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metrumresearchgroup / Torsten

library of C++ functions that support applications of Stan in Pharmacometrics
BSD 3-Clause "New" or "Revised" License
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Example cannot run using torsten #40

Closed nmarusan closed 2 years ago

nmarusan commented 2 years ago

Hi, I'm trying to run the example using Torsten, but can't run following error message. Can you please help?

An example run is as follows: system('git clone https://github.com/metrumresearchgroup/Torsten.git')

install.packages("cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))

Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) also installing the dependencies ‘numDeriv’, ‘abind’, ‘tensorA’, ‘distributional’, ‘matrixStats’, ‘checkmate’, ‘posterior’

library(cmdstanr) Warning message: “package ‘cmdstanr’ was built under R version 4.3.0” This is cmdstanr version 0.5.2

set_cmdstan_path("Torsten/cmdstan") CmdStan path set to: /content/Torsten/cmdstan

rebuild_cmdstan() 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 bin/stansummary bin/print bin/diagnose rm -f -r src/cmdstan/main*.o bin/cmdstan rm -f rm -f examples/bernoulli/bernoulli examples/bernoulli/bernoulli.o examples/bernoulli/bernoulli.d examples/bernoulli/bernoulli.hpp rm -f -r curl -L https://github.com/metrumresearchgroup/stanc3/releases/download/torsten_v0.90.0rc2/linux-stanc -o bin/stanc --retry 5 --retry-delay 10 g++ -pipe -pthread -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 -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 100 9 100 9 0 0 44 0 --:--:-- --:--:-- --:--:-- 44 chmod +x bin/stanc g++ -pipe -pthread -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 -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 g++ -pipe -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 g++ -pipe -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 g++ -pipe -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 -pthread -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 -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 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 -pthread -D_REENTRANT -Wno-sign-compare -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 -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 -pthread -D_REENTRANT -Wno-sign-compare -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 -DBOOST_DISABLE_ASSERTS -c stan/src/stan/model/model_header.hpp -o stan/src/stan/model/model_header.hpp.gch g++ -std=c++1y -pthread -D_REENTRANT -Wno-sign-compare -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 -DBOOST_DISABLE_ASSERTS -c -fvisibility=hidden -o bin/cmdstan/stansummary.o -Wl,-L,"/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" src/cmdstan/stansummary.cpp g++ -std=c++1y -pthread -D_REENTRANT -Wno-sign-compare -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 -DBOOST_DISABLE_ASSERTS -c -fvisibility=hidden -o bin/cmdstan/print.o -Wl,-L,"/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" src/cmdstan/print.cpp g++ -std=c++1y -pthread -D_REENTRANT -Wno-sign-compare -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 -DBOOST_DISABLE_ASSERTS -c -fvisibility=hidden -o bin/cmdstan/diagnose.o -Wl,-L,"/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" src/cmdstan/diagnose.cpp ar -rs stan/lib/stan_math/lib/sundials_6.0.0/lib/libsundials_nvecserial.a stan/lib/stan_math/lib/sundials_6.0.0/src/nvector/serial/nvector_serial.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_math.o ar: creating stan/lib/stan_math/lib/sundials_6.0.0/lib/libsundials_nvecserial.a ar -rs stan/lib/stan_math/lib/sundials_6.0.0/lib/libsundials_cvodes.a stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_spils.o stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_diag.o stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodea.o stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_direct.o stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodea_io.o stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_ls.o stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_nls_stg.o stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_bandpre.o stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_io.o stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_bbdpre.o stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes.o stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_nls.o stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_nls_sim.o stan/lib/stan_math/lib/sundials_6.0.0/src/cvodes/cvodes_nls_stg1.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_matrix.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_linearsolver.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_futils.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_direct.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_version.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_band.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_nonlinearsolver.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_math.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_memory.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_context.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_nvector.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_iterative.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_nvector_senswrapper.