rstan compilation failing on Windows and Mac CI on main

[seabbs]

See https://github.com/epinowcast/epidist/actions/runs/12139031847 for the issue. This issue was first identified in #426 but is not related to that PR.

I hope/assume its a transcient upstream issue but it may also be related to our CI configuration.

[kcharniga]

This happened to me too on a Windows laptop (~1 yr old). The model compiles with the other backend (cmdstanr).

[seabbs]

Thanks for the report @kcharniga. good to know its not just CI but not ideal.

In I looked at removing the use of rstan in the vignette and it indeed moves the fault to the testing setup (the first use of rstan) so this is definitely the issue.

I see the following output which I am investigating:

Loading required package: rstan
Loading required package: StanHeaders

rstan version 2.36.0.9000 (Stan version 2.36.0)

For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
For within-chain threading using `reduce_sum()` or `map_rect()` Stan functions,
change `threads_per_chain` option:
rstan_options(threads_per_chain = 1)

Do not specify '-march=native' in 'LOCAL_CPPFLAGS' or a Makevars file
make cmd is
  make -f "C:/R/etc/x64/Makeconf" -f "C:/R/share/make/winshlib.mk" CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB="file142050c1489.dll" WIN=64 TCLBIN= OBJECTS="file142050c1489.o"

make would use
g++  -std=gnu++17 -I"C:/R/include" -DNDEBUG   -I"D:/a/_temp/Library/Rcpp/include/"  -I"C:/Users/runneradmin/AppData/Local/Temp/Rtmpa0WPz1/RLIBS_[190](https://github.com/epinowcast/epidist/actions/runs/12889663671/job/35937421968?pr=502#step:7:192)02c084db4/RcppEigen/include/"  -I"C:/Users/runneradmin/AppData/Local/Temp/Rtmpa0WPz1/RLIBS_19002c084db4/RcppEigen/include/unsupported"  -I"C:/Users/runneradmin/AppData/Local/Temp/Rtmpa0WPz1/RLIBS_19002c084db4/BH/include" -I"D:/a/_temp/Library/StanHeaders/include/src/"  -I"D:/a/_temp/Library/StanHeaders/include/"  -I"D:/a/_temp/Library/RcppParallel/include/" -DRCPP_PARALLEL_USE_TBB=1 -I"D:/a/_temp/Library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include "D:/a/_temp/Library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp"  -std=c++1y    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c file142050c1489.cpp -o file142050c1489.o
if test "zfile142050c1489.o" != "z"; then \
  if test -e "file142050c1489-win.def"; then \
    echo g++  -shared -s -static-libgcc -o file142050c1489.dll file142050c1489-win.def file142050c1489.o  "D:/a/_temp/Library/rstan/lib/x64/libStanServices.a" -L"D:/a/_temp/Library/StanHeaders/libs/x64" -lStanHeaders -L"D:/a/_temp/Library/RcppParallel/lib/x64" -ltbb -LD:/a/_temp/Library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -L"C:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64" -L"C:/rtools44/x86_64-w64-mingw32.static.posix/lib"  -L"C:/R/bin/x64" -lR ; \
    g++  -shared -s -static-libgcc -o file142050c1489.dll file142050c1489-win.def file142050c1489.o  "D:/a/_temp/Library/rstan/lib/x64/libStanServices.a" -L"D:/a/_temp/Library/StanHeaders/libs/x64" -lStanHeaders -L"D:/a/_temp/Library/RcppParallel/lib/x64" -ltbb -LD:/a/_temp/Library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -L"C:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64" -L"C:/rtools44/x86_64-w64-mingw32.static.posix/lib"  -L"C:/R/bin/x64" -lR ; \
  else \
    echo EXPORTS > tmp.def; \
    nm file142050c1489.o | sed -n 's/^.* [BCDRT] / /p' | sed -e '/[.]refptr[.]/d' -e '/[.]weak[.]/d' | sed 's/[^ ][^ ]*/"&"/g'  >> tmp.def; \
    echo g++  -shared -s -static-libgcc -o file142050c1489.dll tmp.def file142050c1489.o  "D:/a/_temp/Library/rstan/lib/x64/libStanServices.a" -L"D:/a/_temp/Library/StanHeaders/libs/x64" -lStanHeaders -L"D:/a/_temp/Library/RcppParallel/lib/x64" -ltbb -LD:/a/_temp/Library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -L"C:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64" -L"C:/rtools44/x86_64-w64-mingw32.static.posix/lib"  -L"C:/R/bin/x64" -lR ; \
Error: Error: R CMD check found ERRORs
    g++  -shared -s -static-libgcc -o file142050c1489.dll tmp.def file142050c1489.o  "D:/a/_temp/Library/rstan/lib/x64/libStanServices.a" -L"D:/a/_temp/Library/StanHeaders/libs/x64" -lStanHeaders -L"D:/a/_temp/Library/RcppParallel/lib/x64" -ltbb -LD:/a/_temp/Library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -L"C:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64" -L"C:/rtools44/x86_64-w64-mingw32.static.posix/lib"  -L"C:/R/bin/x64" -lR ; \
    rm -f tmp.def; \
  fi \
fi
Error: Error in sink(type = "output") : invalid connection
make cmd is
  make -f "C:/R/etc/x64/Makeconf" -f "C:/R/share/make/winshlib.mk" CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB="file14[201](https://github.com/epinowcast/epidist/actions/runs/12889663671/job/35937421968?pr=502#step:7:203)b6c3a20.dll" WIN=64 TCLBIN= OBJECTS="file14201b6c3a20.o"

