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stan-dev / cmdstanr

CmdStanR: the R interface to CmdStan
https://mc-stan.org/cmdstanr/
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Windows installation problem #333

Closed adamhaber closed 3 years ago

adamhaber commented 3 years ago

Trying to install CmdStanR on a new Windows machine and ran into installation difficulties.

  1. First installed CmdStanR using install.packages("cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOption("repos"))), got the same error reported here.
  2. Installed using devtools::install_github("stan-dev/cmdstanr") instead, which solved the previous issue.
  3. Used check_cmdstan_toolchain(fix = TRUE) to fix RTools installation found but PATH was not properly set..
  4. Tried to install CmdStan: 
    
> check_cmdstan_toolchain(fix = TRUE)
Installing mingw32-make and writing RTools path to ~/.Renviron ...
The CmdStan toolchain is setup properly!
> install_cmdstan(cores=4,overwrite=T)
The CmdStan toolchain is setup properly!
* Latest CmdStan release is v2.25.0
* Installing CmdStan v2.25.0 in C:\Users\adamh\Documents/.cmdstanr/cmdstan-2.25.0
* Downloading cmdstan-2.25.0.tar.gz from GitHub...
* Removing the existing installation of CmdStan...
* Download complete
* Unpacking archive...
* Building CmdStan binaries...
INFO: Could not find files for the given pattern(s).
cp bin/windows-stanc bin/stanc.exe
cd stan/lib/stan_math/lib/boost_1.72.0; ./bootstrap.bat gcc

g++ -std=c++1y -m64 -D_REENTRANT -Wall -Wno-unused-function -Wno-uninitialized -Wno-unused-but-set-variable -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-attributes -Wno-ignored-attributes -I stan/lib/stan_math/lib/tbb_2019_U8/include -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include -D_USE_MATH_DEFINES -DBOOST_DISABLE_ASSERTS -c -fvisibility=hidden -o bin/cmdstan/stansummary.o src/cmdstan/stansummary.cpp g++ -std=c++1y -m64 -D_REENTRANT -Wall -Wno-unused-function -Wno-uninitialized -Wno-unused-but-set-variable -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-attributes -Wno-ignored-attributes -I stan/lib/stan_math/lib/tbb_2019_U8/include -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include -D_USE_MATH_DEFINES -DBOOST_DISABLE_ASSERTS -c -fvisibility=hidden -o bin/cmdstan/print.o src/cmdstan/print.cpp Building Boost.Build engine

g++ -std=c++1y -m64 -D_REENTRANT -Wall -Wno-unused-function -Wno-uninitialized -Wno-unused-but-set-variable -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-attributes -Wno-ignored-attributes -I stan/lib/stan_math/lib/tbb_2019_U8/include -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include -D_USE_MATH_DEFINES -DBOOST_DISABLE_ASSERTS -c -fvisibility=hidden -o bin/cmdstan/diagnose.o src/cmdstan/diagnose.cpp g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/nvector/serial/nvector_serial.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/nvector/serial/nvector_serial.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_math.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_math.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_stg1.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_stg1.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_sim.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_sim.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_ls.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_ls.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodea_io.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodea_io.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_spils.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_spils.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_bandpre.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_bandpre.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_bbdpre.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_bbdpre.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_stg.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_stg.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodea.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodea.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_io.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_io.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_direct.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_direct.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_diag.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_diag.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_dense.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_dense.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector_senswrapper.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector_senswrapper.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_linearsolver.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_linearsolver.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_iterative.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_iterative.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_band.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_band.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_version.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_version.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nonlinearsolver.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nonlinearsolver.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_direct.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_direct.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_futils.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_futils.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_matrix.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_matrix.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/band/sunmatrix_band.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/band/sunmatrix_band.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/dense/sunmatrix_dense.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/dense/sunmatrix_dense.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/band/sunlinsol_band.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/band/sunlinsol_band.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/dense/sunlinsol_dense.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/dense/sunlinsol_dense.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/newton/sunnonlinsol_newton.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/newton/sunnonlinsol_newton.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls_sim.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls_sim.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_ls.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_ls.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_bbdpre.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_bbdpre.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls_stg.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls_stg.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idaa_io.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idaa_io.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_direct.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_direct.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_io.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_io.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idaa.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idaa.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_ic.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_ic.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_spils.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_spils.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_io.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_io.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_spils.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_spils.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_ls.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_ls.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_bbdpre.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_bbdpre.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_direct.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_direct.o if ! [[ mingw32-make.exe =~ mingw32 ]]; then \ echo "ERROR: Please use mingw32-make on Windows to build the Intel TBB library."; \ echo "This is packaged with RTools, for example."; \ exit 1; \ fi

touch stan/lib/stan_math/lib/tbb/tbb-make-check

--- Compiling the main object file. This might take up to a minute. --- g++ -std=c++1y -m64 -D_REENTRANT -Wall -Wno-unused-function -Wno-uninitialized -Wno-unused-but-set-variable -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-attributes -Wno-ignored-attributes -I stan/lib/stan_math/lib/tbb_2019_U8/include -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include -D_USE_MATH_DEFINES -DBOOST_DISABLE_ASSERTS -c -o src/cmdstan/main.o src/cmdstan/main.cpp ar -rs stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_nvecserial.a stan/lib/stan_math/lib/sundials_5.2.0/src/nvector/serial/nvector_serial.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_math.o

--- Compiling pre-compiled header. This might take a few seconds. --- g++ -std=c++1y -m64 -D_REENTRANT -Wall -Wno-unused-function -Wno-uninitialized -Wno-unused-but-set-variable -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-attributes -Wno-ignored-attributes -I stan/lib/stan_math/lib/tbb_2019_U8/include -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include -D_USE_MATH_DEFINES -DBOOST_DISABLE_ASSERTS -c stan/src/stan/model/model_header.hpp -o stan/src/stan/model/model_header.hpp.gch ar: creating stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_nvecserial.a ar -rs stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_cvodes.a stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_stg1.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_sim.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_ls.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodea_io.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_spils.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_bandpre.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_bbdpre.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_stg.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodea.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_io.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_direct.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_diag.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector_senswrapper.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_math.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_linearsolver.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_iterative.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_version.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nonlinearsolver.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_direct.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_futils.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_matrix.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/band/sunmatrix_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/dense/sunmatrix_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/band/sunlinsol_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/dense/sunlinsol_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/newton/sunnonlinsol_newton.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.o ar: creating stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_cvodes.a ar -rs stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_idas.a stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls_sim.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_ls.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_bbdpre.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls_stg.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idaa_io.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_direct.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_io.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idaa.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_ic.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_spils.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector_senswrapper.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_math.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_linearsolver.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_iterative.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_version.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nonlinearsolver.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_direct.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_futils.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_matrix.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/band/sunmatrix_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/dense/sunmatrix_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/band/sunlinsol_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/dense/sunlinsol_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/newton/sunnonlinsol_newton.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.o ar: creating stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_idas.a ar -rs stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_kinsol.a stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_io.o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_spils.o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_ls.o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol.o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_bbdpre.o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_direct.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector_senswrapper.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_math.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_linearsolver.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_iterative.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_version.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nonlinearsolver.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_direct.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_futils.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_matrix.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/band/sunmatrix_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/dense/sunmatrix_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/band/sunlinsol_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/dense/sunlinsol_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/newton/sunnonlinsol_newton.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.o ar: creating stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_kinsol.a

tbb_root="../tbb_2019_U8" CXX="g++" CC="gcc" LDFLAGS='-Wl,-L,"C:/Users/adamh/Documents/.cmdstanr/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"C:/Users/adamh/Documents/.cmdstanr/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb" ' 'mingw32-make.exe' -C "stan/lib/stan_math/lib/tbb" -r -f "C:/Users/adamh/Documents/.cmdstanr/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb_2019_U8/build/Makefile.tbbmalloc" compiler=gcc cfg=release stdver=c++1y malloc CXXFLAGS="-Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation " mingw32-make[1]: Entering directory 'C:/Users/adamh/Documents/.cmdstanr/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb' g++ -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -DMSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -fno-rtti -fno-exceptions -DTBBMALLOC_BUILD=1 -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -flifetime-dse=1 -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include -I../tbb_2019_U8/src/tbbmalloc -I../tbb_2019_U8/src/tbbmalloc ../tbb_2019_U8/src/tbbmalloc/backend.cpp g++ -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -DMSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -fno-rtti -fno-exceptions -DTBBMALLOC_BUILD=1 -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -flifetime-dse=1 -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include -I../tbb_2019_U8/src/tbbmalloc -I../tbb_2019_U8/src/tbbmalloc ../tbb_2019_U8/src/tbbmalloc/large_objects.cpp g++ -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -DMSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -fno-rtti -fno-exceptions -DTBBMALLOC_BUILD=1 -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -flifetime-dse=1 -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include -I../tbb_2019_U8/src/tbbmalloc -I../tbb_2019_U8/src/tbbmalloc ../tbb_2019_U8/src/tbbmalloc/backref.cpp g++ -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -DMSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -fno-rtti -fno-exceptions -DTBBMALLOC_BUILD=1 -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -flifetime-dse=1 -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include -I../tbb_2019_U8/src/tbbmalloc -I../tbb_2019_U8/src/tbbmalloc ../tbb_2019_U8/src/tbbmalloc/tbbmalloc.cpp g++ -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -DMSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -fno-rtti -fno-exceptions -DTBBMALLOC_BUILD=1 -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -flifetime-dse=1 -o itt_notify_malloc.o -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/itt_notify.cpp cmd /C cscript /nologo /E:jscript ../tbb_2019_U8/build/version_info_windows.js gcc intel64 "g++ -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -Wall -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include" > version_string.ver

g++ -E -x c++ ../tbb_2019_U8/src/tbbmalloc/win64-gcc-tbbmalloc-export.def -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -DMSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -Wall -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -fno-rtti -fno-exceptions -DTBBMALLOC_BUILD=1 -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include > tbbmalloc.def g++ -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -DMSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -Wall -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -flifetime-dse=1 -DTBBMALLOC_BUILD=1 -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include -I../tbb_2019_U8/src/tbbmalloc -I../tbb_2019_U8/src/tbbmalloc ../tbb_2019_U8/src/tbbmalloc/proxy.cpp g++ -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -DMSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -Wall -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -flifetime-dse=1 -DTBBMALLOC_BUILD=1 -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include -I../tbb_2019_U8/src/tbbmalloc -I../tbb_2019_U8/src/tbbmalloc ../tbb_2019_U8/src/tbbmalloc/tbb_function_replacement.cpp g++ -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -DMSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -fno-rtti -fno-exceptions -DTBBMALLOC_BUILD=1 -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -flifetime-dse=1 -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include -I../tbb_2019_U8/src/tbbmalloc -I../tbb_2019_U8/src/tbbmalloc -I. ../tbb_2019_U8/src/tbbmalloc/frontend.cpp gcc -o tbbmalloc.dll backend.o large_objects.o backref.o tbbmalloc.o itt_notify_malloc.o frontend.o -lpsapi -shared -m64 -Wl,-L,"C:/Users/adamh/Documents/.cmdstanr/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"C:/Users/adamh/Documents/.cmdstanr/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb" -Wl,--version-script,tbbmalloc.def

g++ -o tbbmalloc_proxy.dll proxy.o tbb_function_replacement.o -lpsapi tbbmalloc.dll -shared -m64 -Wl,-L,"C:/Users/adamh/Documents/.cmdstanr/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"C:/Users/adamh/Documents/.cmdstanr/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb"
mingw32-make[1]: Leaving directory 'C:/Users/adamh/Documents/.cmdstanr/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb' touch stan/lib/stan_math/lib/tbb/version_tbb_2019_U8 tbb_root="../tbb_2019_U8" CXX="g++" CC="gcc" LDFLAGS='-Wl,-L,"C:/Users/adamh/Documents/.cmdstanr/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"C:/Users/adamh/Documents/.cmdstanr/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb" ' 'mingw32-make.exe' -C "stan/lib/stan_math/lib/tbb" -r -f "C:/Users/adamh/Documents/.cmdstanr/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb_2019_U8/build/Makefile.tbb" compiler=gcc cfg=release stdver=c++1y CXXFLAGS="-Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation " mingw32-make[1]: Entering directory 'C:/Users/adamh/Documents/.cmdstanr/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb'