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_dense.o stan/lib/stan_math/lib/sundials_6.0.0/src/sunmatrix/band/sunmatrix_band.o stan/lib/stan_math/lib/sundials_6.0.0/src/sunmatrix/dense/sunmatrix_dense.o stan/lib/stan_math/lib/sundials_6.0.0/src/sunlinsol/band/sunlinsol_band.o stan/lib/stan_math/lib/sundials_6.0.0/src/sunlinsol/dense/sunlinsol_dense.o stan/lib/stan_math/lib/sundials_6.0.0/src/sunnonlinsol/newton/sunnonlinsol_newton.o stan/lib/stan_math/lib/sundials_6.0.0/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.o ar: creating stan/lib/stan_math/lib/sundials_6.0.0/lib/libsundials_cvodes.a ar -rs stan/lib/stan_math/lib/sundials_6.0.0/lib/libsundials_idas.a stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas_spils.o stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas_ic.o stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idaa.o stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas_direct.o stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idaa_io.o stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas_nls_stg.o stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas_bbdpre.o stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas_io.o stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas.o stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas_ls.o stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas_nls_sim.o stan/lib/stan_math/lib/sundials_6.0.0/src/idas/idas_nls.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_matrix.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_linearsolver.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_futils.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_direct.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_version.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_band.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_nonlinearsolver.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_math.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_memory.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_context.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_nvector.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_iterative.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_nvector_senswrapper.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_dense.o stan/lib/stan_math/lib/sundials_6.0.0/src/sunmatrix/band/sunmatrix_band.o stan/lib/stan_math/lib/sundials_6.0.0/src/sunmatrix/dense/sunmatrix_dense.o stan/lib/stan_math/lib/sundials_6.0.0/src/sunlinsol/band/sunlinsol_band.o stan/lib/stan_math/lib/sundials_6.0.0/src/sunlinsol/dense/sunlinsol_dense.o stan/lib/stan_math/lib/sundials_6.0.0/src/sunnonlinsol/newton/sunnonlinsol_newton.o stan/lib/stan_math/lib/sundials_6.0.0/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.o ar: creating stan/lib/stan_math/lib/sundials_6.0.0/lib/libsundials_idas.a ar -rs stan/lib/stan_math/lib/sundials_6.0.0/lib/libsundials_arkode.a stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_matrix.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_linearsolver.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_futils.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_direct.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_version.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_band.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_profiler.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_nonlinearsolver.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_math.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_memory.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_context.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_nvector.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_iterative.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_nvector_senswrapper.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_dense.o stan/lib/stan_math/lib/sundials_6.0.0/src/sunmatrix/band/sunmatrix_band.o stan/lib/stan_math/lib/sundials_6.0.0/src/sunmatrix/dense/sunmatrix_dense.o stan/lib/stan_math/lib/sundials_6.0.0/src/sunlinsol/band/sunlinsol_band.o stan/lib/stan_math/lib/sundials_6.0.0/src/sunlinsol/dense/sunlinsol_dense.o stan/lib/stan_math/lib/sundials_6.0.0/src/sunnonlinsol/newton/sunnonlinsol_newton.o stan/lib/stan_math/lib/sundials_6.0.0/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.o ar: creating stan/lib/stan_math/lib/sundials_6.0.0/lib/libsundials_arkode.a ar -rs stan/lib/stan_math/lib/sundials_6.0.0/lib/libsundials_kinsol.a stan/lib/stan_math/lib/sundials_6.0.0/src/kinsol/kinsol_direct.o stan/lib/stan_math/lib/sundials_6.0.0/src/kinsol/kinsol.o stan/lib/stan_math/lib/sundials_6.0.0/src/kinsol/kinsol_bbdpre.o stan/lib/stan_math/lib/sundials_6.0.0/src/kinsol/kinsol_io.o stan/lib/stan_math/lib/sundials_6.0.0/src/kinsol/kinsol_ls.o stan/lib/stan_math/lib/sundials_6.0.0/src/kinsol/kinsol_spils.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_matrix.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_linearsolver.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_futils.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_direct.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_version.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_band.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_nonlinearsolver.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_math.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_memory.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_context.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_nvector.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_iterative.