search

metrumresearchgroup / Torsten

library of C++ functions that support applications of Stan in Pharmacometrics
BSD 3-Clause "New" or "Revised" License
52 stars 11 forks source link

[BUG] Problems setting up Torsten: mingw32-make error #47

Closed marianklose closed 8 months ago

marianklose commented 8 months ago

Description

Hi there, thanks a lot for developing Torsten. I am currently trying to set up Torsten on my windows machine and encounter an issue when I try to compile the pk2cpt.stan example model.

Example

Before I ran into the error I have already installed cmdstanr. There is also an existing vanilla version of stan on my machine. Here is some output during the steps prior to the error:

library(cmdstanr)

This is cmdstanr version 0.7.0

check_cmdstan_toolchain()

The C++ toolchain required for CmdStan is setup properly!

set_cmdstan_path("G:/Mitarbeiter/Klose/GitHub/Torsten/cmdstan")

CmdStan path set to: G:/Mitarbeiter/Klose/GitHub/Torsten/cmdstan

cmdstan_path()

[1] "G:/Mitarbeiter/Klose/GitHub/Torsten/cmdstan"

rebuild_cmdstan()
Long Output INFORMATION: Es konnten keine Dateien mit dem angegebenen Muster gefunden werden. (translates to _No files with the specified pattern could be found._) 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 cleaning Intel TBB targets rm -f -rf stan/lib/stan_math/lib/tbb rm -f bin/stanc.exe bin/stansummary.exe bin/print.exe bin/diagnose.exe rm -f -r src/cmdstan/main*.o bin/cmdstan rm -f rm -f examples/bernoulli/bernoulli.exe examples/bernoulli/bernoulli.o examples/bernoulli/bernoulli.d examples/bernoulli/bernoulli.hpp rm -f -r INFORMATION: Es konnten keine Dateien mit dem angegebenen Muster gefunden werden. curl -L https://github.com/metrumresearchgroup/stanc3/releases/download/torsten_v0.90.0rc2/windows-stanc -o bin/stanc.exe --retry 5 --retry-delay 10 g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/nvector/serial/nvector_serial.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/nvector/serial/nvector_serial.o % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_math.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_math.o 40 22.3M 40 9267k 0 0 742k 0 0:00:30 0:00:12 0:00:18 742kg++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodea.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodea.o 100 22.3M 100 22.3M 0 0 806k 0 0:00:28 0:00:28 --:--:-- 857k g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodea_io.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodea_io.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_bandpre.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_bandpre.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_bbdpre.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_bbdpre.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_diag.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_diag.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_direct.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_direct.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_io.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_io.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_ls.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_ls.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_nls.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_nls.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_nls_sim.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_nls_sim.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_nls_stg.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_nls_stg.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_nls_stg1.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_nls_stg1.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_spils.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_spils.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_band.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_band.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_context.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_context.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_dense.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_dense.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_direct.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_direct.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_futils.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_futils.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_iterative.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_iterative.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_linearsolver.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_linearsolver.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_matrix.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_matrix.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_memory.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_memory.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_nonlinearsolver.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_nonlinearsolver.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_nvector.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_nvector.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_nvector_senswrapper.