metrumresearchgroup / torsten

library of C++ functions that support applications of Stan in Pharmacometrics

Torsten is a collection of Stan functions to facilitate analysis of pharmacometric data. See the user guide for more details. A slightly outdated web version can be found at https://metrumresearchgroup.github.io/Torsten/.

Changelog

• Version 0.91.0 <2024-03-18 Sun>

  • Changed
    • Update model examples according to new array syntax.
    • Update to Stan version 2.33.1.
    • Removed experimental cross-chain feature.
    • Deprecation of old Torsten functions not using 'pmx\_' prefix.
    • Minor bug fixes.

• Version 0.90.0 <2022-05-18 Wed>

  • Changed
    • Update model examples according to new array syntax.
    • Update to Stan version 2.29.2.

• Version 0.89 <2021-06-15 Tue>

  • Changed
    • New backend for ODE events solvers.
    • Use vector instead of array as ODE function state & return type.
    • Simplified ODE integrator naming, e.g. pmx_ode_bdf[_ctrl].
    • Update to Stan version 2.27.0.

• Version 0.88 <2020-12-18 Fri>

  • Added

    • Bioavailability, lag time, ODE real & integer data are optional in PMX function signatures.
    • Support all EVID options from NM-TRAN and mrgsolve.
    • Support steady-state infusion through multiple interdose intervals.

  • Changed

    • More efficient memory management of COVDES implenmentation.
    • Update of MPI framework to adapt multilevel paralleism.
    • Update to Stan version 2.25.0.
    • Use cmdstanr as R interface.
    • Stop supporting rstan as R interface.

• Version 0.87 <2019-07-26 Fri>

  • Added

    • MPI dynamic load balance for Torsten's population ODE integrators

      • pmx_integrate_ode_group_adams
      • pmx_integrate_ode_group_bdf
      • pmx_integrate_ode_group_rk45

      To invoke dynamic load balance instead of default static balance for MPI, issue TORSTEN_MPI=2 in make/local.

    • Support RATE as parameter in pmx_solve_rk45/bdf/adams functions.

  • Changed
    • Some fixes on steady-state solvers
    • Update to rstan version 2.19.2.

• Version 0.86 <2019-05-15 Wed>

  • Added

    • Torsten's ODE integrator functions

      • pmx_integrate_ode_adams
      • pmx_integrate_ode_bdf
      • pmx_integrate_ode_rk45

      and their counterparts to solve a population/group of subjects governed by an ODE

      • pmx_integrate_ode_group_adams
      • pmx_integrate_ode_group_bdf
      • pmx_integrate_ode_group_rk45

    • Torsten's population PMX solver functions for general ODE models

      • pmx_solve_group_adams
      • pmx_solve_group_bdf
      • pmx_solve_group_rk45

    • Support time step ts as parameter in pmx_integrate_ode_xxx solvers.

  • Changed

    • Renaming Torsten functions in previous releases, the old-new name mapping is

      • PKModelOneCpt → pmx_solve_onecpt
      • PKModelTwoCpt → pmx_solve_onecpt
      • linOdeModel → pmx_solve_linode
      • generalOdeModel_adams → pmx_solve_adams
      • generalOdeModel_bdf → pmx_solve_bdf
      • generalOdeModel_rk45 → pmx_solve_rk45
      • mixOde1CptModel_bdf → pmx_solve_onecpt_bdf
      • mixOde1CptModel_rk45 → pmx_solve_onecpt_rk45
      • mixOde2CptModel_bdf → pmx_solve_twocpt_bdf
      • mixOde2CptModel_rk45 → pmx_solve_twocpt_rk45

      Note that the new version of the above functions return the transpose of the matrix returned by the old versions, in order to improve memory efficiency. The old version are retained but will be deprecated in the future.

    • Update to Stan version 2.19.1.

• Version 0.85 <2018-12-04 Tue>

  • Added
    • Dosing rate as parameter
  • Changed
  • Update to Stan version 2.18.0.

• Version 0.84 <2018-02-24 Sat>

  • Added
    • Piecewise linear interpolation function.
    • Univariate integral functions.
  • Changed
    • Update to Stan version 2.17.1.
    • Minor revisions to User Manual.
    • Bugfixes.