make would use
g++  -std=gnu++17 -I"C:/R/include" -DNDEBUG   -I"D:/a/_temp/Library/Rcpp/include/"  -I"C:/Users/runneradmin/AppData/Local/Temp/Rtmpa0WPz1/RLIBS_19002c084db4/RcppEigen/include/"  -I"C:/Users/runneradmin/AppData/Local/Temp/Rtmpa0WPz1/RLIBS_19002c084db4/RcppEigen/include/unsupported"  -I"C:/Users/runneradmin/AppData/Local/Temp/Rtmpa0WPz1/RLIBS_19002c084db4/BH/include" -I"D:/a/_temp/Library/StanHeaders/include/src/"  -I"D:/a/_temp/Library/StanHeaders/include/"  -I"D:/a/_temp/Library/RcppParallel/include/" -DRCPP_PARALLEL_USE_TBB=1 -I"D:/a/_temp/Library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include "D:/a/_temp/Library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp"  -std=c++1y    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c file14201b6c3a20.cpp -o file14201b6c3a20.o
if test "zfile14201b6c3a20.o" != "z"; then \
  if test -e "file14201b6c3a20-win.def"; then \
    echo g++  -shared -s -static-libgcc -o file14201b6c3a20.dll file14201b6c3a20-win.def file14201b6c3a20.o  "D:/a/_temp/Library/rstan/lib/x64/libStanServices.a" -L"D:/a/_temp/Library/StanHeaders/libs/x64" -lStanHeaders -L"D:/a/_temp/Library/RcppParallel/lib/x64" -ltbb -LD:/a/_temp/Library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -L"C:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64" -L"C:/rtools44/x86_64-w64-mingw32.static.posix/lib"  -L"C:/R/bin/x64" -lR ; \
    g++  -shared -s -static-libgcc -o file14201b6c3a20.dll file14201b6c3a20-win.def file14201b6c3a20.o  "D:/a/_temp/Library/rstan/lib/x64/libStanServices.a" -L"D:/a/_temp/Library/StanHeaders/libs/x64" -lStanHeaders -L"D:/a/_temp/Library/RcppParallel/lib/x64" -ltbb -LD:/a/_temp/Library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -L"C:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64" -L"C:/rtools44/x86_64-w64-mingw32.static.posix/lib"  -L"C:/R/bin/x64" -lR ; \
  else \
    echo EXPORTS > tmp.def; \
    nm file14201b6c3a20.o | sed -n 's/^.* [BCDRT] / /p' | sed -e '/[.]refptr[.]/d' -e '/[.]weak[.]/d' | sed 's/[^ ][^ ]*/"&"/g'  >> tmp.def; \
    echo g++  -shared -s -static-libgcc -o file14201b6c3a20.dll tmp.def file14201b6c3a20.o  "D:/a/_temp/Library/rstan/lib/x64/libStanServices.a" -L"D:/a/_temp/Library/StanHeaders/libs/x64" -lStanHeaders -L"D:/a/_temp/Library/RcppParallel/lib/x64" -ltbb -LD:/a/_temp/Library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -L"C:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64" -L"C:/rtools44/x86_64-w64-mingw32.static.posix/lib"  -L"C:/R/bin/x64" -lR ; \
    g++  -shared -s -static-libgcc -o file14201b6c3a20.dll tmp.def file14201b6c3a20.o  "D:/a/_temp/Library/rstan/lib/x64/libStanServices.a" -L"D:/a/_temp/Library/StanHeaders/libs/x64" -lStanHeaders -L"D:/a/_temp/Library/RcppParallel/lib/x64" -ltbb -LD:/a/_temp/Library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -L"C:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64" -L"C:/rtools44/x86_64-w64-mingw32.static.posix/lib"  -L"C:/R/bin/x64" -lR ; \
    rm -f tmp.def; \
  fi \
fi
Error in `FUN()`:
! In path: "D:\\a\\epidist\\epidist\\check\\epidist.Rcheck\\tests\\testthat\\setup.R"
Caused by error in `compileCode()`:
! >; int Option = 0; Scalar = double]'
D:/a/_temp/Library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:0:   required from 'double stan::mcmc::dense_e_metric<Model, BaseRNG>::T(stan::mcmc::dense_e_point&) [with Model = model142011a91d4f__model_namespace::model142011a91d4f__model; BaseRNG = boost::random::mixmax_engine<17, 36, 0>]'
