stan-dev / stan-dev/rstan

Compiler error on rstan

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Description

Summary:

Compiling errors. I followed the instructions and checked the similar issues, but could not solve the issue. This is on Mac OS.

Description:

fit <- stan(file = 'stan/8schools.stan', data = schools_dat)
Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! clang: warning: no such sysroot directory: '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk' [-Wmissing-sysroot]
In file included from file165bc30a4c1fb.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/
In addition: Warning message:
In system(cmd, intern = !verbose) :
running command '/Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB file165bc30a4c1fb.cpp 2> file165bc30a4c1fb.cpp.err.txt' had status 1
Error in sink(type = "output") : invalid connection

Reproducible Steps:

I was using an older version of rstan on an older version of R. However, after updating both, I can compile any files. If I switch back to the older version, I got an error saying headers are not matched.

Current Output:
Expected Output:

If applicable, the output you expected from RStan.

RStan Version:

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

R Version:

The version of R you are running (e.g., from R.version.string)

Operating System:

Your operating system (e.g., OS X 10.11.3)

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 fit call with stan/8schools.stan and schools_dat, then inspect the reported R CMD SHLIB command and missing MacOSX SDK warning. The issue does not provide RStan, R, or operating-system versions, so collect those details before determining whether the failure is in RStan or the local compiler setup.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
compilers
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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