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_nvector_senswrapper.o stan/lib/stan_math/lib/sundials_6.0.0/src/sundials/sundials_dense.o stan/lib/stan_math/lib/sundials_6.0.0/src/sunmatrix/band/sunmatrix_band.o stan/lib/stan_math/lib/sundials_6.0.0/src/sunmatrix/dense/sunmatrix_dense.o stan/lib/stan_math/lib/sundials_6.0.0/src/sunlinsol/band/sunlinsol_band.o stan/lib/stan_math/lib/sundials_6.0.0/src/sunlinsol/dense/sunlinsol_dense.o stan/lib/stan_math/lib/sundials_6.0.0/src/sunnonlinsol/newton/sunnonlinsol_newton.o stan/lib/stan_math/lib/sundials_6.0.0/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.o ar: creating stan/lib/stan_math/lib/sundials_6.0.0/lib/libsundials_kinsol.a tbb_root="../tbb_2020.3" CXX="g++" CC="gcc" LDFLAGS='-Wl,-L,"/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" ' 'make' -C "stan/lib/stan_math/lib/tbb" -r -f "/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb_2020.3/build/Makefile.tbbmalloc" compiler=gcc cfg=release stdver=c++1y malloc CXXFLAGS="-Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation " make[1]: Entering directory '/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb' g++ -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fno-rtti -fno-exceptions -DTBBMALLOC_BUILD=1 -Wno-parentheses -Wno-sized-deallocation -fPIC -flifetime-dse=1 -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include -I../tbb_2020.3/src/tbbmalloc -I../tbb_2020.3/src/tbbmalloc ../tbb_2020.3/src/tbbmalloc/backend.cpp g++ -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fno-rtti -fno-exceptions -DTBBMALLOC_BUILD=1 -Wno-parentheses -Wno-sized-deallocation -fPIC -flifetime-dse=1 -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include -I../tbb_2020.3/src/tbbmalloc -I../tbb_2020.3/src/tbbmalloc ../tbb_2020.3/src/tbbmalloc/large_objects.cpp g++ -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fno-rtti -fno-exceptions -DTBBMALLOC_BUILD=1 -Wno-parentheses -Wno-sized-deallocation -fPIC -flifetime-dse=1 -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include -I../tbb_2020.3/src/tbbmalloc -I../tbb_2020.3/src/tbbmalloc ../tbb_2020.3/src/tbbmalloc/backref.cpp g++ -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fno-rtti -fno-exceptions -DTBBMALLOC_BUILD=1 -Wno-parentheses -Wno-sized-deallocation -fPIC -flifetime-dse=1 -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include -I../tbb_2020.3/src/tbbmalloc -I../tbb_2020.3/src/tbbmalloc ../tbb_2020.3/src/tbbmalloc/tbbmalloc.cpp g++ -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fno-rtti -fno-exceptions -DTBBMALLOC_BUILD=1 -Wno-parentheses -Wno-sized-deallocation -fPIC -flifetime-dse=1 -o itt_notify_malloc.o -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/itt_notify.cpp sh ../tbb_2020.3/build/version_info_linux.sh g++ -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -Wall -Wextra -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include >version_string.ver echo "INPUT (libtbbmalloc.so.2)" > libtbbmalloc.so g++ -E -x c++ ../tbb_2020.3/src/tbbmalloc/lin64-tbbmalloc-export.def -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -Wall -Wextra -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fno-rtti -fno-exceptions -DTBBMALLOC_BUILD=1 -Wno-parentheses -Wno-sized-deallocation -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include > tbbmalloc.def g++ -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -Wall -Wextra -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -Wno-parentheses -Wno-sized-deallocation -fPIC -flifetime-dse=1 -DTBBMALLOC_BUILD=1 -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include -I../tbb_2020.3/src/tbbmalloc -I../tbb_2020.3/src/tbbmalloc ../tbb_2020.3/src/tbbmalloc/proxy.cpp g++ -std=c++1y -pthread -D_REENTRANT -Wno-sign-compare -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 -DBOOST_DISABLE_ASSERTS -Wl,-L,"/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" bin/cmdstan/stansummary.o -Wl,-L,"/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -o bin/stansummary g++ -std=c++1y -pthread -D_REENTRANT -Wno-sign-compare -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 -DBOOST_DISABLE_ASSERTS -Wl,-L,"/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" bin/cmdstan/print.o -Wl,-L,"/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -o bin/print g++ -std=c++1y -pthread -D_REENTRANT -Wno-sign-compare -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 -DBOOST_DISABLE_ASSERTS -Wl,-L,"/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" bin/cmdstan/diagnose.o -Wl,-L,"/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -o bin/diagnose g++ -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -Wall -Wextra -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -Wno-parentheses -Wno-sized-deallocation -fPIC -flifetime-dse=1 -D__TBBMALLOC_BUILD=1 -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include -I../tbb_2020.3/src/tbbmalloc -I../tbb_2020.3/src/tbbmalloc ../tbb_2020.3/src/tbbmalloc/tbb_function_replacement.cpp echo "INPUT (libtbbmalloc_proxy.so.2)" > libtbbmalloc_proxy.so g++ -E -x c++ ../tbb_2020.3/src/tbbmalloc/lin64-proxy-export.def -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -Wall -Wextra -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -Wno-parentheses -Wno-sized-deallocation -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include > tbbmallocproxy.def g++ -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fno-rtti -fno-exceptions -DTBBMALLOC_BUILD=1 -Wno-parentheses -Wno-sized-deallocation -fPIC -flifetime-dse=1 -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include -I../tbb_2020.3/src/tbbmalloc -I../tbb_2020.3/src/tbbmalloc -I. ../tbb_2020.3/src/tbbmalloc/frontend.cpp