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Moved from Charles' own github - July 31, 2017
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SetupRTorsten doesn't work #1

Closed charlesm93 closed 6 years ago

charlesm93 commented 7 years ago

(April 25th)

A user found an error with SetupRTorsten.R.

The error results from the release of rstan version 2.15 and the fact Torsten is currently built in Stan 2.14. I need to update the installation file so that it picks a version of Stan Torsten has been tested with. The packages get installed and loaded. However, when trying to run a stan file, the following error message appears after compilation:

. . .

Error in compileCode(f, code, language = language, verbose = verbose) : Compilation ERROR, function(s)/method(s) not created!

. . .

charlesm93 commented 7 years ago

I think I found a fix, which is mildly elegant. I could do something simpler with:

install_version("rstan", version = "2.14.1", repos = "http://cran.us.r-project.org") but this procedure overwrites the version of StanHeaders the installation script edits to include Torsten. Any way to prevent rstan from doing this?

charlesm93 commented 7 years ago

The following has been tested on mac and produces the desired results:

charlesm93 commented 7 years ago

@YamingSu writes on April 26th:

My understanding is that we need to ensure rstan_2.14.1 and its associated StanHeaders_2.14.0 are used together with Torsten. My workaround is below, and works for me.

Install rstan as usual (https://github.com/stan-dev/rstan/wiki/Installing-RStan-on-Windows). This will make sure that the necessary dependent packages for rstan are installed. But note that version of rstan_2.15.1 is to be installed as of today (April-26-2017).

I then used your suggested script below to install Torsten. Note that when rstan_2.14.1 is installed at the last step , the dependencies won't get installed as repos = NULL. Otherwise StanHeader_2.14.0 that is edited by Torsten will be overwritten by the latest production version (i.e., StanHeader_2.15.0 as of April-26-2017).

## Install RStan, with Torsten built inside of it.

## Adjust directories to your setting.
libdir <- file.path("C:/Users/XingSu/Documents/R/win-library/3.3")
.libPaths(libdir)
library(devtools)

## Download and edit StanHeaders (version 2.14.0)
install.packages("https://cran.r-project.org/src/contrib/Archive/StanHeaders/StanHeaders_2.14.0.tar.gz", repos = NULL)
setwd(libdir)
system("git clone https://github.com/charlesm93/stan.git")
setwd("stan")
system("git checkout torsten-master")
setwd(libdir)
system("rm -rf StanHeaders/include/src/stan")
system("mv stan/src/stan StanHeaders/include/src/stan")
system("rm -rf stan")
system("git clone https://github.com/charlesm93/math.git")
setwd("math")
system("git checkout torsten-master")
setwd(libdir)
system("rm -rf StanHeaders/include/stan")
system("mv math/stan StanHeaders/include/stan")
system("rm -rf math")

## Download rstan 2.14.1 without the dependencies.
install.packages("https://cran.r-project.org/src/contrib/Archive/rstan/rstan_2.14.1.tar.gz"
charlesm93 commented 7 years ago

Nice! This is a more elegant approach and doesn't require running pkgSetup.R. The repos = NULL argument was what I was missing. I wonder if we can install all dependencies, except StanHeaders when downloading rstan. That would avoid having to install rstan twice.

charlesm93 commented 7 years ago

(update, today) The issue gets fixed when Torsten is up to date with Stan's current version. Just got torsten up to date with stan 2.16 and updated setupRTorsten on the issue-8-mixedOdeCpt branch.