• Version 0.83 <2017-08-02 Wed>

  • Added
    • Work with TorstenHeaders
    • Each chain has a different initial estimate
  • Changed
    • User manual
    • Fix misspecification in ODE system for TwoCpt example.
    • Other bugfixes

• Version 0.82 <2017-01-29 Sun>

  • Added
    • Allow parameter arguments to be passed as 1D or 2D arrays
    • More unit tests
    • Unit tests check automatic differentiation against finite differentiation.
  • Changed
    • Split the parameter argument into three arguments: pMatrix (parameters for the ODEs – note: for linOdeModel, pMatrix is replaced by the constant rate matrix K), biovar (parameters for the biovariability), and tlag (parameters for the lag time).
    • bugfixes

• Version 0.81 <2016-09-27 Tue>

  • Added
    • linCptModel (linear compartmental model) function

• Version 0.80a <2016-09-21 Wed>

  • Added
    • check_finite statements in pred_1 and pred_2 to reject metropolis proposal if initial conditions are not finite

torsten's Issues

Torsten integration with Stan

Hi, the current(latest) release of Torsten requires a bundled installation of stan-2.19 and doesnt play well with an system installation of stan. I would like to understand if your plans for a more loosely coupled integration with a standard installation of stan has materialized and when the next release of Torsten compatible with the current release of rstan (2.21 at the moment) is being planned. Thanks,

-Vijay

Torsten Installation on a Mac

I've attempted to run the 2-compartment PK model using the R interface to Torsten which has generated the following error message:

Compiling Stan program...

Semantic error in '/var/folders/k_/t891xypn0vvd7x5lfdv6txmh0000gn/T/RtmpvhNll8/model-a7d43e46fd25.stan', line 87, column 26 to line 95, column 20:

85:      parms = {CL[j], V[j], ka[j]};
86:  
87:      x[start[j]:end[j],] = PKModelOneCpt(time[start[j]:end[j]], 
                               ^
88:  					amt[start[j]:end[j]],
89:  					rate[start[j]:end[j]],

---

A returning function was expected but an undeclared identifier 'PKModelOneCpt' was supplied.

make: *** [/var/folders/k_/t891xypn0vvd7x5lfdv6txmh0000gn/T/RtmpvhNll8/model-a7d43e46fd25.hpp] Error 1
Error: An error occured during compilation! See the message above for more information.
Called from: self$compile(...)

---

I've had challenges installing the R interface to Torsten and, so far, I'm thinking I've not been successful. I would appreciate some guidance. Apologies for the open ended request, but I'm new to Torsten/Stan. Thanks in advance for your help in this matter.

posterior predictive distributions code

I have fit a number of Torsten population models with different residual variability options and the diagnostics look ok. However I did not find any code that I can use to extract posterior distributions and plot individual and population prediction to further evaluate the fit and guide model selection.

I am new Stan user and would appreciate any help.

Best regards

[DOC] twocpt_population is not a hierarchical population model

Description

The twocpt_population model in the example-models directory is not an appropriately constructed population model, i.e., a hierarchical model with inter-individual variability in model parameters. It is instead a simultaneous fit of a set of individual models---one model per individual. While this is suitable for demonstrating the use of the pmx_solve_group functions, it does not demonstrate good PK modeling practice. The model should be replaced by a correctly structured model.

Expected documentation

Revise or replace twocpt_population with a corrected model. This also needs to be changed in the Users Guide.

Current Version:

v0.90.0

[BUG] bioavailability calculation error on MacOS with LLVM 15

Description

From a user report I was able to trace the error to bioavailability calculation at

Torsten/cmdstan/stan/lib/stan_math/stan/math/torsten/ev_manager.hpp

Line 251 in 2d9076f

return params.bioavailability(i, event_his.cmt(i) - 1) * event_his.amt(i);

Example

• build pk2cpt example with llvm 15 toolchain
• the pk2cpt will sample with initialization error.

Expected Output

Pass all tests and example models run w/o issue.

Current Version:

v0.89.0

Compilation requires write access to the installation folder

Hi Yi,

I have tried running "pk2cpt" example-model in a centos-8, gcc-8.3.1 and R-4.0.4 environment. When I run as a root user the execution goes through successfully as root has write access to all the locations. However, when running as a non-root user.. I am seeing the below errors, also below is the source code for pk2cpt example model..:

R version 4.0.4 (2021-02-15) -- "Lost Library Book"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

library("cmdstanr")
This is cmdstanr version 0.4.0

• Online documentation and vignettes at mc-stan.org/cmdstanr
• Use set_cmdstan_path() to set the path to CmdStan
• Use install_cmdstan() to install CmdStan

set_cmdstan_path("/pkpd/Torsten/cmdstan")
CmdStan path set to: /pkpd/Torsten/cmdstan
file.dir <- file.path("/pkpd/Torsten", "example-models", "pk2cpt")
file <- file.path(file.dir, "pk2cpt.stan")
model <- cmdstan_model(file)
: fatal error: opening dependency file stan/src/stan/model/model_header.d: Permission denied
compilation terminated.
: fatal error: opening dependency file src/cmdstan/main.d: Permission denied
compilation terminated.
mkdir: cannot create directory ‘bin/’: Permission denied
make: *** [make/stanc:74: bin/stanc] Error 1
Error: An error occured during compilation! See the message above for more information.
Execution halted