D:/a/_temp/Library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:0:   required from here
C:/Users/runneradmin/AppData/Local/Temp/Rtmpa0WPz1/RLIBS_19002c084db4/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits<double>::type' {aka '__m128d'} [-Wignored-attributes]
  654 |   return internal::first_aligned<int(unpacket_traits<DefaultPacketType>::alignment),Derived>(m);
      |                                                                          ^~~~~~~~~
make: *** [C:/R/etc/x64/Makeconf:296: file14201b6c3a20.o] Error 1
Backtrace:
     ▆
  1. ├─testthat::test_check("epidist")
  2. │ └─testthat::test_dir(...)
  3. │   └─testthat:::test_files(...)
  4. │     └─testthat:::test_files_serial(...)
  5. │       └─testthat:::test_files_setup_state(...)
  6. │         └─testthat::source_test_setup(".", env)
  7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
  8. │             └─base::lapply(...)
  9. │               └─testthat (local) FUN(X[[i]], ...)
 10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
 11. │                   ├─base::withCallingHandlers(...)
 12. │                   └─base::eval(exprs, env)
 13. │                     └─base::eval(exprs, env)
 14. │                       └─epidist::epidist(...) at D:\a\epidist\epidist\check\epidist.Rcheck\tests\testthat\setup.R:133:3
 15. │                         └─brms (local) fn(...) at epidist/R/epidist.R:52:3
 16. │                           └─brms::do_call(compile_model, compile_args)
 17. │                             └─brms:::eval2(call, envir = args, enclos = envir)
 18. │                               └─base::eval(expr, envir, ...)
 19. │                                 └─base::eval(expr, envir, ...)
 20. │                                   └─brms (local) .fun(...)
 21. │                                     └─brms (local) .compile_model(model, ...)
 22. │                                       ├─brms:::eval_silent(...)
 23. │                                       │ └─base::eval(expr, envir)
 24. │                                       │   └─base::eval(expr, envir)
 25. │                                       └─brms::do_call(rstan::stan_model, args)
 26. │                                         └─brms:::eval2(call, envir = args, enclos = envir)
 27. │                                           └─base::eval(expr, envir, ...)
 28. │                                             └─base::eval(expr, envir, ...)
 29. │                                               └─rstan (local) .fun(model_code = .x1)
 30. │                                                 └─rstan:::cxxfunctionplus(...)
 31. │                                                   ├─pkgbuild::with_build_tools(...)
 32. │                                                   │ └─pkgbuild:::withr_with_path(rtools_path(), code)
 33. │                                                   │   └─base::force(code)
 34. │                                                   └─inline::cxxfunction(...)
 35. │                                                     └─inline:::compileCode(f, code, language = language, verbose = verbose)
 36. │                                                       └─base::stop(...)
 37. └─base::.handleSimpleError(...)
 38.   └─testthat (local) h(simpleError(msg, call))
 39.     └─rlang::abort(...)
Error in `FUN()`:
! In path: "D:\\a\\epidist\\epidist\\check\\epidist.Rcheck\\tests\\testthat\\setup.R"