Generating Boost.Build configuration in project-config.jam for gcc...Bootstrapping is done. To build, run: .\b2 To adjust configuration, edit 'project-config.jam'.

Further information:

cd stan/lib/stan_math/lib/boost_1.72.0; ./b2 address-model=64 --visibility=hidden --with-program_options cxxstd=11 variant=release link=static

C:/Users/adamh/Documents/.cmdstanr/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb_2019_U8/build/Makefile.tbb:28: CONFIG: cfg=release arch=intel64 compiler=gcc target=windows runtime=mingw8.3.0

g++ -o concurrent_hash_map.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -DMSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/concurrent_hash_map.cpp g++ -o concurrent_queue.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/concurrent_queue.cpp g++ -o concurrent_vector.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/concurrent_vector.cpp g++ -o dynamic_link.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/dynamic_link.cpp g++ -o itt_notify.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/itt_notify.cpp Performing configuration checks

- default address-model    : 64-bit

g++ -o cache_aligned_allocator.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/cache_aligned_allocator.cpp

Building the Boost C++ Libraries.Component configuration:

- atomic                   : not building
- chrono                   : not building
- container                : not building
- context                  : not building
- contract                 : not building
- coroutine                : not building
- date_time                : not building
- exception                : not building
- fiber                    : not building
- filesystem               : not building
- graph                    : not building
- graph_parallel           : not building
- headers                  : not building
- iostreams                : not building
- locale                   : not building
- log                      : not building
- math                     : not building
- mpi                      : not building
- program_options          : building
- python                   : not building
- random                   : not building
- regex                    : not building
- serialization            : not building
- stacktrace               : not building
- system                   : not building
- test                     : not building
- thread                   : not building
- timer                    : not building
- type_erasure             : not building
- wave                     : not building

...patience... g++ -o pipeline.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/pipeline.cpp ...found 1072 targets... ...updating 48 targets... common.copy C:\Users\adamh\Documents.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\cmake\BoostDetectToolset-1.72.0.cmake C:\Users\adamh\Documents.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\tools\boost_install\BoostDetectToolset.cmake

    1 file(s) copied.

boost-install.generate-cmake-config-version- bin.v2\tools\boost_install\BoostConfigVersion.cmake common.copy C:\Users\adamh\Documents.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\cmake\Boost-1.72.0\BoostConfig.cmake C:\Users\adamh\Documents.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\tools\boost_install\BoostConfig.cmake

    1 file(s) copied.

boost-install.generate-cmake-config- bin.v2\libs\program_options\build\stage\boost_program_options-config.cmake boost-install.generate-cmake-config-version- bin.v2\libs\program_options\build\stage\boost_program_options-config-version.cmake boost-install.generate-cmake-config- bin.v2\libs\headers\build\stage\boost_headers-config.cmake boost-install.generate-cmake-config-version- bin.v2\libs\headers\build\stage\boost_headers-config-version.cmake common.copy C:\Users\adamh\Documents.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\cmake\Boost-1.72.0\BoostConfigVersion.cmake bin.v2\tools\boost_install\BoostConfigVersion.cmake

    1 file(s) copied.

common.copy C:\Users\adamh\Documents.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\cmake\boost_program_options-1.72.0\boost_program_options-config.cmake bin.v2\libs\program_options\build\stage\boost_program_options-config.cmake

    1 file(s) copied.

common.copy C:\Users\adamh\Documents.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\cmake\boost_headers-1.72.0\boost_headers-config.cmake bin.v2\libs\headers\build\stage\boost_headers-config.cmake

    1 file(s) copied.

common.copy C:\Users\adamh\Documents.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\cmake\boost_program_options-1.72.0\boost_program_options-config-version.cmake bin.v2\libs\program_options\build\stage\boost_program_options-config-version.cmake

    1 file(s) copied.

common.copy C:\Users\adamh\Documents.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\cmake\boost_headers-1.72.0\boost_headers-config-version.cmake bin.v2\libs\headers\build\stage\boost_headers-config-version.cmake

    1 file(s) copied.

g++ -o queuing_mutex.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/queuing_mutex.cpp gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\utf8_codecvt_facet.o

gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\positional_options.o

g++ -o queuing_rw_mutex.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -DMSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/queuing_rw_mutex.cpp g++ -o reader_writer_lock.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -DMSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/reader_writer_lock.cpp gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\convert.o

g++ -o spin_rw_mutex.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/spin_rw_mutex.cpp gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\winmain.o

gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\config_file.o

g++ -o x86_rtm_rw_mutex.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/x86_rtm_rw_mutex.cpp gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\split.o

gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\variables_map.o

g++ -o spin_mutex.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/spin_mutex.cpp gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\value_semantic.o

gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\options_description.o

gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\cmdline.o

g++ -o critical_section.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/critical_section.cpp gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\parsers.o

g++ -o mutex.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/mutex.cpp gcc.archive bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\libboost_program_options-mgw83-mt-x64-1_72.a

boost-install.generate-cmake-variant- bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\libboost_program_options-variant-mgw83-mt-x64-1_72-static.cmake common.copy C:\Users\adamh\Documents.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\libboost_program_options-mgw83-mt-x64-1_72.a bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\libboost_program_options-mgw83-mt-x64-1_72.a

    1 file(s) copied.

type "C:\Users\adamh\AppData\Local\Temp\jam1330adba.000" > "bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\libboost_program_options-variant-mgw83-mt-x64-1_72-static.cmake"

...failed text-action bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\libboost_program_options-variant-mgw83-mt-x64-1_72-static.cmake... ...skipped <pC:\Users\adamh\Documents.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\cmake\boost_program_options-1.72.0>libboost_program_options-variant-mgw83-mt-x64-1_72-static.cmake for lack of <pbin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden>libboost_program_options-variant-mgw83-mt-x64-1_72-static.cmake... ...failed updating 1 target... ...skipped 1 target... ...updated 46 targets... g++ -o recursive_mutex.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/recursive_mutex.cpp

mingw32-make.exe: ** [make/command:40: stan/lib/stan_math/lib/boost_1.72.0/stage/lib/libboost_program_options.a] Error 1

mingw32-make.exe: *** Waiting for unfinished jobs.... g++ -o condition_variable.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -DMSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/condition_variable.cpp g++ -o tbb_thread.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -DMSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/tbb_thread.cpp g++ -o concurrent_monitor.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -DMSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/concurrent_monitor.cpp g++ -o semaphore.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/semaphore.cpp g++ -o private_server.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -DMSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/private_server.cpp g++ -o rml_tbb.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -DMSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/rml/client/rml_tbb.cpp g++ -o tbb_misc.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -DMSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include -I. ../tbb_2019_U8/src/tbb/tbb_misc.cpp g++ -o tbb_misc_ex.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -DMSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/tbb_misc_ex.cpp g++ -o task.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -DMSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/task.cpp g++ -o task_group_context.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -DMSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/task_group_context.cpp g++ -o governor.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -DMSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/governor.cpp g++ -o market.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -DMSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/market.cpp g++ -o arena.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -DMSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/arena.cpp g++ -o scheduler.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -DMSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/scheduler.cpp g++ -o observer_proxy.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/observer_proxy.cpp g++ -o tbb_statistics.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/tbb_statistics.cpp g++ -o tbb_main.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/tbb_main.cpp g++ -o concurrent_vector_v2.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -DMSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/old/concurrent_vector_v2.cpp g++ -o concurrent_queue_v2.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -DMSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/old/concurrent_queue_v2.cpp g++ -o spin_rw_mutex_v2.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/old/spin_rw_mutex_v2.cpp g++ -o task_v2.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/old/task_v2.cpp cmd /C "..\tbb_2019_U8\build\generate_tbbvars.bat"

Generating local tbbvars.bat

Generating local tbbvars.sh

Generating local tbbvars.csh

g++ -E -x c++ ../tbb_2019_U8/src/tbb/win64-gcc-tbb-export.def -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION=0x0700 -msse -mthreads -m64 -mrtm -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include > tbb.def

g++ -o tbb.dll concurrent_hash_map.o concurrent_queue.o concurrent_vector.o dynamic_link.o itt_notify.o cache_aligned_allocator.o pipeline.o queuing_mutex.o queuing_rw_mutex.o reader_writer_lock.o spin_rw_mutex.o x86_rtm_rw_mutex.o spin_mutex.o critical_section.o mutex.o recursive_mutex.o condition_variable.o tbb_thread.o concurrent_monitor.o semaphore.o private_server.o rml_tbb.o tbb_misc.o tbb_misc_ex.o task.o task_group_context.o governor.o market.o arena.o scheduler.o observer_proxy.o tbb_statistics.o tbb_main.o concurrent_vector_v2.o concurrent_queue_v2.o spin_rw_mutex_v2.o task_v2.o -lpsapi -shared -m64 -Wl,-L,"C:/Users/adamh/Documents/.cmdstanr/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"C:/Users/adamh/Documents/.cmdstanr/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb" -Wl,--version-script,tbb.def

task.o: duplicate section `.rdata$_ZTIN3tbb4taskE[_ZTIN3tbb4taskE]' has different size

arena.o: duplicate section `.rdata$_ZTIN3tbb4taskE[_ZTIN3tbb4taskE]' has different size

scheduler.o: duplicate section `.rdata$_ZTIN3tbb4taskE[_ZTIN3tbb4taskE]' has different size

mingw32-make[1]: Leaving directory 'C:/Users/adamh/Documents/.cmdstanr/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb'