Source:
library("cmdstanr")
set_cmdstan_path("/pkpd/Torsten/cmdstan")
file.dir <- file.path("./")
file <- file.path(file.dir, "pk2cpt.stan")
model <- cmdstan_model(file)
fit <- model$sample(data = file.path(file.dir, "pk2cpt.data.R"),
init = file.path(file.dir, "pk2cpt.init.R"),
seed = 123,
chains = 4,
parallel_chains = 2,
refresh = 500)
bayesplot::mcmc_dens_overlay(fit$draws("CL"))

troubleshoting installation

This is potentially related to #3 but I can not find a solution after trying the source install.R recommended and the alternative install_torsten from the submodule torstenHeaders.

I have tried to install the R interface of Torsten
install_error.txt
but I can not troubleshot the follwoing error (atttached).
I have made sure that my .R/Makevars look like this:
CXX14 = g++ -fPIC

CXXFLAGS=-O3 -std=c++1y -mtune=native -march=native -Wno-unused-variable -Wno-unused-function
CXXFLAGS += -DBOOST_MPL_CFG_NO_PREPROCESSED_HEADERS -DBOOST_MPL_LIMIT_LIST_SIZE=30

CXX14FLAGS=-O3 -std=c++1y -mtune=native -march=native -Wno-unused-variable -Wno-unused-function
CXX14FLAGS += -DBOOST_MPL_CFG_NO_PREPROCESSED_HEADERS -DBOOST_MPL_LIMIT_LIST_SIZE=30

My session info is:
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /opt/scp/software/mro/3.5.1-foss-2017a/lib64/R/lib/libRblas.so
LAPACK: /opt/scp/software/mro/3.5.1-foss-2017a/lib64/R/lib/libRlapack.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] rstan_2.19.1 StanHeaders_2.18.1 RevoUtils_11.0.1
[4] RevoUtilsMath_11.0.0

loaded via a namespace (and not attached):
[1] Rcpp_1.0.1.3 pillar_1.3.1.9000 compiler_3.5.1
[4] plyr_1.8.4 torstenHeaders_0.1.1 tools_3.5.1
[7] digest_0.6.15 pkgbuild_1.0.0 memoise_1.1.0
[10] tibble_2.1.1.9000 gtable_0.2.0 debugme_1.1.0
[13] pkgconfig_2.0.2 rlang_0.3.99.9003 rstudioapi_0.7
[16] curl_3.2 yaml_2.2.0 parallel_3.5.1
[19] loo_2.1.0.9000 gridExtra_2.3 xml2_1.2.0
[22] httr_1.3.1 withr_2.1.2 dplyr_0.8.1.9000
[25] devtools_1.13.6 stats4_3.5.1 grid_3.5.1
[28] tidyselect_0.2.5.9000 inline_0.3.15 glue_1.3.1.9000
[31] R6_2.4.0 processx_3.1.0 ggplot2_3.0.0
[34] callr_2.0.4 purrr_0.2.5 magrittr_1.5
[37] scales_0.5.0 matrixStats_0.54.0 rvest_0.3.2
[40] assertthat_0.2.1.9000 colorspace_1.3-2 lazyeval_0.2.1
[43] munsell_0.5.0 crayon_1.3.4

[BUG] Torsten installation issue

Hello,

I'm keen to utilize the event schedule functionality of Torsten, and I've encountered an installation issue.

my information:
Windows 10;
R version 4.0.4;
rstan version 2.21.2;
cmdstan version 2.27.0;

cmdstan_path() 
[1] "D:/OneDrive/Documents/.cmdstanr/cmdstan-2.27.0"

check_cmdstan_toolchain()
The C++ toolchain required for CmdStan is setup properly!

I am able to compile models via cmdstan using code from this page.

I next cloned the Torsten repo, and set the cmdstan path to the version of cmdstan within the cloned Torsten repo (per the directions on your installation page):

cmdstanr::set_cmdstan_path("C:/Programs/Git/Torsten/cmdstan/")
CmdStan path set to: C:/Programs/Git/Torsten/cmdstan/

Next I tried to compile example models from the Torsten repo (via code from the Installation page):

library(cmdstanr)
library(posterior)
library(bayesplot)

file.dir <- file.path("C:/Programs/Git/Torsten", "example-models", "pk2cpt")
file  <- file.path(file.dir, "pk2cpt.stan")
model <- cmdstan_model(file)`` 

which produced the following error:

Compiling Stan program...
process_begin: CreateProcess(NULL, https://github.com/metrumresearchgroup/stanc3/releases/download/torsten_v0.89rc2/windows-stanc -o bin/stanc.exe --retry 5 --retry-delay 10, ...) failed.
make (e=2): The system cannot find the file specified.
mingw32-make.exe: *** [make/stanc:70: bin/stanc.exe] Error 2
Error: An error occured during compilation! See the message above for more information.