[seabbs]

I see that the march = native flag is not recommended on the stan install guide for rstan so perhaps this is the problem. I am not clear why this would suddenly have become a problem. I can't see anything about this in the brms repo. I also see that the mac issue is still in the vignette suggesting it is a different problem. For this reason I have created sub issues.

[kcharniga]

This is my error message:

make cmd is
make -f "C:/Users/kcharnig/AppData/Local/Programs/R/R-431.2/etc/x64/Makeconf" -f "C:/Users/kcharnig/AppData/Local/Programs/R/R-431.2/share/make/winshlib.mk" CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB="file63d83f787834.dll" WIN=64 TCLBIN= OBJECTS="file63d83f787834.o"

make would use
g++ -std=gnu++17 -I"C:/Users/kcharnig/AppData/Local/Programs/R/R-431.2/include" -DNDEBUG -I"C:/Users/kcharnig/AppData/Local/Programs/R/R-4.3.2/library/Rcpp/include/" -I"C:/Users/kcharnig/AppData/Local/Programs/R/R-4.3.2/library/RcppEigen/include/" -I"C:/Users/kcharnig/AppData/Local/Programs/R/R-4.3.2/library/RcppEigen/include/unsupported" -I"C:/Users/kcharnig/AppData/Local/Programs/R/R-4.3.2/library/BH/include" -I"C:/Users/kcharnig/AppData/Local/Programs/R/R-4.3.2/library/StanHeaders/include/src/" -I"C:/Users/kcharnig/AppData/Local/Programs/R/R-4.3.2/library/StanHeaders/include/" -I"C:/Users/kcharnig/AppData/Local/Programs/R/R-4.3.2/library/RcppParallel/include/" -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/kcharnig/AppData/Local/Programs/R/R-4.3.2/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include "C:/Users/kcharnig/AppData/Local/Programs/R/R-4.3.2/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp" -std=c++1y -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c file63d83f787834.cpp -o file63d83f787834.o
if test "zfile63d83f787834.o" != "z"; then
if test -e "file63d83f787834-win.def"; then
echo g++ -shared -s -static-libgcc -o file63d83f787834.dll file63d83f787834-win.def file63d83f787834.o "C:/Users/kcharnig/AppData/Local/Programs/R/R-4.3.2/library/rstan/lib/x64/libStanServices.a" -L"C:/Users/kcharnig/AppData/Local/Programs/R/R-4.3.2/library/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/kcharnig/AppData/Local/Programs/R/R-4.3.2/library/RcppParallel/lib/x64" -ltbb -LC:/Users/kcharnig/AppData/Local/Programs/R/R-4.3.2/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -L"C:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64" -L"C:/rtools43/x86_64-w64-mingw32.static.posix/lib" -L"C:/Users/kcharnig/AppData/Local/Programs/R/R-431.2/bin/x64" -lR ;