Warning message: There was a problem during installation. See the error message(s) above.

rok-cesnovar commented 3 years ago

Hi,

thanks for reporting. We are tracking down all these common Windows issue to handle them automatically. Can you post the output of the following: 

Sys.getenv("PATH")
Sys.getenv("RTOOLS40_HOME")
rok-cesnovar commented 3 years ago

And additionaly:

Sys.which("g++") Sys.which("mingw32-make")

adamhaber commented 3 years ago

Sys.getenv("PATH")

"C:\rtools40\usr\bin;C:\rtools40\mingw64\bin;C:\rtools40\usr\bin;C:\ProgramData\DockerDesktop\version-bin;C:\Program Files\Docker\Docker\Resources\bin;C:\Program Files\Haskell\bin;C:\Program Files\Haskell Platform\8.6.5\lib\extralibs\bin;C:\Program Files\Haskell Platform\8.6.5\bin;C:\texlive\2018\bin\win32;C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v9.2\bin;C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v9.2\libnvvp;C:\ProgramData\Anaconda3;C:\ProgramData\Anaconda3\Library\mingw-w64\bin;C:\ProgramData\Anaconda3\Library\usr\bin;C:\ProgramData\Anaconda3\Library\bin;C:\ProgramData\Anaconda3\Scripts;C:\ProgramData\Oracle\Java\javapath;C:\windows\system32;C:\windows;C:\windows\System32\Wbem;C:\windows\System32\WindowsPowerShell\v1.0\;C:\Program Files (x86)\Sennheiser\SoftphoneSDK\;C:\Program Files\MATLAB\R2018a\runtime\win64;C:\Program Files\MATLAB\R2018a\bin;C:\Program Files\Microsoft VS Code\bin;C:\Program Files\dotnet\;C:\Program Files (x86)\NVIDIA Corporation\PhysX\Common;C:\Program Files\Git\cmd;C:\Program Files\MiKTeX 2.9\miktex\bin\x64\;C:\Strawberry\c\bin;C:\Strawberry\perl\site\bin;C:\Strawberry\perl\bin;C:\Program Files\Haskell Platform\8.6.5\mingw\bin;C:\Users\adamh\AppData\Roaming\cabal\bin;C:\Users\adamh\AppData\Roaming\local\bin;C:\Users\adamh\AppData\Local\Microsoft\WindowsApps;C:\Users\adamh\AppData\Local\hyper\app-3.0.2\resources\bin;C:\Users\adamh\AppData\Local\Programs\Microsoft VS Code Insiders\bin;C:\Users\adamh\.dotnet\tools;C:\rtools40\usr\bin;C:\rtools40\mingw64\bin;"

Sys.getenv("RTOOLS40_HOME")

"C:\rtools40"

Sys.which("g++")

""

Sys.which("mingw32-make")

""

The last two were a little weird to me, so I checked in cmd:

which g++
/c/Strawberry/c/bin/g++

which mingw32-make
/mingw64/bin/mingw32-make

which make
/usr/bin/make

g++ --version
g++ (x86_64-posix-seh, Built by strawberryperl.com project) 7.1.0
rok-cesnovar commented 3 years ago

Sys.which("g++") and Sys.which("mingw32-make") should both actually return C:\rtools40\mingw64\bin because of what you have in Sys.getenv("PATH"). The g++.exe and mingw32-make.exe should both be in that folder? And given that this folder is second in PATH it should be picked up. Weird.

What does processx::run("g++", args = c("--version")) return?

adamhaber commented 3 years ago 
> processx::run("g++", args = c("--version"))
$status
[1] 0

$stdout
[1] "g++ (Built by Jeroen for the R-project) 8.3.0\r\nCopyright (C) 2018 Free Software Foundation, Inc.\r\nThis is free software; see the source for copying conditions.  There is NO\r\nwarranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.\r\n\r\n"

$stderr
[1] ""

$timeout
[1] FALSE
adamhaber commented 3 years ago

Oh, sorry - I used getenv instead of which. Here's the correct output:

> Sys.which("mingw32-make")
                              mingw32-make 
"C:\\rtools40\\mingw64\\bin\\MINGW3~1.EXE" 
> Sys.which("g++")
                                    g++ 
"C:\\rtools40\\mingw64\\bin\\G__~1.EXE" 
>
rok-cesnovar commented 3 years ago

Ok, those are both correct. This error actually does not prevent you from working with cmdstan now. The cmdstan summary function wont work (due to the build error) but you dont need it in cmdstanr. The first model you will build will take a bit longer but then it will work. Its not ideal though.

Can you try a rebuild_cmdstan() again and see if you get the same output? I would still like to get to the bottom of this case, but understand if you dont have time to debug this :)

adamhaber commented 3 years ago

Of course, thanks for helping!

> rebuild_cmdstan()
INFO: Could not find files for the given pattern(s).

rm -f -r test

rm -f 

rm -f 

rm -f 

rm -f 

  removing dependency files
rm -f    

rm -f   

rm -f   

  cleaning sundials targets
rm -f stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_cvodes.a stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_idas.a stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_kinsol.a stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_nvecserial.a stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodea.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodea_io.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_bandpre.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_bbdpre.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_diag.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_direct.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_io.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_ls.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_sim.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_stg.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_stg1.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_spils.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idaa.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idaa_io.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_bbdpre.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_direct.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_ic.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_io.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_ls.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls_sim.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls_stg.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_spils.o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol.o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_bbdpre.o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_direct.o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_io.o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_ls.o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_spils.o stan/lib/stan_math/lib/sundials_5.2.0/src/nvector/serial/nvector_serial.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_direct.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_futils.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_iterative.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_linearsolver.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_math.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_matrix.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nonlinearsolver.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector_senswrapper.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_version.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/band/sunlinsol_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/dense/sunlinsol_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/band/sunmatrix_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/dense/sunmatrix_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/newton/sunnonlinsol_newton.o

  cleaning Intel TBB targets
rm -f -rf stan/lib/stan_math/lib/tbb

rm -f bin/stanc.exe bin/stanc2.exe bin/stansummary.exe bin/print.exe bin/diagnose.exe

rm -f -r src/cmdstan/main*.o bin/cmdstan

rm -f stan/src/stan/model/model_header.hpp.gch

rm -f examples/bernoulli/bernoulli.exe examples/bernoulli/bernoulli.o examples/bernoulli/bernoulli.d examples/bernoulli/bernoulli.hpp

rm -f -r stan/lib/stan_math/lib/boost_1.72.0/stage/lib stan/lib/stan_math/lib/boost_1.72.0/bin.v2 stan/lib/stan_math/lib/boost_1.72.0/project-config.jam stan/lib/stan_math/lib/boost_1.72.0/bootstrap.log

INFO: Could not find files for the given pattern(s).

cp bin/windows-stanc bin/stanc.exe

g++ -std=c++1y -m64 -D_REENTRANT -Wall -Wno-unused-function -Wno-uninitialized -Wno-unused-but-set-variable -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-attributes -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2019_U8/include   -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include  -D_USE_MATH_DEFINES  -DBOOST_DISABLE_ASSERTS        -c -fvisibility=hidden -o bin/cmdstan/stansummary.o src/cmdstan/stansummary.cpp

cd stan/lib/stan_math/lib/boost_1.72.0; ./bootstrap.bat gcc

Building Boost.Build engine

g++ -std=c++1y -m64 -D_REENTRANT -Wall -Wno-unused-function -Wno-uninitialized -Wno-unused-but-set-variable -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-attributes -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2019_U8/include   -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include  -D_USE_MATH_DEFINES  -DBOOST_DISABLE_ASSERTS        -c -fvisibility=hidden -o bin/cmdstan/print.o src/cmdstan/print.cpp

g++ -std=c++1y -m64 -D_REENTRANT -Wall -Wno-unused-function -Wno-uninitialized -Wno-unused-but-set-variable -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-attributes -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2019_U8/include   -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include  -D_USE_MATH_DEFINES  -DBOOST_DISABLE_ASSERTS        -c -fvisibility=hidden -o bin/cmdstan/diagnose.o src/cmdstan/diagnose.cpp

Generating Boost.Build configuration in project-config.jam for gcc...

Bootstrapping is done. To build, run:

    .\b2

To adjust configuration, edit 'project-config.jam'.

Further information:

    - Command line help:

    .\b2 --help

    - Getting started guide: 

    http://boost.org/more/getting_started/windows.html

    - Boost.Build documentation:

    http://www.boost.org/build/

cd stan/lib/stan_math/lib/boost_1.72.0; ./b2  address-model=64 --visibility=hidden --with-program_options cxxstd=11 variant=release link=static

Performing configuration checks

    - default address-model    : 64-bit

    - default architecture     : x86

Building the Boost C++ Libraries.

Component configuration:

    - atomic                   : not building

    - chrono                   : not building

    - container                : not building

    - context                  : not building

    - contract                 : not building

    - coroutine                : not building

    - date_time                : not building

    - exception                : not building

    - fiber                    : not building

    - filesystem               : not building

    - graph                    : not building

    - graph_parallel           : not building

    - headers                  : not building

    - iostreams                : not building

    - locale                   : not building

    - log                      : not building

    - math                     : not building

    - mpi                      : not building

    - program_options          : building

    - python                   : not building

    - random                   : not building

    - regex                    : not building

    - serialization            : not building

    - stacktrace               : not building

    - system                   : not building

    - test                     : not building

    - thread                   : not building

    - timer                    : not building

    - type_erasure             : not building

    - wave                     : not building

...patience...

...found 1072 targets...