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_nvector_senswrapper.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_version.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_version.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/sunmatrix/band/sunmatrix_band.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/sunmatrix/band/sunmatrix_band.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/sunmatrix/dense/sunmatrix_dense.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/sunmatrix/dense/sunmatrix_dense.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/sunlinsol/band/sunlinsol_band.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/sunlinsol/band/sunlinsol_band.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/sunlinsol/dense/sunlinsol_dense.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/sunlinsol/dense/sunlinsol_dense.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/sunnonlinsol/newton/sunnonlinsol_newton.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/sunnonlinsol/newton/sunnonlinsol_newton.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idaa.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idaa.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idaa_io.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idaa_io.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas_bbdpre.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas_bbdpre.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas_direct.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas_direct.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas_ic.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas_ic.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas_io.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas_io.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas_ls.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas_ls.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas_nls.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas_nls.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas_nls_sim.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas_nls_sim.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas_nls_stg.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas_nls_stg.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas_spils.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas_spils.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_profiler.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_profiler.o In file included from stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_profiler.c:37: stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_hashmap.h: In function 'fnv1a_hash': stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_hashmap.h:35:31: warning: conversion from 'long long unsigned int' to 'long unsigned int' changes value from '14695981039346656037' to '2216829733' [-Woverflow] 35 | const unsigned long prime = 14695981039346656037U; /* prime */ | ^~~~~~~~~~~~~~~~~~~~~ stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_hashmap.h:36:31: warning: conversion from 'long long unsigned int' to 'long unsigned int' changes value from '1099511628211' to '435' [-Woverflow] 36 | unsigned long hash = 1099511628211U; /* offset basis */ | ^~~~~~~~~~~~~~ g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/kinsol/kinsol.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/kinsol/kinsol.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/kinsol/kinsol_bbdpre.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/kinsol/kinsol_bbdpre.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/kinsol/kinsol_direct.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/kinsol/kinsol_direct.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/kinsol/kinsol_io.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/kinsol/kinsol_io.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/kinsol/kinsol_ls.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/kinsol/kinsol_ls.o g++ -pipe -m64 -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DNO_FPRINTF_OUTPUT -D_USE_MATH_DEFINES -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.0.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.0.0/src/kinsol/kinsol_spils.c -o stan/lib/stan_math/lib/sundials_6.0.0/src/kinsol/kinsol_spils.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_2020.3/include -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I lib/CLI11-1.9.1/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.9 -I stan/lib/stan_math/lib/boost_1.75.0 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DBOOST_MPL_CFG_NO_PREPROCESSED_HEADERS -DBOOST_MPL_LIMIT_LIST_SIZE=30 -D_USE_MATH_DEFINES -DBOOST_DISABLE_ASSERTS -c -o src/cmdstan/main.o src/cmdstan/main.cpp --- 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_2020.3/include -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I lib/CLI11-1.9.1/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.9 -I stan/lib/stan_math/lib/boost_1.75.0 -I stan/lib/stan_math/lib/sundials_6.0.0/include -I stan/lib/stan_math/lib/sundials_6.0.0/src/sundials -DBOOST_MPL_CFG_NO_PREPROCESSED_HEADERS -DBOOST_MPL_LIMIT_LIST_SIZE=30 -D_USE_MATH_DEFINES -DBOOST_DISABLE_ASSERTS -c stan/src/stan/model/model_header.hpp -o stan/src/stan/model/model_header.hpp.gch In file included from stan/lib/stan_math/lib/boost_1.75.0/boost/multi_array/multi_array_ref.hpp:32, from stan/lib/stan_math/lib/boost_1.75.0/boost/multi_array.hpp:34, from stan/lib/stan_math/lib/boost_1.75.0/boost/numeric/odeint/algebra/multi_array_algebra.hpp:22, from stan/lib/stan_math/lib/boost_1.75.0/boost/numeric/odeint.hpp:63, from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9, from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6, from stan/lib/stan_math/stan/math/prim/functor.hpp:14, from stan/lib/stan_math/stan/math/rev/fun.hpp:193, from stan/lib/stan_math/stan/math/rev.hpp:10, from stan/lib/stan_math/stan/math.hpp:19, from stan/src/stan/model/model_header.hpp:4: stan/lib/stan_math/lib/boost_1.75.0/boost/functional.hpp:180:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 180 | : public boost::functional::detail::unary_function::argument_type,bool> | ^~~~~~~~~~~~~~ In file included from C:/rtools43/ucrt64/include/c++/13.2.0/string:49, from C:/rtools43/ucrt64/include/c++/13.2.0/bits/locale_classes.h:40, from C:/rtools43/ucrt64/include/c++/13.2.0/bits/ios_base.h:41, from C:/rtools43/ucrt64/include/c++/13.2.0/ios:44, from C:/rtools43/ucrt64/include/c++/13.2.0/istream:40, from C:/rtools43/ucrt64/include/c++/13.2.0/sstream:40, from C:/rtools43/ucrt64/include/c++/13.2.0/complex:45, from stan/lib/stan_math/lib/eigen_3.3.9/Eigen/Core:96, from stan/lib/stan_math/lib/eigen_3.3.9/Eigen/Dense:1, from stan/lib/stan_math/stan/math/prim/fun/Eigen.hpp:22, from stan/lib/stan_math/stan/math/rev.hpp:4: C:/rtools43/ucrt64/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ stan/lib/stan_math/lib/boost_1.75.0/boost/functional.hpp:214:45: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 214 | : public boost::functional::detail::binary_function< | ^~~~~~~~~~~~~~~ C:/rtools43/ucrt64/include/c++/13.2.0/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ stan/lib/stan_math/lib/boost_1.75.0/boost/functional.hpp:252:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 252 | : public boost::functional::detail::unary_function< | ^~~~~~~~~~~~~~ C:/rtools43/ucrt64/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ stan/lib/stan_math/lib/boost_1.75.0/boost/functional.hpp:299:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 299 | : public boost::functional::detail::unary_function< | ^~~~~~~~~~~~~~ C:/rtools43/ucrt64/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here **[truncated some of the output]** stan/lib/stan_math/lib/boost_1.75.0/boost/concept/detail/has_constraints.hpp:42:5: required from 'const bool boost::concepts::not_satisfied > > > >::value' stan/lib/stan_math/lib/boost_1.75.0/boost/concept/detail/has_constraints.hpp:45:51: required from 'struct boost::concepts::not_satisfied > > > >' stan/lib/stan_math/lib/boost_1.75.0/boost/concept/detail/general.hpp:51:8: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] C:/rtools43/ucrt64/include/c++/13.2.0/bits/stl_vector.h:708:23: required from 'std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = boost::iterators::transform_iterator, __gnu_cxx::__normal_iterator > >, boost::algorithm::split_iterator<__gnu_cxx::__normal_iterator > >, boost::use_default, boost::use_default>; = void; _Tp = std::__cxx11::basic_string; _Alloc = std::allocator >; allocator_type = std::allocator >]' stan/lib/stan_math/lib/boost_1.75.0/boost/algorithm/string/iter_find.hpp:186:31: required from 'SequenceSequenceT& boost::algorithm::iter_split(SequenceSequenceT&, RangeT&&, FinderT) [with SequenceSequenceT = std::vector >; RangeT = std::__cxx11::basic_string&; FinderT = detail::token_finderF >]' stan/lib/stan_math/lib/boost_1.75.0/boost/algorithm/string/split.hpp:158:50: required from 'SequenceSequenceT& boost::algorithm::split(SequenceSequenceT&, RangeT&&, PredicateT, token_compress_mode_type) [with SequenceSequenceT = std::vector >; RangeT = std::__cxx11::basic_string&; PredicateT = detail::is_any_ofF]' stan/src/stan/services/sample/standalone_gqs.hpp:39:0: required from 'void stan::services::get_model_parameters(const Model&, std::vector >&, std::vector >&) [with Model = stan::model::model_base]' stan/src/stan/services/sample/standalone_gqs.hpp:110:0: required from 'int stan::services::standalone_generate(const Model&, const Eigen::MatrixXd&, unsigned int, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&) [with Model = stan::model::model_base; Eigen::MatrixXd = Eigen::Matrix]' src/cmdstan/command.hpp:678:0: required from here stan/lib/stan_math/lib/boost_1.75.0/boost/concept/usage.hpp:16:48: warning: 'this' pointer is null [-Wnonnull] 16 | ~usage_requirements() { ((Model*)0)->~Model(); } | ~~~~~~~~~~~~~~~~~~~^~ stan/lib/stan_math/lib/boost_1.75.0/boost/concept/usage.hpp:30:7: note: in a call to non-static member function 'boost::SinglePassRangeConcept::~SinglePassRangeConcept() [with T = const boost::iterator_range<__gnu_cxx::__normal_iterator > >]' 30 | ~model() | ^ stan/lib/stan_math/lib/boost_1.75.0/boost/range/concepts.hpp:284:9: note: in expansion of macro 'BOOST_CONCEPT_USAGE' 284 | BOOST_CONCEPT_USAGE(SinglePassRangeConcept) | ^~~~~~~~~~~~~~~~~~~