gcc -fPIC -o libtbbmalloc.so.2 backend.o large_objects.o backref.o tbbmalloc.o itt_notify_malloc.o frontend.o -ldl -lrt -shared -Wl,-soname=libtbbmalloc.so.2 -pthread -m64 -Wl,-L,"/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,--version-script,tbbmalloc.def g++ -fPIC -o libtbbmalloc_proxy.so.2 proxy.o tbb_function_replacement.o -ldl -lrt libtbbmalloc.so -shared -Wl,-soname=libtbbmalloc_proxy.so.2 -pthread -m64 -Wl,-L,"/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,--version-script,tbbmallocproxy.def make[1]: Leaving directory '/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb' touch stan/lib/stan_math/lib/tbb/version_tbb_2020.3 tbb_root="../tbb_2020.3" CXX="g++" CC="gcc" LDFLAGS='-Wl,-L,"/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" ' 'make' -C "stan/lib/stan_math/lib/tbb" -r -f "/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb_2020.3/build/Makefile.tbb" compiler=gcc cfg=release stdver=c++1y CXXFLAGS="-Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation " make[1]: Entering directory '/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb' /content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb_2020.3/build/Makefile.tbb:28: CONFIG: cfg=release arch=intel64 compiler=gcc target=linux runtime=cc7.5.0_libc2.27_kernel5.4.188+ g++ -o concurrent_hash_map.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/concurrent_hash_map.cpp g++ -o concurrent_queue.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/concurrent_queue.cpp g++ -o concurrent_vector.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/concurrent_vector.cpp g++ -o dynamic_link.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/dynamic_link.cpp g++ -o itt_notify.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/itt_notify.cpp g++ -o cache_aligned_allocator.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/cache_aligned_allocator.cpp g++ -o pipeline.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/pipeline.cpp g++ -o queuing_mutex.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/queuing_mutex.cpp g++ -o queuing_rw_mutex.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/queuing_rw_mutex.cpp g++ -o reader_writer_lock.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/reader_writer_lock.cpp g++ -o spin_rw_mutex.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/spin_rw_mutex.cpp g++ -o x86_rtm_rw_mutex.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/x86_rtm_rw_mutex.cpp g++ -o spin_mutex.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/spin_mutex.cpp g++ -o critical_section.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/critical_section.cpp g++ -o mutex.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/mutex.cpp g++ -o recursive_mutex.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/recursive_mutex.cpp g++ -o condition_variable.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/condition_variable.cpp g++ -o tbb_thread.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/tbb_thread.cpp g++ -o concurrent_monitor.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/concurrent_monitor.cpp g++ -o semaphore.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/semaphore.cpp g++ -o private_server.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/private_server.cpp g++ -o rml_tbb.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/rml/client/rml_tbb.cpp g++ -o tbb_misc.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include -I. ../tbb_2020.3/src/tbb/tbb_misc.cpp g++ -o tbb_misc_ex.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/tbb_misc_ex.cpp g++ -o task.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/task.cpp g++ -o task_group_context.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/task_group_context.cpp g++ -o governor.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/governor.cpp g++ -o market.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/market.cpp g++ -o arena.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/arena.cpp g++ -o scheduler.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/scheduler.cpp g++ -o observer_proxy.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/observer_proxy.cpp g++ -o tbb_statistics.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/tbb_statistics.cpp g++ -o tbb_main.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/tbb/tbb_main.cpp g++ -o concurrent_vector_v2.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/old/concurrent_vector_v2.cpp g++ -o concurrent_queue_v2.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/old/concurrent_queue_v2.cpp g++ -o spin_rw_mutex_v2.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/old/spin_rw_mutex_v2.cpp g++ -o task_v2.o -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -DTBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -std=c++1y -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include ../tbb_2020.3/src/old/task_v2.cpp sh ../tbb_2020.3/build/generate_tbbvars.sh echo "INPUT (libtbb.so.2)" > libtbb.so g++ -E -x c++ ../tbb_2020.3/src/tbb/lin64-tbb-export.def -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -fPIC -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-sized-deallocation -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include > tbb.def g++ -fPIC -o libtbb.so.2 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 -ldl -lrt -shared -Wl,-soname=libtbb.so.2 -pthread -m64 -Wl,-L,"/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,--version-script,tbb.def make[1]: Leaving directory '/content/Torsten/cmdstan/stan/lib/stan_math/lib/tbb'