...updating 48 targets...

common.copy C:\Users\adamh\Documents\.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\cmake\BoostDetectToolset-1.72.0.cmake

C:\Users\adamh\Documents\.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\tools\boost_install\BoostDetectToolset.cmake

        1 file(s) copied.

boost-install.generate-cmake-config-version- bin.v2\tools\boost_install\BoostConfigVersion.cmake

common.copy C:\Users\adamh\Documents\.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\cmake\Boost-1.72.0\BoostConfig.cmake

C:\Users\adamh\Documents\.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\tools\boost_install\BoostConfig.cmake

        1 file(s) copied.

common.copy C:\Users\adamh\Documents\.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\cmake\Boost-1.72.0\BoostConfigVersion.cmake

bin.v2\tools\boost_install\BoostConfigVersion.cmake

        1 file(s) copied.

boost-install.generate-cmake-config- bin.v2\libs\headers\build\stage\boost_headers-config.cmake

boost-install.generate-cmake-config-version- bin.v2\libs\headers\build\stage\boost_headers-config-version.cmake

boost-install.generate-cmake-config- bin.v2\libs\program_options\build\stage\boost_program_options-config.cmake

boost-install.generate-cmake-config-version- bin.v2\libs\program_options\build\stage\boost_program_options-config-version.cmake

common.copy C:\Users\adamh\Documents\.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\cmake\boost_headers-1.72.0\boost_headers-config-version.cmake

bin.v2\libs\headers\build\stage\boost_headers-config-version.cmake

        1 file(s) copied.

common.copy C:\Users\adamh\Documents\.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\cmake\boost_program_options-1.72.0\boost_program_options-config.cmake

bin.v2\libs\program_options\build\stage\boost_program_options-config.cmake

        1 file(s) copied.

common.copy C:\Users\adamh\Documents\.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\cmake\boost_headers-1.72.0\boost_headers-config.cmake

bin.v2\libs\headers\build\stage\boost_headers-config.cmake

        1 file(s) copied.

common.copy C:\Users\adamh\Documents\.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\cmake\boost_program_options-1.72.0\boost_program_options-config-version.cmake

bin.v2\libs\program_options\build\stage\boost_program_options-config-version.cmake

        1 file(s) copied.

gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\utf8_codecvt_facet.o

gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\positional_options.o

gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\convert.o

gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\winmain.o

gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\config_file.o

gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\split.o

gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\variables_map.o

gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\options_description.o

gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\cmdline.o

gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\value_semantic.o

gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\parsers.o

gcc.archive bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\libboost_program_options-mgw83-mt-x64-1_72.a

boost-install.generate-cmake-variant- bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\libboost_program_options-variant-mgw83-mt-x64-1_72-static.cmake

    type "C:\Users\adamh\AppData\Local\Temp\jam2074d350.000" > "bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\libboost_program_options-variant-mgw83-mt-x64-1_72-static.cmake"

...failed text-action bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\libboost_program_options-variant-mgw83-mt-x64-1_72-static.cmake...

...skipped <pC:\Users\adamh\Documents\.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\cmake\boost_program_options-1.72.0>libboost_program_options-variant-mgw83-mt-x64-1_72-static.cmake for lack of <pbin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden>libboost_program_options-variant-mgw83-mt-x64-1_72-static.cmake...

common.copy C:\Users\adamh\Documents\.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\libboost_program_options-mgw83-mt-x64-1_72.a

bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\libboost_program_options-mgw83-mt-x64-1_72.a

        1 file(s) copied.

...failed updating 1 target...

...skipped 1 target...

...updated 46 targets...

mingw32-make.exe: *** [make/command:40: stan/lib/stan_math/lib/boost_1.72.0/stage/lib/libboost_program_options*.a] Error 1

mingw32-make.exe: *** Waiting for unfinished jobs....
rok-cesnovar commented 3 years ago

Ok, so the same thing. Can you see if there is some log file generated inside C:\Users\adamh\Documents\.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0 somewhere?

This is related to the boost library not building which will eventually not be necessary once we fix https://github.com/stan-dev/cmdstan/issues/929 One reason this error occurs is if the non-Rtools g++ is used on windows. But that is not the case here as the correct g++ and mingw32-make are used. So I am interested in what causes it here.

adamhaber commented 3 years ago

There's bootstrap.log, containing:

###
### Using 'gcc' toolset.
###

C:\Users\adamh\Documents\.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\tools\build\src\engine>g++ -x c++ -std=c++11 -s -O3 -o b2.exe   -DNDEBUG  builtins.cpp class.cpp command.cpp compile.cpp constants.cpp cwd.cpp debug.cpp debugger.cpp execcmd.cpp execnt.cpp filent.cpp filesys.cpp frames.cpp function.cpp glob.cpp hash.cpp hcache.cpp hdrmacro.cpp headers.cpp jam.cpp jambase.cpp jamgram.cpp lists.cpp make.cpp make1.cpp md5.cpp mem.cpp modules.cpp native.cpp object.cpp option.cpp output.cpp parse.cpp pathnt.cpp pathsys.cpp regexp.cpp rules.cpp scan.cpp search.cpp strings.cpp subst.cpp sysinfo.cpp timestamp.cpp variable.cpp w32_getreg.cpp modules/order.cpp modules/path.cpp modules/property-set.cpp modules/regex.cpp modules/sequence.cpp modules/set.cpp  

C:\Users\adamh\Documents\.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\tools\build\src\engine>dir *.exe 
 Volume in drive C is Windows
 Volume Serial Number is 4A86-6AC4

 Directory of C:\Users\adamh\Documents\.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\tools\build\src\engine

11/02/2020  11:37 AM           449,536 b2.exe
11/02/2020  10:38 AM           449,536 bjam.exe
               2 File(s)        899,072 bytes
               0 Dir(s)  216,752,287,744 bytes free

C:\Users\adamh\Documents\.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\tools\build\src\engine>copy /b .\b2.exe .\bjam.exe 
        1 file(s) copied.
rok-cesnovar commented 3 years ago

Ok, one more debug thing. 

processx::run("./bootstrap.bat", args = c("gcc"), wd = "C:\\Users\\adamh\\Documents\\.cmdstanr\\cmdstan-2.25.0\\stan\\lib\\stan_math\\lib\\boost_1.72.0")

and then

processx::run("./b2", args = c("address-model=64", "--visibility=hidden", "--with-program_options", "cxxstd=11", "variant=release", "link=static"), wd = "C:\\Users\\adamh\\Documents\\.cmdstanr\\cmdstan-2.25.0\\stan\\lib\\stan_math\\lib\\boost_1.72.0")

Thanks!!

adamhaber commented 3 years ago 
> processx::run("bootstrap.bat", args = c("gcc"), wd = "C:\\Users\\adamh\\Documents\\.cmdstanr\\cmdstan-2.25.0\\stan\\lib\\stan_math\\lib\\boost_1.72.0")
$status
[1] 0

$stdout
[1] "Building Boost.Build engine\r\n\r\nGenerating Boost.Build configuration in project-config.jam for gcc...\r\n\r\nBootstrapping is done. To build, run:\r\n\r\n    .\\b2\r\n\r\nTo adjust configuration, edit 'project-config.jam'.\r\nFurther information:\r\n\r\n    - Command line help:\r\n    .\\b2 --help\r\n     \r\n    - Getting started guide: \r\n    http://boost.org/more/getting_started/windows.html\r\n     \r\n    - Boost.Build documentation:\r\n    http://www.boost.org/build/\r\n\r\n"

$stderr
[1] ""

$timeout
[1] FALSE

and 

processx::run("b2.exe", args = c("address-model=64", "--visibility=hidden", "--with-program_options", "cxxstd=11", "variant=release", "link=static"), wd = "C:\\Users\\adamh\\Documents\\.cmdstanr\\cmdstan-2.25.0\\stan\\lib\\stan_math\\lib\\boost_1.72.0")
Error in processx::run("b2.exe", args = c("address-model=64", "--visibility=hidden",  : 
  System command 'b2.exe' failed, exit status: 1, stderr empty
Type .Last.error.trace to see where the error occured
> .Last.error.trace

 Stack trace:

 1. processx::run("b2.exe", args = c("address-model=64", "--visibility=hidden",  ...
 2. throw(new_process_error(res, call = sys.call(), echo = echo,  ...

 x System command 'b2.exe' failed, exit status: 1, stderr empty
rok-cesnovar commented 3 years ago

I think its just b2 without the .exe? Or does that also not work?

EDIT: nevermind, its fine.

adamhaber commented 3 years ago

Tried it as well, got the same result.

rok-cesnovar commented 3 years ago

So there is no b2.exe in C:\Users\adamh\Documents\.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0?

adamhaber commented 3 years ago

Yes, there is. When I tried to run it from cmd, this is what I get:

C:\Users\adamh\Documents\.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0>b2 address-model=64 --visibility=hidden --with-program_options cxxstd=11 variant=release link=static
Performing configuration checks

    - default address-model    : 64-bit (cached)
    - default architecture     : x86 (cached)

Building the Boost C++ Libraries.

Component configuration:

    - atomic                   : not building
    - chrono                   : not building
    - container                : not building
    - context                  : not building
    - contract                 : not building
    - coroutine                : not building
    - date_time                : not building
    - exception                : not building
    - fiber                    : not building
    - filesystem               : not building
    - graph                    : not building
    - graph_parallel           : not building
    - headers                  : not building
    - iostreams                : not building
    - locale                   : not building
    - log                      : not building
    - math                     : not building
    - mpi                      : not building
    - program_options          : building
    - python                   : not building
    - random                   : not building
    - regex                    : not building
    - serialization            : not building
    - stacktrace               : not building
    - system                   : not building
    - test                     : not building
    - thread                   : not building
    - timer                    : not building
    - type_erasure             : not building
    - wave                     : not building

...patience...
...found 1072 targets...
...updating 2 targets...
boost-install.generate-cmake-variant- bin.v2\libs\program_options\build\gcc-7.1.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\libboost_program_options-variant-mgw71-mt-x64-1_72-static.cmake

    type "C:\Users\adamh\AppData\Local\Temp\jam5470e47d.000" > "bin.v2\libs\program_options\build\gcc-7.1.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\libboost_program_options-variant-mgw71-mt-x64-1_72-static.cmake"

...failed text-action bin.v2\libs\program_options\build\gcc-7.1.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\libboost_program_options-variant-mgw71-mt-x64-1_72-static.cmake...
...skipped <pC:\Users\adamh\Documents\.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\cmake\boost_program_options-1.72.0>libboost_program_options-variant-mgw71-mt-x64-1_72-static.cmake for lack of <pbin.v2\libs\program_options\build\gcc-7.1.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden>libboost_program_options-variant-mgw71-mt-x64-1_72-static.cmake...
...failed updating 1 target...
...skipped 1 target...
rok-cesnovar commented 3 years ago

Can you try this:

processx::run("b2.exe", args = c("address-model=64", "--visibility=hidden", "--with-program_options", "cxxstd=11", "variant=release", "link=static"), wd = "C:\\Users\\adamh\\Documents\\.cmdstanr\\cmdstan-2.25.0\\stan\\lib\\stan_math\\lib\\boost_1.72.0", echo = TRUE, error_on_status = FALSE)
adamhaber commented 3 years ago 
> processx::run("b2.exe", args = c("address-model=64", "--visibility=hidden", "--with-program_options", "cxxstd=11", "variant=release", "link=static"), wd = "C:\\Users\\adamh\\Documents\\.cmdstanr\\cmdstan-2.25.0\\stan\\lib\\stan_math\\lib\\boost_1.72.0", echo = TRUE, error_on_status = FALSE)
Performing configuration checks

    - default address-model    : 64-bit (cached)
    - default architecture     : x86 (cached)

Building the Boost C++ Libraries.