At this point I am not sure if these warnings and notes should already concern me or not. At least the process seems to finish properly without any fatal errors and now a bin folder with stanc.exe pops up inside cmdstan. Now I try to compile the model:

model <- cmdstan_model("G:/Mitarbeiter/Klose/GitHub/Torsten/example-models/pk2cpt/pk2cpt.stan")
Output and Error Compiling Stan program... INFORMATION: Es konnten keine Dateien mit dem angegebenen Muster gefunden werden. INFORMATION: Es konnten keine Dateien mit dem angegebenen Muster gefunden werden. ar: creating stan/lib/stan_math/lib/sundials_6.0.0/lib/libsundials_nvecserial.a ar: creating stan/lib/stan_math/lib/sundials_6.0.0/lib/libsundials_cvodes.a ar: creating stan/lib/stan_math/lib/sundials_6.0.0/lib/libsundials_idas.a ar: creating stan/lib/stan_math/lib/sundials_6.0.0/lib/libsundials_arkode.a ar: creating stan/lib/stan_math/lib/sundials_6.0.0/lib/libsundials_kinsol.a In file included from C:/rtools43/ucrt64/include/c++/13.2.0/stdlib.h:36, from C:/rtools43/ucrt64/lib/gcc/x86_64-w64-mingw32/13.2.0/include/mm_malloc.h:27, from C:/rtools43/ucrt64/lib/gcc/x86_64-w64-mingw32/13.2.0/include/xmmintrin.h:34, from C:/rtools43/ucrt64/lib/gcc/x86_64-w64-mingw32/13.2.0/include/immintrin.h:31, from ../tbb_2020.3/include/tbb/machine/gcc_itsx.h:57, from ../tbb_2020.3/include/tbb/machine/gcc_ia32_common.h:107, from ../tbb_2020.3/include/tbb/machine/gcc_generic.h:232, from ../tbb_2020.3/include/tbb/tbb_machine.h:197, from ../tbb_2020.3/src/tbbmalloc/Synchronize.h:20, from ../tbb_2020.3/src/tbbmalloc/Customize.h:29, from ../tbb_2020.3/src/tbbmalloc/TypeDefinitions.h:54, from ../tbb_2020.3/src/tbbmalloc/tbbmalloc_internal.h:21, from ../tbb_2020.3/src/tbbmalloc/backend.cpp:19: C:/rtools43/ucrt64/include/c++/13.2.0/cstdlib:141:11: error: 'at_quick_exit' has not been declared in '::' 141 | using ::at_quick_exit; | ^~~~~~~~~~~~~ C:/rtools43/ucrt64/include/c++/13.2.0/cstdlib:164:11: error: 'quick_exit' has not been declared in '::' 164 | using ::quick_exit; | ^~~~~~~~~~ C:/rtools43/ucrt64/include/c++/13.2.0/stdlib.h:43:14: error: 'at_quick_exit' has not been declared in 'std' 43 | using std::at_quick_exit; | ^~~~~~~~~~~~~ C:/rtools43/ucrt64/include/c++/13.2.0/stdlib.h:46:14: error: 'quick_exit' has not been declared in 'std' 46 | using std::quick_exit; | ^~~~~~~~~~ cc1plus.exe: note: unrecognized command-line option '-Wno-unknown-warning-option' may have been intended to silence earlier diagnostics mingw32-make[1]: *** [G:/Mitarbeiter/Klose/GitHub/Torsten/cmdstan/stan/lib/stan_math/lib/tbb_2020.3/build/Makefile.tbbmalloc:65: backend.o] Error 1 mingw32-make: *** [stan/lib/stan_math/make/libraries:187: stan/lib/stan_math/lib/tbb/tbbmalloc.def] Error 2 Fehler: An error occured during compilation! See the message above for more information.

Expected Output

Successful compilation of the test model.

Current Version:

v0.90.0

Additional Information

RSesssion

sessionInfo()

R version 4.3.0 (2023-04-21 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale: [1] LC_COLLATE=German_Germany.utf8 LC_CTYPE=German_Germany.utf8 LC_MONETARY=German_Germany.utf8 LC_NUMERIC=C
[5] LC_TIME=German_Germany.utf8

time zone: Europe/Berlin tzcode source: internal

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] cmdstanr_0.7.0

loaded via a namespace (and not attached): [1] vctrs_0.6.4 knitr_1.45 cli_3.6.1 xfun_0.40 rlang_1.1.1 processx_3.8.2 generics_0.1.3
[8] tensorA_0.36.2.1 jsonlite_1.8.7 glue_1.6.2 colorspace_2.1-0 backports_1.4.1 ps_1.7.5 distributional_0.3.2 [15] scales_1.2.1 fansi_1.0.5 grid_4.3.0 munsell_0.5.0 tibble_3.2.1 abind_1.4-5 lifecycle_1.0.3
[22] compiler_4.3.0 dplyr_1.1.2 posterior_1.5.0 pkgconfig_2.0.3 rstudioapi_0.15.0 farver_2.1.1 R6_2.5.1
[29] tidyselect_1.2.0 utf8_1.2.4 pillar_1.9.0 magrittr_2.0.3 checkmate_2.2.0 withr_2.5.2 tools_4.3.0
[36] gtable_0.3.4 ggplot2_3.4.3

g++ version

H:\>g++ --version

g++ (x86_64-posix-seh, Built by strawberryperl.com project) 8.3.0 Copyright (C) 2018 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

make version

H:\>make --version

GNU Make 4.4.1 Built for x86_64-pc-msys Copyright (C) 1988-2023 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later https://gnu.org/licenses/gpl.html This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law.

