Installing rstanarm

[Peter Li]

How do I install rstanarm? I tried using the r package dev tools but when I run install_github("rstanarm") I get client error (406) not acceptable.


Peter

[Ben Goodrich]

I haven't figured it out yet. I would just download either

https://github.com/stan-dev/rstanarm/archive/master.zip # Windows
https://github.com/stan-dev/rstanarm/archive/master.tar.gz # !Windows

and then follow the procedure to install a package from a local file.

Ben

[Peter Li]

I'm using the r package installer and getting this error:

2: In install.packages(file.choose(), "/Users/Peter/rstanarm", NULL,  :
  installation of package ‘/Users/Peter/rstanarm/rstanarm.tar.gz’ had non-zero exit status


Peter

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[Ben Goodrich]

On Thursday, July 25, 2013 11:43:40 AM UTC-4, Peter Li wrote:

I'm using the r package installer and getting this error:

2: In install.packages(file.choose(), "/Users/Peter/rstanarm", NULL,  :
  installation of package ‘/Users/Peter/rstanarm/rstanarm.tar.gz’ had non-zero exit status

What does the output say when you do it from a shell? Mine is working:

goodrich@CYBERPOWERPC:/tmp$ R CMD INSTALL rstanarm.tar.gz
Warning in untar2(tarfile, files, list, exdir, restore_times) :
  skipping pax global extended headers
* installing to library ‘/opt/site-library’                                                                                                                            
* installing *source* package ‘rstanarm’ ...                                                                                                                          
** R                                                                                                                                                                  
** exec                                                                                                                                                                
** preparing package for lazy loading

TRANSLATING MODEL 'Gaussian GLM' FROM Stan CODE TO C++ CODE NOW.
COMPILING THE C++ CODE FOR MODEL 'Gaussian GLM' NOW.
Error : variable does not exist; processing stage=data initialization; variable name=N; base type=int
failed to create the sampler; sampling not done

TRANSLATING MODEL 'Discrete GLM' FROM Stan CODE TO C++ CODE NOW.
COMPILING THE C++ CODE FOR MODEL 'Discrete GLM' NOW.
Error : variable does not exist; processing stage=data initialization; variable name=N; base type=int
failed to create the sampler; sampling not done
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (rstanarm)
goodrich@CYBERPOWERPC:/tmp$ echo $?
0

Ben

[Peter Li]

I get this error:
Error in untar2(tarfile, files, list, exdir) : unsupported entry type ‘g’

[Ben Goodrich]

On Thursday, July 25, 2013 1:04:07 PM UTC-4, Peter Li wrote:

I get this error:
Error in untar2(tarfile, files, list, exdir) : unsupported entry type ‘g’

I have no idea about that. Do you have some ancient version of tar or gzip installed?

I suppose you could try

git clone https://github.com/stan-dev/rstanarm.git
R CMD INSTALL rstanarm/

Ben

[Peter Li]

I'm not sure what version of tar I have but that seemed to have worked. Thanks. I'll let you know which models (if any) can't be run with rstanarm.


Peter

[Peter Li]

Just kidding.. Now it says there's something missing.

Cloning into 'rstanarm'...
remote: Counting objects: 24, done.
remote: Compressing objects: 100% (16/16), done.
remote: Total 24 (delta 3), reused 18 (delta 3)
Unpacking objects: 100% (24/24), done.
Chinese-Secret-Service-Van-4:~ Peter$ R CMD INSTALL rstanarm/
* installing to library ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library’

* installing *source* package ‘rstanarm’ ...
** R
** exec
** preparing package for lazy loading

Warning: package ‘Rcpp’ was built under R version 2.15.3

TRANSLATING MODEL 'Gaussian GLM' FROM Stan CODE TO C++ CODE NOW.
COMPILING THE C++ CODE FOR MODEL 'Gaussian GLM' NOW.
Error : variable does not exist; processing stage=data initialization; variable name=N; base type=int
failed to create the sampler; sampling not done

TRANSLATING MODEL 'Discrete GLM' FROM Stan CODE TO C++ CODE NOW.
COMPILING THE C++ CODE FOR MODEL 'Discrete GLM' NOW.
Error : variable does not exist; processing stage=data initialization; variable name=N; base type=int
failed to create the sampler; sampling not done
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

*** arch - i386
Error : package ‘rstan’ is not installed for 'arch=i386'
Error: loading failed
Execution halted
*** arch - x86_64
Warning: package ‘Rcpp’ was built under R version 2.15.3
ERROR: loading failed for ‘i386’
* removing ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/rstanarm’

[Ben Goodrich]

On Thursday, July 25, 2013 1:09:13 PM UTC-4, Peter Li wrote:

I'm not sure what version of tar I have but that seemed to have worked. Thanks. I'll let you know which models (if any) can't be run with rstanarm.