Component configuration:

    - atomic                   : not building
    - chrono                   : not building
    - container                : not building
    - context                  : not building
    - contract                 : not building
    - coroutine                : not building
    - date_time                : not building
    - exception                : not building
    - fiber                    : not building
    - filesystem               : not building
    - graph                    : not building
    - graph_parallel           : not building
    - headers                  : not building
    - iostreams                : not building
    - locale                   : not building
    - log                      : not building
    - math                     : not building
    - mpi                      : not building
    - program_options          : building
    - python                   : not building
    - random                   : not building
    - regex                    : not building
    - serialization            : not building
    - stacktrace               : not building
    - system                   : not building
    - test                     : not building
    - thread                   : not building
    - timer                    : not building
    - type_erasure             : not building
    - wave                     : not building

...patience...
...found 1072 targets...
...updating 2 targets...
boost-install.generate-cmake-variant- bin.v2\libs\program_options\build\gcc-7.1.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\libboost_program_options-variant-mgw71-mt-x64-1_72-static.cmake

    type "C:\Users\adamh\AppData\Local\Temp\jam5888e8f2.000" > "bin.v2\libs\program_options\build\gcc-7.1.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\libboost_program_options-variant-mgw71-mt-x64-1_72-static.cmake"

...failed text-action bin.v2\libs\program_options\build\gcc-7.1.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\libboost_program_options-variant-mgw71-mt-x64-1_72-static.cmake...
...skipped <pC:\Users\adamh\Documents\.cmdstanr\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\cmake\boost_program_options-1.72.0>libboost_program_options-variant-mgw71-mt-x64-1_72-static.cmake for lack of <pbin.v2\libs\program_options\build\gcc-7.1.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden>libboost_program_options-variant-mgw71-mt-x64-1_72-static.cmake...
...failed updating 1 target...
...skipped 1 target...
$status
[1] 1

$stdout
[1] "Performing configuration checks\r\n\r\n    - default address-model    : 64-bit (cached)\r\n    - default architecture     : x86 (cached)\r\n\r\nBuilding the Boost C++ Libraries.\r\n\r\n\r\n\r\nComponent configuration:\r\n\r\n    - atomic                   : not building\r\n    - chrono                   : not building\r\n    - container                : not building\r\n    - context                  : not building\r\n    - contract                 : not building\r\n    - coroutine                : not building\r\n    - date_time                : not building\r\n    - exception                : not building\r\n    - fiber                    : not building\r\n    - filesystem               : not building\r\n    - graph                    : not building\r\n    - graph_parallel           : not building\r\n    - headers                  : not building\r\n    - iostreams                : not building\r\n    - locale                   : not building\r\n    - log                      : not building\r\n    - math                     : not building\r\n    - mpi                      : not building\r\n    - program_options          : building\r\n    - python                   : not building\r\n    - random                   : not building\r\n    - regex                    : not building\r\n    - serialization            : not building\r\n    - stacktrace               : not building\r\n    - system                   : not building\r\n    - test                     : not building\r\n    - thread                   : not building\r\n    - timer                    : not building\r\n    - type_erasure             : not building\r\n    - wave                     : not building\r\n\r\n...patience...\r\n...found 1072 targets...\r\n...updating 2 targets...\r\nboost-install.generate-cmake-variant- bin.v2\\libs\\program_options\\build\\gcc-7.1.0\\release\\cxxstd-11-iso\\link-static\\threading-multi\\visibility-hidden\\libboost_program_options-variant-mgw71-mt-x64-1_72-static.cmake\r\n\r\n    type \"C:\\Users\\adamh\\AppData\\Local\\Temp\\jam5888e8f2.000\" > \"bin.v2\\libs\\program_options\\build\\gcc-7.1.0\\release\\cxxstd-11-iso\\link-static\\threading-multi\\visibility-hidden\\libboost_program_options-variant-mgw71-mt-x64-1_72-static.cmake\"\r\n\r\n...failed text-action bin.v2\\libs\\program_options\\build\\gcc-7.1.0\\release\\cxxstd-11-iso\\link-static\\threading-multi\\visibility-hidden\\libboost_program_options-variant-mgw71-mt-x64-1_72-static.cmake...\r\n...skipped <pC:\\Users\\adamh\\Documents\\.cmdstanr\\cmdstan-2.25.0\\stan\\lib\\stan_math\\lib\\boost_1.72.0\\stage\\lib\\cmake\\boost_program_options-1.72.0>libboost_program_options-variant-mgw71-mt-x64-1_72-static.cmake for lack of <pbin.v2\\libs\\program_options\\build\\gcc-7.1.0\\release\\cxxstd-11-iso\\link-static\\threading-multi\\visibility-hidden>libboost_program_options-variant-mgw71-mt-x64-1_72-static.cmake...\r\n...failed updating 1 target...\r\n...skipped 1 target...\r\n"

$stderr
[1] ""

$timeout
[1] FALSE
rok-cesnovar commented 3 years ago

Hm, OK, maybe one hunch.

Can you go in your windows path and place C:\rtools40\mingw64\bin at the front? Its currently in last place (its placed in front for the R session only). and then try rebuild_cmdstan() again.

adamhaber commented 3 years ago

Same error:

image
rok-cesnovar commented 3 years ago

Did you restart the RStudio or R terminal?

adamhaber commented 3 years ago

Yes.

rok-cesnovar commented 3 years ago

I have one more idea for now. Can you make a directory, lets say "C:\test" and then run install_cmdstan(dir = "C:\test")

rok-cesnovar commented 3 years ago

Or even better, before you do that enable "long paths": https://docs.microsoft.com/en-us/windows/win32/fileio/maximum-file-path-limitation#enable-long-paths-in-windows-10-version-1607-and-later

rok-cesnovar commented 3 years ago

Really appreciate your time and help Adam!

adamhaber commented 3 years ago

I have one more idea for now. Can you make a directory, lets say "C:\test" and then run install_cmdstan(dir = "C:\test")

Thanks! That worked. What was the problem?

I'm attaching the installation output, in case you're interested:

> install_cmdstan(dir = "C:\\Users\\adamh\\Downloads\\test")
The CmdStan toolchain is setup properly!
* Latest CmdStan release is v2.25.0
* Installing CmdStan v2.25.0 in C:/Users/adamh/Downloads/test/cmdstan-2.25.0
* Downloading cmdstan-2.25.0.tar.gz from GitHub...
* Download complete
* Unpacking archive...
* Building CmdStan binaries...
INFO: Could not find files for the given pattern(s).

cp bin/windows-stanc bin/stanc.exe

g++ -std=c++1y -m64 -D_REENTRANT -Wall -Wno-unused-function -Wno-uninitialized -Wno-unused-but-set-variable -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-attributes -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2019_U8/include   -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include  -D_USE_MATH_DEFINES  -DBOOST_DISABLE_ASSERTS        -c -fvisibility=hidden -o bin/cmdstan/stansummary.o src/cmdstan/stansummary.cpp

cd stan/lib/stan_math/lib/boost_1.72.0; ./bootstrap.bat gcc

Building Boost.Build engine

g++ -std=c++1y -m64 -D_REENTRANT -Wall -Wno-unused-function -Wno-uninitialized -Wno-unused-but-set-variable -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-attributes -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2019_U8/include   -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include  -D_USE_MATH_DEFINES  -DBOOST_DISABLE_ASSERTS        -c -fvisibility=hidden -o bin/cmdstan/print.o src/cmdstan/print.cpp

g++ -std=c++1y -m64 -D_REENTRANT -Wall -Wno-unused-function -Wno-uninitialized -Wno-unused-but-set-variable -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-attributes -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2019_U8/include   -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include  -D_USE_MATH_DEFINES  -DBOOST_DISABLE_ASSERTS        -c -fvisibility=hidden -o bin/cmdstan/diagnose.o src/cmdstan/diagnose.cpp

Generating Boost.Build configuration in project-config.jam for gcc...

Bootstrapping is done. To build, run:

    .\b2

To adjust configuration, edit 'project-config.jam'.

Further information:

    - Command line help:

    .\b2 --help

    - Getting started guide: 

    http://boost.org/more/getting_started/windows.html

    - Boost.Build documentation:

    http://www.boost.org/build/

cd stan/lib/stan_math/lib/boost_1.72.0; ./b2  address-model=64 --visibility=hidden --with-program_options cxxstd=11 variant=release link=static

Performing configuration checks

    - default address-model    : 64-bit

    - default architecture     : x86

Building the Boost C++ Libraries.

Component configuration:

    - atomic                   : not building

    - chrono                   : not building

    - container                : not building

    - context                  : not building

    - contract                 : not building

    - coroutine                : not building

    - date_time                : not building

    - exception                : not building

    - fiber                    : not building

    - filesystem               : not building

    - graph                    : not building

    - graph_parallel           : not building

    - headers                  : not building

    - iostreams                : not building

    - locale                   : not building

    - log                      : not building

    - math                     : not building

    - mpi                      : not building

    - program_options          : building

    - python                   : not building

    - random                   : not building

    - regex                    : not building

    - serialization            : not building

    - stacktrace               : not building

    - system                   : not building

    - test                     : not building

    - thread                   : not building

    - timer                    : not building

    - type_erasure             : not building

    - wave                     : not building

...patience...

...found 1072 targets...