--- CmdStan v2.29.0 built --- --- Torsten v0.90.0 built ---

nmarusan commented 2 years ago

The problem is as follows: cmdstan_model("/content/Torsten/cmdstan/examples/TwoCptModelPopulation/TwoCptModelPopulation.stan",quiet=FALSE)

g++ -std=c++1y -pthread -D_REENTRANT -Wno-sign-compare -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 -DBOOST_DISABLE_ASSERTS -c -MT stan/src/stan/model/model_header.hpp.gch -MT stan/src/stan/model/model_header.d -MM -E -MG -MP -MF stan/src/stan/model/model_header.d stan/src/stan/model/model_header.hpp g++ -std=c++1y -pthread -D_REENTRANT -Wno-sign-compare -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 -DBOOST_DISABLE_ASSERTS -c -MT src/cmdstan/main.o -MM -E -MG -MP -MF src/cmdstan/main.d src/cmdstan/main.cpp

--- Translating Stan model to C++ code --- bin/stanc --name='TwoCptModelPopulation_model' --o=/tmp/Rtmp7uh7Bi/model-456b36d7d4.hpp /tmp/Rtmp7uh7Bi/model-456b36d7d4.stan bin/stanc: line 1: Not: command not found bin/stanc: line 1: Not: command not found

make/program:48: recipe for target '/tmp/Rtmp7uh7Bi/model-456b36d7d4.hpp' failed make: [/tmp/Rtmp7uh7Bi/model-456b36d7d4.hpp] Error 127 make: [/tmp/Rtmp7uh7Bi/model-456b36d7d4.hpp] Error 127

Error: An error occured during compilation! See the message above for more information. Traceback:

  1. cmdstanr::cmdstan_model("/content/Torsten/cmdstan/examples/TwoCptModelPopulation/TwoCptModelPopulation.stan", . quiet = FALSE)
  2. CmdStanModel$new(stan_file = stan_file, exe_file = exe_file, . compile = compile, ...)
  3. initialize(...)
  4. self$compile(...)
  5. stop("An error occured during compilation! See the message above for more information.", . call. = FALSE)

Current Version:

R version 4.2.0 (2022-04-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.5 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] cmdstanr_0.5.2

loaded via a namespace (and not attached): [1] pillar_1.7.0 compiler_4.2.0 base64enc_0.1-3
[4] tools_4.2.0 digest_0.6.29 uuid_1.1-0
[7] jsonlite_1.8.0 evaluate_0.15 lifecycle_1.0.1
[10] tibble_3.1.7 checkmate_2.1.0 gtable_0.3.0
[13] pkgconfig_2.0.3 rlang_1.0.2 DBI_1.1.2
[16] IRdisplay_1.1 cli_3.3.0 IRkernel_1.3
[19] xfun_0.30 fastmap_1.1.0 withr_2.5.0
[22] knitr_1.39 dplyr_1.0.9 repr_1.1.4
[25] generics_0.1.2 vctrs_0.4.1 tidyselect_1.1.2
[28] grid_4.2.0 glue_1.6.2 R6_2.5.1
[31] processx_3.5.3 fansi_1.0.3 distributional_0.3.0 [34] tensorA_0.36.2 pbdZMQ_0.3-7 purrr_0.3.4
[37] farver_2.1.0 ggplot2_3.3.6 posterior_1.2.1
[40] magrittr_2.0.3 ps_1.7.0 backports_1.4.1
[43] scales_1.2.0 ellipsis_0.3.2 htmltools_0.5.2
[46] assertthat_0.2.1 abind_1.4-5 colorspace_2.0-3
[49] utf8_1.2.2 munsell_0.5.0 crayon_1.5.1
image image

yizhang-yiz commented 2 years ago

I found the bug: I missed the ARCH_TAG in the stanc3 fork so that linux platform doesn't download proper transpiler. Fix on the way.

nmarusan commented 2 years ago

Thank Dr. Yi for responding to my question.

yizhang-yiz commented 2 years ago

I just updated stanc3 artifacts. Can you try it again?