H:\>mingw32-make --version

Der Befehl "mingw32-make" ist entweder falsch geschrieben oder konnte nicht gefunden werden. (= not found)

H:\>mingw64-make --version

Der Befehl "mingw64-make" ist entweder falsch geschrieben oder konnte nicht gefunden werden. (= not found)

Any ideas what could be the issue? Thanks a lot in advance!

marianklose commented 8 months ago

Maybe two additional comments:

I have a fresh installation of Rtools (rtools43) and apparently the distribution doesn't come with mingw32-make (see https://github.com/stan-dev/cmdstan/issues/1064). I have followed 2 steps there to make mingw32-make available:

  • Add C:\rtools43\usr\bin and C:\rtools43\ucrt64\bin to the PATH
  • Run pacman -Sy mingw-w64-ucrt-x86_64-make mingw-w64-ucrt-x86_64-gcc in a freshly opened Powershell

Now I get

H:\>mingw32-make --version

GNU Make 4.4 Built for Windows32 Copyright (C) 1988-2022 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later https://gnu.org/licenses/gpl.html This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law.

But the issue is still persistent unfortunately. There was another advice to put two lines into make/local, but I was not sure where exactly I need to put them (make/local is not existent) so I skipped this for now.

Add the following two lines to the make/local: CXXFLAGS += -Wno-nonnull TBB_CXXFLAGS= -UMSVCRT_VERSION -DMSVCRT_VERSION=0x0E00

Furthermore, I have no problems running / compiling an example .stan model using the vanilla cmdstan version:

set_cmdstan_path("C:/.cmdstan/cmdstan-2.33.1")

CmdStan path set to: C:/.cmdstan/cmdstan-2.33.1

cmdstan_path()

[1] "C:/.cmdstan/cmdstan-2.33.1"

file <- file.path(cmdstan_path(), "examples", "bernoulli", "bernoulli.stan")
mod <- cmdstan_model(file)

Model executable is up to date!

mod$print()

data { int N; array[N] int y; } parameters { real theta; } model { theta ~ beta(1,1); // uniform prior on interval 0,1 y ~ bernoulli(theta); }

mod$exe_file()

[1] "C:/.cmdstan/cmdstan-2.33.1/examples/bernoulli/bernoulli.exe"

# names correspond to the data block in the Stan program
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 = 4,
     refresh = 500 # print update every 500 iters
 )

Running MCMC with 4 parallel chains...

Chain 1 Iteration: 1 / 2000 [ 0%] (Warmup) Chain 1 Iteration: 500 / 2000 [ 25%] (Warmup) Chain 1 Iteration: 1000 / 2000 [ 50%] (Warmup) ...

marianklose commented 8 months ago

Okay, so apparently following the full instructions from https://github.com/stan-dev/cmdstan/issues/1064 did the job for me.

To run CmdStan with Rtools42 you need to do the following (This assumes Rtools42:

  1. Add C:\rtools42\usr\bin and C:\rtools42\ucrt64\bin to the PATH
  2. Run pacman -Sy mingw-w64-ucrt-x86_64-make mingw-w64-ucrt-x86_64-gcc in a freshly opened Powershell
  3. Add the following two lines to the make/local:

CXXFLAGS += -Wno-nonnull TBB_CXXFLAGS= -UMSVCRT_VERSION -DMSVCRT_VERSION=0x0E00

And that should do it.

Explanation of the steps:

The second step installs ucrt64 versions of mingw32-make and g++ (11.2) that are not installed by default. RTools42 by default uses mingw32.static.posix for which we can not install mingw32-make.

The first line we need to add to make/local is to silence some warnings caused by TBB with g++ 11. Newer versions of TBB do not spit out this warning.

The second line to make/local is due to a bug in MinGW that incorrectly sets the version of MSVCRT which causes the compiler to think it does not have support for some functions, though it does have it - this mainly affects std::at_quick_exit and std::quick_exit. That causes errors like the one here. This had been fixed in MinGW as I can see here but seems to not make its way into Rtools42 I guess. We should report this to Rtools I think, though I am not sure where is the best place to do that.

However, since Torsten/cmdstan/make does not have a local file, I have copied the local file over from the vanilla cmdstan version and modified it accordingly. This is how the file looks like:

CXXFLAGS += -Wno-nonnull
TBB_CXXFLAGS= -U__MSVCRT_VERSION__ -D__MSVCRT_VERSION__=0x0E00
CXXFLAGS += -Wno-deprecated-declarations

I am now able to compile the example pk2cpt.stan file and the output was similar to the one described in this blog post, so I assume it is correct. If my assessment is correct and mingw32-make is not part of the newer RTools versions, maybe a hint somewhere on the installation page would be helpful. Feel free to close this issue (unless there is something to add). Thanks!

yizhang-yiz commented 8 months ago

Thanks a lot for investigating on this. I'll add instructions to the new release.