...updating 48 targets...

common.copy C:\Users\adamh\Downloads\test\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\cmake\BoostDetectToolset-1.72.0.cmake

C:\Users\adamh\Downloads\test\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\tools\boost_install\BoostDetectToolset.cmake

        1 file(s) copied.

common.copy C:\Users\adamh\Downloads\test\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\cmake\Boost-1.72.0\BoostConfig.cmake

C:\Users\adamh\Downloads\test\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\tools\boost_install\BoostConfig.cmake

        1 file(s) copied.

boost-install.generate-cmake-config-version- bin.v2\tools\boost_install\BoostConfigVersion.cmake

boost-install.generate-cmake-config- bin.v2\libs\program_options\build\stage\boost_program_options-config.cmake

boost-install.generate-cmake-config-version- bin.v2\libs\program_options\build\stage\boost_program_options-config-version.cmake

boost-install.generate-cmake-config- bin.v2\libs\headers\build\stage\boost_headers-config.cmake

boost-install.generate-cmake-config-version- bin.v2\libs\headers\build\stage\boost_headers-config-version.cmake

common.copy C:\Users\adamh\Downloads\test\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\cmake\Boost-1.72.0\BoostConfigVersion.cmake

bin.v2\tools\boost_install\BoostConfigVersion.cmake

        1 file(s) copied.

common.copy C:\Users\adamh\Downloads\test\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\cmake\boost_program_options-1.72.0\boost_program_options-config.cmake

bin.v2\libs\program_options\build\stage\boost_program_options-config.cmake

        1 file(s) copied.

common.copy C:\Users\adamh\Downloads\test\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\cmake\boost_program_options-1.72.0\boost_program_options-config-version.cmake

bin.v2\libs\program_options\build\stage\boost_program_options-config-version.cmake

        1 file(s) copied.

common.copy C:\Users\adamh\Downloads\test\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\cmake\boost_headers-1.72.0\boost_headers-config.cmake

bin.v2\libs\headers\build\stage\boost_headers-config.cmake

        1 file(s) copied.

common.copy C:\Users\adamh\Downloads\test\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\cmake\boost_headers-1.72.0\boost_headers-config-version.cmake

bin.v2\libs\headers\build\stage\boost_headers-config-version.cmake

        1 file(s) copied.

gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\utf8_codecvt_facet.o

gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\positional_options.o

gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\convert.o

gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\winmain.o

gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\config_file.o

gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\split.o

gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\variables_map.o

gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\options_description.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/nvector/serial/nvector_serial.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/nvector/serial/nvector_serial.o

gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\cmdline.o

gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\value_semantic.o

gcc.compile.c++ bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\parsers.o

gcc.archive bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\libboost_program_options-mgw83-mt-x64-1_72.a

boost-install.generate-cmake-variant- bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\libboost_program_options-variant-mgw83-mt-x64-1_72-static.cmake

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_math.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_math.o

common.copy C:\Users\adamh\Downloads\test\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\libboost_program_options-mgw83-mt-x64-1_72.a

bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\libboost_program_options-mgw83-mt-x64-1_72.a

        1 file(s) copied.

common.copy C:\Users\adamh\Downloads\test\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib\cmake\boost_program_options-1.72.0\libboost_program_options-variant-mgw83-mt-x64-1_72-static.cmake

bin.v2\libs\program_options\build\gcc-8.3.0\release\cxxstd-11-iso\link-static\threading-multi\visibility-hidden\libboost_program_options-variant-mgw83-mt-x64-1_72-static.cmake

        1 file(s) copied.

...updated 48 targets...

The Boost C++ Libraries were successfully built!

The following directory should be added to compiler include paths:

    C:\Users\adamh\Downloads\test\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0

The following directory should be added to linker library paths:

    C:\Users\adamh\Downloads\test\cmdstan-2.25.0\stan\lib\stan_math\lib\boost_1.72.0\stage\lib

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_stg1.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_stg1.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_sim.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_sim.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_ls.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_ls.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodea_io.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodea_io.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_spils.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_spils.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_bandpre.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_bandpre.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_bbdpre.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_bbdpre.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_stg.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_stg.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodea.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodea.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_io.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_io.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_direct.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_direct.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_diag.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_diag.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_dense.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_dense.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector_senswrapper.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector_senswrapper.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_linearsolver.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_linearsolver.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_iterative.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_iterative.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_band.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_band.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_version.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_version.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nonlinearsolver.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nonlinearsolver.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_direct.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_direct.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_futils.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_futils.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_matrix.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_matrix.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/band/sunmatrix_band.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/band/sunmatrix_band.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/dense/sunmatrix_dense.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/dense/sunmatrix_dense.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/band/sunlinsol_band.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/band/sunlinsol_band.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/dense/sunlinsol_dense.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/dense/sunlinsol_dense.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/newton/sunnonlinsol_newton.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/newton/sunnonlinsol_newton.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls_sim.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls_sim.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_ls.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_ls.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_bbdpre.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_bbdpre.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls_stg.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls_stg.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idaa_io.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idaa_io.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_direct.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_direct.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_io.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_io.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idaa.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idaa.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_ic.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_ic.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_spils.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_spils.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_io.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_io.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_spils.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_spils.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_ls.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_ls.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_bbdpre.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_bbdpre.o

g++ -pipe   -m64 -D_REENTRANT  -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT   -D_USE_MATH_DEFINES  -O3  -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_direct.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_direct.o

if ! [[ mingw32-make.exe =~ mingw32 ]]; then \

        echo "ERROR: Please use mingw32-make on Windows to build the Intel TBB library."; \

        echo "This is packaged with RTools, for example."; \

        exit 1; \

fi

touch stan/lib/stan_math/lib/tbb/tbb-make-check

--- Compiling the main object file. This might take up to a minute. ---
--- Compiling pre-compiled header. This might take a few seconds. ---
g++ -std=c++1y -m64 -D_REENTRANT -Wall -Wno-unused-function -Wno-uninitialized -Wno-unused-but-set-variable -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-attributes -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2019_U8/include   -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include  -D_USE_MATH_DEFINES  -DBOOST_DISABLE_ASSERTS        -c stan/src/stan/model/model_header.hpp -o stan/src/stan/model/model_header.hpp.gch

g++ -std=c++1y -m64 -D_REENTRANT -Wall -Wno-unused-function -Wno-uninitialized -Wno-unused-but-set-variable -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-attributes -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2019_U8/include   -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include  -D_USE_MATH_DEFINES  -DBOOST_DISABLE_ASSERTS        -c -o src/cmdstan/main.o src/cmdstan/main.cpp

g++ -std=c++1y -m64 -D_REENTRANT -Wall -Wno-unused-function -Wno-uninitialized -Wno-unused-but-set-variable -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-attributes -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2019_U8/include   -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include  -D_USE_MATH_DEFINES  -DBOOST_DISABLE_ASSERTS              -Wl,-L,"C:/Users/adamh/Downloads/test/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"C:/Users/adamh/Downloads/test/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb"      bin/cmdstan/stansummary.o stan/lib/stan_math/lib/boost_1.72.0/stage/lib/libboost_program_options*.a stan/lib/stan_math/lib/boost_1.72.0/stage/lib/libboost_program_options*.a  -static-libgcc -static-libstdc++       -o bin/stansummary.exe

g++ -std=c++1y -m64 -D_REENTRANT -Wall -Wno-unused-function -Wno-uninitialized -Wno-unused-but-set-variable -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-attributes -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2019_U8/include   -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include  -D_USE_MATH_DEFINES  -DBOOST_DISABLE_ASSERTS              -Wl,-L,"C:/Users/adamh/Downloads/test/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"C:/Users/adamh/Downloads/test/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb"      bin/cmdstan/print.o stan/lib/stan_math/lib/boost_1.72.0/stage/lib/libboost_program_options*.a stan/lib/stan_math/lib/boost_1.72.0/stage/lib/libboost_program_options*.a  -static-libgcc -static-libstdc++       -o bin/print.exe

g++ -std=c++1y -m64 -D_REENTRANT -Wall -Wno-unused-function -Wno-uninitialized -Wno-unused-but-set-variable -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-attributes -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2019_U8/include   -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include  -D_USE_MATH_DEFINES  -DBOOST_DISABLE_ASSERTS              -Wl,-L,"C:/Users/adamh/Downloads/test/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"C:/Users/adamh/Downloads/test/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb"      bin/cmdstan/diagnose.o stan/lib/stan_math/lib/boost_1.72.0/stage/lib/libboost_program_options*.a stan/lib/stan_math/lib/boost_1.72.0/stage/lib/libboost_program_options*.a  -static-libgcc -static-libstdc++       -o bin/diagnose.exe

ar -rs stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_nvecserial.a stan/lib/stan_math/lib/sundials_5.2.0/src/nvector/serial/nvector_serial.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_math.o

ar: creating stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_nvecserial.a

ar -rs stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_cvodes.a stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_stg1.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_sim.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_ls.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodea_io.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_spils.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_bandpre.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_bbdpre.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_stg.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodea.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_io.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_direct.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_diag.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector_senswrapper.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_math.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_linearsolver.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_iterative.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_version.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nonlinearsolver.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_direct.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_futils.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_matrix.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/band/sunmatrix_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/dense/sunmatrix_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/band/sunlinsol_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/dense/sunlinsol_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/newton/sunnonlinsol_newton.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.o

ar: creating stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_cvodes.a

ar -rs stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_idas.a stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls_sim.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_ls.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_bbdpre.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls_stg.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idaa_io.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_direct.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_io.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idaa.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_ic.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_spils.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector_senswrapper.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_math.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_linearsolver.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_iterative.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_version.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nonlinearsolver.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_direct.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_futils.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_matrix.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/band/sunmatrix_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/dense/sunmatrix_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/band/sunlinsol_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/dense/sunlinsol_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/newton/sunnonlinsol_newton.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.o

ar: creating stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_idas.a

ar -rs stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_kinsol.a stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_io.o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_spils.o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_ls.o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol.o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_bbdpre.o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_direct.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector_senswrapper.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_math.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_linearsolver.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_iterative.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_version.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nonlinearsolver.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_direct.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_futils.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_matrix.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/band/sunmatrix_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/dense/sunmatrix_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/band/sunlinsol_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/dense/sunlinsol_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/newton/sunnonlinsol_newton.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.o

ar: creating stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_kinsol.a

tbb_root="../tbb_2019_U8" CXX="g++" CC="gcc" LDFLAGS='-Wl,-L,"C:/Users/adamh/Downloads/test/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"C:/Users/adamh/Downloads/test/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb"  ' 'mingw32-make.exe' -C "stan/lib/stan_math/lib/tbb" -r -f "C:/Users/adamh/Downloads/test/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb_2019_U8/build/Makefile.tbbmalloc" compiler=gcc cfg=release stdver=c++1y malloc CXXFLAGS="-Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation  "

mingw32-make[1]: Entering directory 'C:/Users/adamh/Downloads/test/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb'

g++ -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -fno-rtti -fno-exceptions -D__TBBMALLOC_BUILD=1 -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor  -flifetime-dse=1 -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include -I../tbb_2019_U8/src/tbbmalloc -I../tbb_2019_U8/src/tbbmalloc ../tbb_2019_U8/src/tbbmalloc/backend.cpp

g++ -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -fno-rtti -fno-exceptions -D__TBBMALLOC_BUILD=1 -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor  -flifetime-dse=1 -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include -I../tbb_2019_U8/src/tbbmalloc -I../tbb_2019_U8/src/tbbmalloc ../tbb_2019_U8/src/tbbmalloc/large_objects.cpp

g++ -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -fno-rtti -fno-exceptions -D__TBBMALLOC_BUILD=1 -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor  -flifetime-dse=1 -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include -I../tbb_2019_U8/src/tbbmalloc -I../tbb_2019_U8/src/tbbmalloc ../tbb_2019_U8/src/tbbmalloc/backref.cpp

g++ -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -fno-rtti -fno-exceptions -D__TBBMALLOC_BUILD=1 -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor  -flifetime-dse=1 -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include -I../tbb_2019_U8/src/tbbmalloc -I../tbb_2019_U8/src/tbbmalloc ../tbb_2019_U8/src/tbbmalloc/tbbmalloc.cpp