For more details (@billgillespie ): cmdstan now requires more specific machine information. For linux, make will check machine architecture and build/download corresponding stanc. I fixed the issue momentarily by removing all the architecture information detected by make and only supply ubuntu for linux platform. I believe this works for metworx and hopefully resolve the current issue.

nmarusan commented 2 years ago

I tried it again, but the next error message is as follows:

cmdstanr::cmdstan_model("/content/Torsten/cmdstan/examples/TwoCptModelPopulation/TwoCptModelPopulation.stan",quiet=FALSE)

g++ -std=c++1y -pthread -D_REENTRANT -Wno-sign-compare -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 -DBOOST_DISABLE_ASSERTS -c -MT stan/src/stan/model/model_header.hpp.gch -MT stan/src/stan/model/model_header.d -MM -E -MG -MP -MF stan/src/stan/model/model_header.d stan/src/stan/model/model_header.hpp g++ -std=c++1y -pthread -D_REENTRANT -Wno-sign-compare -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 -DBOOST_DISABLE_ASSERTS -c -MT src/cmdstan/main.o -MM -E -MG -MP -MF src/cmdstan/main.d src/cmdstan/main.cpp

--- Translating Stan model to C++ code --- bin/stanc --name='TwoCptModelPopulation_model' --o=/tmp/RtmpfPHQCQ/model-45363bdefd.hpp /tmp/RtmpfPHQCQ/model-45363bdefd.stan bin/stanc: /lib/x86_64-linux-gnu/libm.so.6: version GLIBC_2.29' not found (required by bin/stanc) bin/stanc: /lib/x86_64-linux-gnu/libm.so.6: versionGLIBC_2.29' not found (required by bin/stanc)

make/program:48: recipe for target '/tmp/RtmpfPHQCQ/model-45363bdefd.hpp' failed bin/stanc: /lib/x86_64-linux-gnu/libc.so.6: version GLIBC_2.28' not found (required by bin/stanc) make: *** [/tmp/RtmpfPHQCQ/model-45363bdefd.hpp] Error 1 bin/stanc: /lib/x86_64-linux-gnu/libc.so.6: versionGLIBC_2.28' not found (required by bin/stanc) make: *** [/tmp/RtmpfPHQCQ/model-45363bdefd.hpp] Error 1

Error: An error occured during compilation! See the message above for more information. Traceback:

  1. cmdstanr::cmdstan_model("/content/Torsten/cmdstan/examples/TwoCptModelPopulation/TwoCptModelPopulation.stan", . quiet = FALSE)
  2. CmdStanModel$new(stan_file = stan_file, exe_file = exe_file, . compile = compile, ...)
  3. initialize(...)
  4. self$compile(...)
  5. stop("An error occured during compilation! See the message above for more information.", . call. = FALSE)
billgillespie commented 2 years ago

Hi Yi (@yizhang-yiz). I was able to replicate nmarusan's result on Metworx. I got the following messages:

Compiling Stan program...
bin/stanc: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by bin/stanc)
bin/stanc: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.28' not found (required by bin/stanc)
make: *** [/tmp/RtmphRkM89/model-6aef6fe05ec7.hpp] Error 1
billgillespie commented 2 years ago

@nmarusan, if you need a working version while we resolve the issues with the most recent release, you can install the previous release. The following code will do that and compile the test example:

system("git clone -b torsten_v0.89.1 https://github.com/metrumresearchgroup/Torsten.git")

library(cmdstanr)
set_cmdstan_path(path = file.path(getwd(), "Torsten", "cmdstan")) 
rebuild_cmdstan()

model <- cmdstan_model(file.path(getwd(), "Torsten",
                                 "example-models/pk2cpt/pk2cpt.stan"))

Yo will need to edit the file paths for your environment...

nmarusan commented 2 years ago

Hi BIll(@billgillespie), I followed your advice, solving the problem. Thanks for the help. I implemented the process from Torsten install to example execution with google colaboratory, so please use it if you like.

https://colab.research.google.com/drive/1Xck-nZY95llKQ_Oa02n_hLeFhWTD8z4P?usp=sharing

yizhang-yiz commented 2 years ago

Looks like I need build a static version. I'll fixed it asap, afterwards will need @billgillespie 's assistance on testing it on metworx.

yizhang-yiz commented 2 years ago

I finally set up ubuntu and updated the stanc3 binary. @nmarusan @billgillespie could you give another try by rebuilding cmdstan? Namely.

cd Torsten/cmdstan
make clean-all
make -j4 ../example-models/pk2cpt_ode/pk2cpt_ode
nmarusan commented 2 years ago

@yizhang-yiz, I tried the latest Torsten on my environment, which was successful. Thank you for developing it!

billgillespie commented 2 years ago

Hi @yizhang-yiz. I was also able to successfully install Torsten and compile the example on Metworx. Thanks