to Stan then it also has an option in 
the brm() function to use cmdstanr as the backend rather than rstan.

regards

Milani



Dr Milani Chaloupka
Ecological Modelling Services P/L
PO Box 6150, University of Queensland
St Lucia, Queensland, 4067, Australia

Honorary Associate Professor
School of Biological Sciences, University of Queensland
Brisbane, Queensland, 4072, Australia

Scientific Advisory Committee (Member)
Caribbean Conservation Corporation
Gainesville, Florida, USA

Science and Statistics Committee (Member)
Western Pacific Regional Fisheries Management Council
NOAA, US Dept of Commerce, Honolulu, Hawaii, USA

[email protected]
mobile: (local) 0419180554  (international) + 61 419180554
skype: milani2005



On 10 Nov 2020, at 6:03 am, Goncalo Ferraz via R-SIG-Mac 
mailto:[email protected]>> wrote:

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 
mailto:[email protected]>> 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.



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Re: [R-SIG-Mac] Rstan compilation hangs misterisouly

2020-11-09 Thread Goncalo Ferraz via R-SIG-Mac 
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  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
> [email protected] 
> 
> ```
> 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 
>> mailto:[email protected]>> 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 >> > 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 
 mailto:[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 
 mailto:[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  > 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 > > 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 >> > 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 mailto:[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://d

Re: [R-SIG-Mac] Rstan compilation hangs misterisouly

2020-11-09 Thread Robert Goedman via R-SIG-Mac 
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
[email protected]

```
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 
>  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  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 
>>>  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 
>>>  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  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  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  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 
>>>  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 
  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
  
 
  to the letter, but when I try to compile any model R leaves me 
 hanging indefinitely (I’ve waited up to 30 minutes with ridiculou

Re: [R-SIG-Mac] Rstan compilation hangs misterisouly

2020-11-09 Thread Goncalo Ferraz via R-SIG-Mac 
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  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 
>>  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 
>>  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  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  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  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 
>>   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 
>> >  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
>> >  
>> > 
>> >  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]

Re: [R-SIG-Mac] Rstan compilation hangs misterisouly

2020-11-09 Thread Goncalo Ferraz via R-SIG-Mac 
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 
>  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 
> mailto:[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  > > 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  >> > 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  >>> > 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 
>  mailto:[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 
> > mailto:[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
> >  
> > 
> >  
> >  >  
> > >
> >  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."
>

Re: [R-SIG-Mac] Rstan compilation hangs misterisouly

2020-11-09 Thread 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 <
[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  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  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  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  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
> R-SIG

Re: [R-SIG-Mac] Rstan compilation hangs misterisouly

2020-11-08 Thread Ken Beath 
It looks like what used to be suggested for stan. Move it elsewhere and then 
see what happens.

Ken

> On 9 Nov 2020, at 2:57 pm, Goncalo Ferraz  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  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  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  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 
>  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 
>>  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
>>  
>> 
>>  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
 
>>> 
>> 
> 

___

Re: [R-SIG-Mac] Rstan compilation hangs misterisouly

2020-11-08 Thread Goncalo Ferraz via R-SIG-Mac 
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  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  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  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 
  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 
>  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
>  
> 
>  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

Re: [R-SIG-Mac] Rstan compilation hangs misterisouly

2020-11-08 Thread Ken Beath 
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  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  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 
>>>  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 
  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
  
 
  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

Re: [R-SIG-Mac] Rstan compilation hangs misterisouly

2020-11-08 Thread Goncalo Ferraz via R-SIG-Mac 
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  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 
>>  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 
>>>  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
>>>  
>>> 
>>>  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

Re: [R-SIG-Mac] Rstan compilation hangs misterisouly

2020-11-08 Thread Ken Beath 
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 
>  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 
>>  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
>>  
>> 
>>  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.
> 
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> R-SIG-Mac mailing list
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Re: [R-SIG-Mac] Rstan compilation hangs misterisouly

2020-11-08 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac 
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 
>  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 
> 
>  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.

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