g++ -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -fno-rtti -fno-exceptions -D__TBBMALLOC_BUILD=1 -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor  -flifetime-dse=1 -o itt_notify_malloc.o -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/itt_notify.cpp

cmd /C cscript /nologo /E:jscript ../tbb_2019_U8/build/version_info_windows.js gcc intel64 "g++ -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm  -Wall -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation    -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include" > version_string.ver

g++ -E -x c++ ../tbb_2019_U8/src/tbbmalloc/win64-gcc-tbbmalloc-export.def -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm  -Wall -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation    -fno-rtti -fno-exceptions -D__TBBMALLOC_BUILD=1  -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include > tbbmalloc.def

g++ -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm  -Wall -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation    -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor  -flifetime-dse=1 -D__TBBMALLOC_BUILD=1 -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include -I../tbb_2019_U8/src/tbbmalloc -I../tbb_2019_U8/src/tbbmalloc ../tbb_2019_U8/src/tbbmalloc/proxy.cpp

g++ -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm  -Wall -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation    -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor  -flifetime-dse=1 -D__TBBMALLOC_BUILD=1 -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include -I../tbb_2019_U8/src/tbbmalloc -I../tbb_2019_U8/src/tbbmalloc ../tbb_2019_U8/src/tbbmalloc/tbb_function_replacement.cpp

g++ -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -fno-rtti -fno-exceptions -D__TBBMALLOC_BUILD=1 -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor  -flifetime-dse=1 -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include -I../tbb_2019_U8/src/tbbmalloc -I../tbb_2019_U8/src/tbbmalloc -I. ../tbb_2019_U8/src/tbbmalloc/frontend.cpp

gcc  -o tbbmalloc.dll backend.o large_objects.o backref.o  tbbmalloc.o  itt_notify_malloc.o frontend.o   -lpsapi -shared -m64 -Wl,-L,"C:/Users/adamh/Downloads/test/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"C:/Users/adamh/Downloads/test/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb"   -Wl,--version-script,tbbmalloc.def

g++  -o tbbmalloc_proxy.dll proxy.o tbb_function_replacement.o   -lpsapi tbbmalloc.dll  -shared -m64 -Wl,-L,"C:/Users/adamh/Downloads/test/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"C:/Users/adamh/Downloads/test/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb"  

mingw32-make[1]: Leaving directory 'C:/Users/adamh/Downloads/test/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb'

touch stan/lib/stan_math/lib/tbb/version_tbb_2019_U8

tbb_root="../tbb_2019_U8" CXX="g++" CC="gcc" LDFLAGS='-Wl,-L,"C:/Users/adamh/Downloads/test/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"C:/Users/adamh/Downloads/test/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb"  ' 'mingw32-make.exe' -C "stan/lib/stan_math/lib/tbb" -r -f "C:/Users/adamh/Downloads/test/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb_2019_U8/build/Makefile.tbb" compiler=gcc cfg=release stdver=c++1y  CXXFLAGS="-Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation  "

mingw32-make[1]: Entering directory 'C:/Users/adamh/Downloads/test/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb'

C:/Users/adamh/Downloads/test/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb_2019_U8/build/Makefile.tbb:28: CONFIG: cfg=release arch=intel64 compiler=gcc target=windows runtime=mingw8.3.0

g++ -o concurrent_hash_map.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/concurrent_hash_map.cpp

g++ -o concurrent_queue.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/concurrent_queue.cpp

g++ -o concurrent_vector.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/concurrent_vector.cpp

g++ -o dynamic_link.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/dynamic_link.cpp

g++ -o itt_notify.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/itt_notify.cpp

g++ -o cache_aligned_allocator.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/cache_aligned_allocator.cpp

g++ -o pipeline.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/pipeline.cpp

g++ -o queuing_mutex.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/queuing_mutex.cpp

g++ -o queuing_rw_mutex.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/queuing_rw_mutex.cpp

g++ -o reader_writer_lock.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/reader_writer_lock.cpp

g++ -o spin_rw_mutex.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/spin_rw_mutex.cpp

g++ -o x86_rtm_rw_mutex.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/x86_rtm_rw_mutex.cpp

g++ -o spin_mutex.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/spin_mutex.cpp

g++ -o critical_section.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/critical_section.cpp

g++ -o mutex.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/mutex.cpp

g++ -o recursive_mutex.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/recursive_mutex.cpp

g++ -o condition_variable.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/condition_variable.cpp

g++ -o tbb_thread.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/tbb_thread.cpp

g++ -o concurrent_monitor.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/concurrent_monitor.cpp

g++ -o semaphore.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/semaphore.cpp

g++ -o private_server.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/private_server.cpp

g++ -o rml_tbb.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/rml/client/rml_tbb.cpp

g++ -o tbb_misc.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include -I. ../tbb_2019_U8/src/tbb/tbb_misc.cpp

g++ -o tbb_misc_ex.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/tbb_misc_ex.cpp

g++ -o task.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/task.cpp

g++ -o task_group_context.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/task_group_context.cpp

g++ -o governor.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/governor.cpp

g++ -o market.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/market.cpp

g++ -o arena.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/arena.cpp

g++ -o scheduler.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/scheduler.cpp

g++ -o observer_proxy.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/observer_proxy.cpp

g++ -o tbb_statistics.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/tbb_statistics.cpp

g++ -o tbb_main.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/tbb_main.cpp

g++ -o concurrent_vector_v2.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/old/concurrent_vector_v2.cpp

g++ -o concurrent_queue_v2.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/old/concurrent_queue_v2.cpp

g++ -o spin_rw_mutex_v2.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/old/spin_rw_mutex_v2.cpp

g++ -o task_v2.o -c -MMD -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -std=c++1y  -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/old/task_v2.cpp

cmd /C "..\tbb_2019_U8\build\generate_tbbvars.bat"

Generating local tbbvars.bat

Generating local tbbvars.sh

Generating local tbbvars.csh

g++ -E -x c++ ../tbb_2019_U8/src/tbb/win64-gcc-tbb-export.def -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-uninitialized -Wno-non-virtual-dtor -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include > tbb.def

g++  -o tbb.dll concurrent_hash_map.o concurrent_queue.o concurrent_vector.o dynamic_link.o itt_notify.o cache_aligned_allocator.o pipeline.o queuing_mutex.o queuing_rw_mutex.o reader_writer_lock.o spin_rw_mutex.o x86_rtm_rw_mutex.o spin_mutex.o critical_section.o mutex.o recursive_mutex.o condition_variable.o tbb_thread.o concurrent_monitor.o semaphore.o private_server.o rml_tbb.o tbb_misc.o tbb_misc_ex.o task.o task_group_context.o governor.o market.o arena.o scheduler.o observer_proxy.o tbb_statistics.o tbb_main.o concurrent_vector_v2.o concurrent_queue_v2.o spin_rw_mutex_v2.o task_v2.o    -lpsapi -shared -m64 -Wl,-L,"C:/Users/adamh/Downloads/test/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"C:/Users/adamh/Downloads/test/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb"   -Wl,--version-script,tbb.def

task.o: duplicate section `.rdata$_ZTIN3tbb4taskE[_ZTIN3tbb4taskE]' has different size

arena.o: duplicate section `.rdata$_ZTIN3tbb4taskE[_ZTIN3tbb4taskE]' has different size

scheduler.o: duplicate section `.rdata$_ZTIN3tbb4taskE[_ZTIN3tbb4taskE]' has different size

mingw32-make[1]: Leaving directory 'C:/Users/adamh/Downloads/test/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb'

NOTE: Please add C:/Users/adamh/Downloads/test/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb to your PATH variable.
You may call

mingw32-make install-tbb

to automatically update your user configuration.
--- CmdStan v2.25.0 built ---
INFO: Could not find files for the given pattern(s).

g++ -std=c++1y -m64 -D_REENTRANT -Wall -Wno-unused-function -Wno-uninitialized -Wno-unused-but-set-variable -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-attributes -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2019_U8/include   -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include  -D_USE_MATH_DEFINES  -DBOOST_DISABLE_ASSERTS        -c -MT stan/src/stan/model/model_header.hpp.gch -MT stan/src/stan/model/model_header.d -M -E -MG -MP -MF stan/src/stan/model/model_header.d stan/src/stan/model/model_header.hpp

g++ -std=c++1y -m64 -D_REENTRANT -Wall -Wno-unused-function -Wno-uninitialized -Wno-unused-but-set-variable -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-attributes -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2019_U8/include   -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include  -D_USE_MATH_DEFINES  -DBOOST_DISABLE_ASSERTS        -c -MT src/cmdstan/main.o -M -E -MG -MP -MF src/cmdstan/main.d src/cmdstan/main.cpp

INFO: Could not find files for the given pattern(s).

--- Translating Stan model to C++ code ---
bin/stanc.exe  --o=examples/bernoulli/bernoulli.hpp examples/bernoulli/bernoulli.stan

--- Compiling, linking C++ code ---
g++ -std=c++1y -m64 -D_REENTRANT -Wall -Wno-unused-function -Wno-uninitialized -Wno-unused-but-set-variable -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-attributes -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2019_U8/include   -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include  -D_USE_MATH_DEFINES  -DBOOST_DISABLE_ASSERTS        -c -Wno-ignored-attributes   -x c++ -o examples/bernoulli/bernoulli.o examples/bernoulli/bernoulli.hpp

g++ -std=c++1y -m64 -D_REENTRANT -Wall -Wno-unused-function -Wno-uninitialized -Wno-unused-but-set-variable -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-attributes -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2019_U8/include   -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include  -D_USE_MATH_DEFINES  -DBOOST_DISABLE_ASSERTS              -Wl,-L,"C:/Users/adamh/Downloads/test/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"C:/Users/adamh/Downloads/test/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb"      examples/bernoulli/bernoulli.o src/cmdstan/main.o  -static-libgcc -static-libstdc++       stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_nvecserial.a stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_cvodes.a stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_idas.a stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_kinsol.a  stan/lib/stan_math/lib/tbb/tbb.dll -o examples/bernoulli/bernoulli.exe

rm -f examples/bernoulli/bernoulli.o

Intel TBB is not in PATH.
Consider calling 
mingw32-make install-tbb
to avoid copying Intel TBB library files.
'stan/lib/stan_math/lib/tbb/tbb.dll' -> 'examples/bernoulli/tbb.dll'
* Finished installing CmdStan to C:/Users/adamh/Downloads/test/cmdstan-2.25.0

CmdStan path set to: C:/Users/adamh/Downloads/test/cmdstan-2.25.0
rok-cesnovar commented 3 years ago

Not completely sure to be honest. Wild guess based on an issue @martinmodrak had and fixed a while back.

install_cmdstan() tried to install to: C:\Users\adamh\Documents/.cmdstanr/ (notice the weird slash and backward slash combo - looking into that). The weird slash backslash being a problem is one possible explanation. If this is the problem then install_cmdstan(dir = "C:/Users/adamh/Documents/.cmdstanr/") would work.

