stan-dev / stan-dev/rstan

Updated R to 3.6 and all hell broke loose

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Description

Summary:

Updated R and Rstudio, and all hell broke loose

Description:

I've been running the rethinking package, which uses rstan, for about 6 months - no problem. I updated R today, and all of a sudden things have gone haywire.

I uninstalled and re-installed rstan (and all other packages, for that matter), including updating Rtools. No luck. When I try to run the schools example directly from the Rstan "getting started" page, I get the error listed below

The C++ toolchain passes the test
I have also tried disabling the C++ toolchain configuration (which is noted to sometimes cause problems). No luck. Exact same issue.

I have de-installed and re-installed from scratch (R, then Rstan, then other toolboxes), but still no luck.

Any advice would be GREATLY appreciated. BTW - I'm just an ordinary scientist, not a developer or c-scientist ...so I would appreciate advice being "dummed down" as much as possible. TIA

Reproducible Steps:

Followed the steps on the Get Started page EXACTLY

Current Output:

Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! In file included from C:/Users/schwa/Documents/R/win-library/3.6/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from C:/Users/schwa/Documents/R/win-library/3.6/BH/include/boost/random/detail/int_float_pair.hpp:26,
from C:/Users/schwa/Documents/R/win-library/3.6/BH/include/boost/random/exponential_distribution.hpp:27,
from C:/Users/schwa/Documents/R/win-library/3.6/BH/include/boost/random/gamma_distribution.hpp:25,
from C:/Users/schwa/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_rng.hpp:5,
from C:/Users/schwa/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/mat.hpp:276,
from C:/Users/schwa/Documents/R/win-library/3.6/StanHeaders/include/stan/math/rev/mat.hpp:12,
from C:/Users/schwa/Documents/R/win-library/3.6/StanHeaders/include/stan/math.hpp:4,

Error in sink(type = "output") : invalid connection

Expected Output:
RStan Version:

The version of RStan you are running (e.g., from packageVersion("rstan"))

R Version:

2.18.12

Operating System:

Windows 10

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing the schools example from the RStan Get Started page on Windows 10, using the reported R, RStan, Rtools, and RStudio versions. Inspect the compiler output beginning with the Boost and StanHeaders paths, then compare the result with the documented toolchain configuration. Done means identifying the environment mismatch or compilation failure and confirming a working example.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
build-system
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
20/100

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