g++ -shared -s -static-libgcc -o file63d83f787834.dll file63d83f787834-win.def file63d83f787834.o "C:/Users/kcharnig/AppData/Local/Programs/R/R-4.3.2/library/rstan/lib/x64/libStanServices.a" -L"C:/Users/kcharnig/AppData/Local/Programs/R/R-4.3.2/library/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/kcharnig/AppData/Local/Programs/R/R-4.3.2/library/RcppParallel/lib/x64" -ltbb -LC:/Users/kcharnig/AppData/Local/Programs/R/R-4.3.2/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -L"C:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64" -L"C:/rtools43/x86_64-w64-mingw32.static.posix/lib" -L"C:/Users/kcharnig/AppData/Local/Programs/R/R-431.2/bin/x64" -lR ;
else
echo EXPORTS > tmp.def;
nm file63d83f787834.o | sed -n 's/^.* [BCDRT] / /p' | sed -e '/[.]refptr[.]/d' -e '/[.]weak[.]/d' | sed 's/[^ ][^ ]*/"&"/g' >> tmp.def;
echo g++ -shared -s -static-libgcc -o file63d83f787834.dll tmp.def file63d83f787834.o "C:/Users/kcharnig/AppData/Local/Programs/R/R-4.3.2/library/rstan/lib/x64/libStanServices.a" -L"C:/Users/kcharnig/AppData/Local/Programs/R/R-4.3.2/library/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/kcharnig/AppData/Local/Programs/R/R-4.3.2/library/RcppParallel/lib/x64" -ltbb -LC:/Users/kcharnig/AppData/Local/Programs/R/R-4.3.2/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -L"C:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64" -L"C:/rtools43/x86_64-w64-mingw32.static.posix/lib" -L"C:/Users/kcharnig/AppData/Local/Programs/R/R-431.2/bin/x64" -lR ;
g++ -shared -s -static-libgcc -o file63d83f787834.dll tmp.def file63d83f787834.o "C:/Users/kcharnig/AppData/Local/Programs/R/R-4.3.2/library/rstan/lib/x64/libStanServices.a" -L"C:/Users/kcharnig/AppData/Local/Programs/R/R-4.3.2/library/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/kcharnig/AppData/Local/Programs/R/R-4.3.2/library/RcppParallel/lib/x64" -ltbb -LC:/Users/kcharnig/AppData/Local/Programs/R/R-4.3.2/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -L"C:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64" -L"C:/rtools43/x86_64-w64-mingw32.static.posix/lib" -L"C:/Users/kcharnig/AppData/Local/Programs/R/R-431.2/bin/x64" -lR ;
rm -f tmp.def;
fi
fi
Error in compileCode(f, code, language = language, verbose = verbose) :
c/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from 'double stan::mcmc::dense_e_metric<Model, BaseRNG>::T(stan::mcmc::dense_e_point&) [with Model = model63d857d87eae__model_namespace::model63d857d87eae__model; BaseRNG = boost::random::mixmax_engine<17, 36, 0>]'
C:/Users/kcharnig/AppData/Local/Programs/R/R-4.3.2/library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here
C:/Users/kcharnig/AppData/Local/Programs/R/R-4.3.2/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes]
654 | return internal::first_aligned<int(unpacket_traits::alignment),Derived>(m);
| ^~~~~~~~~
make: *** [C:/Users/kcharnig/AppData/Local/Programs/R/R-431.2/etc/x64/Makeconf:272: file63d83f787834.o
Error in sink(type = "output") : invalid connection

[seabbs]

Now that both sub issues have been addressed moving to close this. Feel free to reopen if anyone sees te behaviour again or anything related.