We already know that anything multilevel won't work yet because we don't have a stanlmer() function yet. Basically, we just have stanglm() so far, although I guess that is sufficient to do a lot. I made a wiki page

https://github.com/stan-dev/rstanarm/wiki/Models-from-ARM-Book

that I think you can edit.

Ben

[Ben Goodrich]

You need rstan first

https://code.google.com/p/stan/wiki/RStanGettingStarted

Ben

[Peter Li]

I have rstan installed. Do I need to have the version in the develop repo?

As for the wiki, I also made one on the stan page to list all of the model code that we have (https://github.com/stan-dev/stan/wiki/ARM-Models). I'll be sure to link the two.


Peter

On 7/25/13 1:16 PM, Ben Goodrich wrote:

You need rstan first

https://code.google.com/p/stan/wiki/RStanGettingStarted

Ben

On Thu, Jul 25, 2013 at 1:12 PM, Peter Li <li.pe...@gmail.com> wrote:

Just kidding.. Now it says there's something missing.

Cloning into 'rstanarm'...
remote: Counting objects: 24, done.
remote: Compressing objects: 100% (16/16), done.
remote: Total 24 (delta 3), reused 18 (delta 3)
Unpacking objects: 100% (24/24), done.
Chinese-Secret-Service-Van-4:~ Peter$ R CMD INSTALL rstanarm/

* installing to library �/Library/Frameworks/R.framework/Versions/2.15/Resources/library�

* installing *source* package �rstanarm� ...

** R
** exec
** preparing package for lazy loading

Warning: package �Rcpp� was built under R version 2.15.3

TRANSLATING MODEL 'Gaussian GLM' FROM Stan CODE TO C++ CODE NOW.
COMPILING THE C++ CODE FOR MODEL 'Gaussian GLM' NOW.
Error : variable does not exist; processing stage=data initialization; variable name=N; base type=int
failed to create the sampler; sampling not done

TRANSLATING MODEL 'Discrete GLM' FROM Stan CODE TO C++ CODE NOW.
COMPILING THE C++ CODE FOR MODEL 'Discrete GLM' NOW.
Error : variable does not exist; processing stage=data initialization; variable name=N; base type=int
failed to create the sampler; sampling not done
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

*** arch - i386

Error : package �rstan� is not installed for 'arch=i386'

Error: loading failed
Execution halted
*** arch - x86_64

Warning: package �Rcpp� was built under R version 2.15.3
ERROR: loading failed for �i386�
* removing �/Library/Frameworks/R.framework/Versions/2.15/Resources/library/rstanarm�

On 7/25/13 1:09 PM, Peter Li wrote:

I'm not sure what version of tar I have but that seemed to have worked. Thanks. I'll let you know which models (if any) can't be run with rstanarm.


Peter

On 7/25/13 1:07 PM, Ben Goodrich wrote:

On Thursday, July 25, 2013 1:04:07 PM UTC-4, Peter Li wrote:

I get this error:
Error in untar2(tarfile, files, list, exdir) : unsupported entry type �g�

[Ben Goodrich]

On Thursday, July 25, 2013 1:20:06 PM UTC-4, Peter Li wrote:

I have rstan installed. Do I need to have the version in the develop repo?

No, actually I think it should only work if you have rstan 1.3 installed, which R complained about

** testing if installed package can be loaded
*** arch - i386
Error : package �rstan� is not installed for 'arch=i386'
Error: loading failed
Execution halted
*** arch - x86_64
Warning: package �Rcpp� was built under R version 2.15.3
ERROR: loading failed for �i386�

 
Do you maybe need to do

export R_ARCH='/x86_64'

or something.

 

As for the wiki, I also made one on the stan page to list all of the model code that we have (https://github.com/stan-dev/stan/wiki/ARM-Models). I'll be sure to link the two.

OK, or just note on your wikipage whether it is also working from rstanarm.

Ben

[Peter Li]

Same error still. I'll try reinstalling RStan.

[Peter Li]

Ok, so I got the same error using command line. As a side note, I figured out how to get the install to run (but not work--same error still) with the r package devtools:

library(devtools)
install_github("rstanarm","stan-dev")

[Jiqiang Guo]

The error might be still due to that rstan is installed for only one bitness, 64 or 32.  If it is, one way is to install rstan for both 64 and 32 bits by using 

install.packages('rstan', type = 'source', INSTALL_opts = "--merge-multiarch")

The other way is to update your R.  R 3.0.1 on mac only has 64 bits now. 

--

Jiqiang

[Peter Li]

That did the trick, though it took quite a while to install (~20+ min).

Peter