If that does not work then it may be due to the path being shorter in which case https://docs.microsoft.com/en-us/windows/win32/fileio/maximum-file-path-limitation#enable-long-paths-in-windows-10-version-1607-and-later would also help, I honestly dont know. Windows is a gift that keeps on giving :)

adamhaber commented 3 years ago

Thanks again for all your help, Rok!

I checked and the bernoulli example works fine:

library(cmdstanr)
library(posterior)
library(bayesplot)
set_cmdstan_path("C:\\Users\\adamh\\Downloads\\test\\cmdstan-2.25.0")
color_scheme_set("brightblue")
file <- file.path(cmdstan_path(), "examples", "bernoulli", "bernoulli.stan")
mod <- cmdstan_model(file)
data_list <- list(N = 10, y = c(0,1,0,0,0,0,0,0,0,1))

fit <- mod$sample(
  data = data_list,
  seed = 123,
  chains = 4,
  parallel_chains = 2,
  refresh = 500
)

I then proceeded to try the following (based on this):

generator = function(seed = 0, n = 1000, k = 10) {

  inv_logit <- function(x) {
    1 / (1 + exp(-x))
  }

  set.seed(seed)
  X <- matrix(rnorm(n * k), ncol = k)

  y <- 3 * X[,1] - 2 * X[,2] + 1
  p <- runif(n)
  y <- ifelse(p < inv_logit(y), 1, 0)

  list(k = ncol(X), n = nrow(X), y = y, X = X)
}

data <- generator(1, 2000, 50)

opencl_options = list(
  stan_opencl = TRUE,
  opencl_platform_id = 0, # replace the ID based on step 3
  opencl_device_id = 0 # replace the ID based on step 3
)

mod <- cmdstan_model("c:/Users/adamh/Downloads/lr_glm.stan", cpp_options = opencl_options, quiet = FALSE)
fit <- mod$sample(data = data, num_samples=500, num_warmup = 500, num_chains = 1, num_cores = 1)

which crashes with:

an_model("c:/Users/adamh/Downloads/lr_glm.stan", cpp_options = opencl_options, quiet = FALSE)
Compiling Stan program...
Running mingw32-make.exe "C:/Users/adamh/AppData/Local/Temp/RtmpWwp4Ex/model-21007598250a.exe" \
  "STAN_OPENCL=TRUE OPENCL_PLATFORM_ID=0 OPENCL_DEVICE_ID=0" "STANCFLAGS += --use-opencl --name='lr_glm_model'"

--- Compiling pre-compiled header. This might take a few seconds. ---
g++ -std=c++1y -m64 -D_REENTRANT -Wall -Wno-unused-function -Wno-uninitialized -Wno-unused-but-set-variable -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-attributes -Wno-ignored-attributes   -I stan/lib/stan_math/lib/opencl_2.2.0   -I stan/lib/stan_math/lib/tbb_2019_U8/include   -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include  -D_USE_MATH_DEFINES  -DBOOST_DISABLE_ASSERTS  -DSTAN_OPENCL -DOPENCL_DEVICE_ID=0 -DOPENCL_PLATFORM_ID=0 -DCL_HPP_TARGET_OPENCL_VERSION=120 -DCL_HPP_MINIMUM_OPENCL_VERSION=120 -DCL_HPP_ENABLE_EXCEPTIONS -Wno-ignored-attributes      -c stan/src/stan/model/model_header.hpp -o stan/src/stan/model/model_header_opencl.hpp.gch
In file included from stan/src/stan/model/model_header.hpp:16:
stan/src/stan/services/util/create_rng.hpp:35:1: internal compiler error: in gt_pch_note_object, at ggc-common.c:276
 }  // namespace stan
 ^
In file included from stan/src/stan/model/model_header.hpp:16:
stan/src/stan/services/util/create_rng.hpp:35:1: internal compiler error: in gt_pch_note_object, at ggc-common.c:276
 }  // namespace stan
 ^
libbacktrace could not find executable to open
Please submit a full bug report,
with preprocessed source if appropriate.
See <https://github.com/r-windows> for instructions.
libbacktrace could not find executable to open
Please submit a full bug report,
with preprocessed source if appropriate.
See <https://github.com/r-windows> for instructions.
mingw32-make.exe: *** [make/program:25: stan/src/stan/model/model_header_opencl.hpp.gch] Error 1
mingw32-make.exe: *** [make/program:25: stan/src/stan/model/model_header_opencl.hpp.gch] Error 1
Error: An error occured during compilation! See the message above for more information.

When I remove the cpp_options the model compiles and samples.

rok-cesnovar commented 3 years ago

Glad to help and sorry for the troubles. This looks like an issue with precompiled headers with OpenCL on.

Can you post the output of

cmdstan_make_local()

adamhaber commented 3 years ago 
> cmdstan_make_local()
[1] "PRECOMPILED_HEADERS=true"
rok-cesnovar commented 3 years ago

Ok, try cmdstan_make_local(””) and rebuild cmdstan and try again. Maybe Windows + precompiled headers + opencl combo does not work.

adamhaber commented 3 years ago

I deleted the content of make/local, and I'm getting a different error (seems to be related to what's reported here):

Compiling Stan program...
Running mingw32-make.exe "C:/Users/adamh/AppData/Local/Temp/RtmpEhT48p/model-412426f55c74.exe" \
  "STAN_OPENCL=TRUE OPENCL_PLATFORM_ID=0 OPENCL_DEVICE_ID=0" "STANCFLAGS += --use-opencl --name='lr_glm_model'"

--- Compiling the main object file. This might take up to a minute. ---
g++ -std=c++1y -m64 -D_REENTRANT -Wall -Wno-unused-function -Wno-uninitialized -Wno-unused-but-set-variable -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-attributes -Wno-ignored-attributes   -I stan/lib/stan_math/lib/opencl_2.2.0   -I stan/lib/stan_math/lib/tbb_2019_U8/include   -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include  -D_USE_MATH_DEFINES  -DBOOST_DISABLE_ASSERTS  -DSTAN_OPENCL -DOPENCL_DEVICE_ID=0 -DOPENCL_PLATFORM_ID=0 -DCL_HPP_TARGET_OPENCL_VERSION=120 -DCL_HPP_MINIMUM_OPENCL_VERSION=120 -DCL_HPP_ENABLE_EXCEPTIONS -Wno-ignored-attributes      -c -o src/cmdstan/main_opencl.o src/cmdstan/main.cpp

--- Translating Stan model to C++ code ---
bin/stanc.exe --use-opencl --name='lr_glm_model' --o=C:/Users/adamh/AppData/Local/Temp/RtmpEhT48p/model-412426f55c74.hpp C:/Users/adamh/AppData/Local/Temp/RtmpEhT48p/model-412426f55c74.stan

--- Compiling, linking C++ code ---
g++ -std=c++1y -m64 -D_REENTRANT -Wall -Wno-unused-function -Wno-uninitialized -Wno-unused-but-set-variable -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-attributes -Wno-ignored-attributes   -I stan/lib/stan_math/lib/opencl_2.2.0   -I stan/lib/stan_math/lib/tbb_2019_U8/include   -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include  -D_USE_MATH_DEFINES  -DBOOST_DISABLE_ASSERTS  -DSTAN_OPENCL -DOPENCL_DEVICE_ID=0 -DOPENCL_PLATFORM_ID=0 -DCL_HPP_TARGET_OPENCL_VERSION=120 -DCL_HPP_MINIMUM_OPENCL_VERSION=120 -DCL_HPP_ENABLE_EXCEPTIONS -Wno-ignored-attributes      -c  -x c++ -o C:/Users/adamh/AppData/Local/Temp/RtmpEhT48p/model-412426f55c74.o C:/Users/adamh/AppData/Local/Temp/RtmpEhT48p/model-412426f55c74.hpp
g++ -std=c++1y -m64 -D_REENTRANT -Wall -Wno-unused-function -Wno-uninitialized -Wno-unused-but-set-variable -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-attributes -Wno-ignored-attributes   -I stan/lib/stan_math/lib/opencl_2.2.0   -I stan/lib/stan_math/lib/tbb_2019_U8/include   -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include  -D_USE_MATH_DEFINES  -DBOOST_DISABLE_ASSERTS  -DSTAN_OPENCL -DOPENCL_DEVICE_ID=0 -DOPENCL_PLATFORM_ID=0 -DCL_HPP_TARGET_OPENCL_VERSION=120 -DCL_HPP_MINIMUM_OPENCL_VERSION=120 -DCL_HPP_ENABLE_EXCEPTIONS -Wno-ignored-attributes            -Wl,-L,"C:/Users/adamh/Downloads/test/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"C:/Users/adamh/Downloads/test/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb"      C:/Users/adamh/AppData/Local/Temp/RtmpEhT48p/model-412426f55c74.o src/cmdstan/main_opencl.o  -static-libgcc -static-libstdc++    -lOpenCL   stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_nvecserial.a stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_cvodes.a stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_idas.a stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_kinsol.a  stan/lib/stan_math/lib/tbb/tbb.dll -o C:/Users/adamh/AppData/Local/Temp/RtmpEhT48p/model-412426f55c74.exe
C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: cannot find -lOpenCL
collect2.exe: error: ld returned 1 exit status
C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: cannot find -lOpenCL
collect2.exe: error: ld returned 1 exit status
mingw32-make.exe: *** [make/program:62: C:/Users/adamh/AppData/Local/Temp/RtmpEhT48p/model-412426f55c74.exe] Error 1
mingw32-make.exe: *** [make/program:62: C:/Users/adamh/AppData/Local/Temp/RtmpEhT48p/model-412426f55c74.exe] Error 1
Error: An error occured during compilation! See the message above for more information.
rok-cesnovar commented 3 years ago

Ok, so we are now finnaly there :)

On Windows for OpenCL we need to add a linker flag. See the end of step 3 here: https://github.com/bstatcomp/stan_gpu_install_docs/blob/master/install_docs/INSTALL_CMDSTANR.md

path_to_opencl_lib <- "C:/Program Files (x86)/OCL_SDK_Light/lib/x86_64"
write(paste0("LDFLAGS= -L\"",path_to_opencl_lib,"\" -lOpenCL"), file.path(cmdstan_path(), "make", "local"), append = TRUE)

switch the path to OpenCL in path_to_opencl_lib and you should be good.

Added Windows + precompiled headers + OpenCL on my todo list.

adamhaber commented 3 years ago

Thanks a lot! And apologies for extending your todo list. 🙃

Just in case someone else reads this and the information might be useful - OpenCL.lib was in C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v9.2\lib\x64 on my machine.