After examining the error and after reading posts online, I realized Torsten's version of cmdstan did not contain a stanc.exe file . . . specifically, there was no stanc.exe file in Torsten/cmdstan/bin.

So, in a fit of improvisation, I copied the stanc.exe file from the "standard" cmdstan into Torsten's cmdstan
(which may be highly inappropriate -- I apologize -- I'm at the very edge of my competence here).

Running the above model then returned:

Compiling Stan program...
Semantic error in 'C:/Users/rande/AppData/Local/Temp/RtmpMhm7gw/model-7a101c7d73a3.stan', line 50, column 6 to column 71:
   -------------------------------------------------
    48:    theta[5] = ka;
    49:  
    50:    x = pmx_solve_twocpt(time, amt, rate, ii, evid, cmt, addl, ss, theta);
               ^
    51:  
    52:    cHat = x[2, :] ./ V1; // we're interested in the amount in the second compartment
   -------------------------------------------------
A returning function was expected but an undeclared identifier 'pmx_solve_twocpt' was supplied.mingw32-make.exe: *** [make/program:47: C:\Users\rande\AppData\Local\Temp\RtmpMhm7gw\model-7a101c7d73a3.hpp] Error 1
Error: An error occured during compilation! See the message above for more information.

I'm assuming my copying of the stanc.exe file somewhat patched one issue, but created another? Or is there an underlying issue with my Make? I'm assuming since cmdstan works properly, my g++ and Make toolchain are in place?

I very much appreciate any assistance here!!

[BUG] KA=0 is not allowed in one/two cpt models.

Description

ka=0 leads to exception instead of eliminating absorption in one/two cut models.

Example

  y0(0) = 745;
  y0(1) = 100;
  rate[0] = 1200;
  rate[1] = 200;
  ka = 0.0;
  using model_t = PMXOneCptModel<double, double, double, double>;
  model_t model(t0, y0, rate, CL, V2, ka);
  auto y = model.solve(ts[0]);

The above model throws exception when check_positive_finite is applied to ka, removing this check will give NaN in output y because ka is used in denominators in the solver.

Expected Output

Solution with no absorption

Current Version:

v0.87.1

[FEATURE] Allow tolerance and max_step controls for steady states solver's algebraic solver

Description

Referenced in
metrumresearchgroup/math#29

Example

Description:

PredSS_general has f_tol hard-coded as

    double rel_tol = 1e-10;  // default
    double f_tol = 1e-4;  // empirical
    long int max_num_steps = 1e3;  // default // NOLINT

We need to avoid the above hard-coded solver parameters. In particular, when ODE coefficients are not normalized, f_tol may cause solver failure due to large abs error.

Expected Output:

Allow user to specify tolerance or provide a normalization in the ODE solver.

Current Version:

v0.87.1

Compilation failure

Trying to install Torsten.
During installation of Torsten (as R interface on Windows) it crashes when trying to include <stan/lang/grammars/term_grammar_def.hpp>. Other headers are included successfully.
Rstan itself has no such an error during installation. All C++14 flags are present, gcc 4.9.3.
Here is R console output:
g++ -fPIC -I"D:/Personal_folders/user1/R-3.5.1/include" -DNDEBUG -I"../inst/include" -I"." -I"D:/Personal_folders/user1/Test_Torsten/Work/R_project/packrat/lib/x86_64-w64-mingw32/3.5.1/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"D:/Personal_folders/user1/Test_Torsten/Work/R_project/packrat/lib/x86_64-w64-mingw32/3.5.1/Rcpp/include" -I"D:/Personal_folders/user1/Test_Torsten/Work/R_project/packrat/lib/x86_64-w64-mingw32/3.5.1/RcppEigen/include" -I"D:/Personal_folders/user1/Test_Torsten/Work/R_project/packrat/lib/x86_64-w64-mingw32/3.5.1/BH/include" -I"D:/Personal_folders/user1/Test_Torsten/Work/R_project/packrat/lib/x86_64-w64-mingw32/3.5.1/StanHeaders/include" -O3 -std=c++1y -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -DBOOST_MPL_CFG_NO_PREPROCESSED_HEADERS -DBOOST_MPL_LIMIT_LIST_SIZE=30 -c stan/lang/grammars/term_grammar_inst.cpp -o stan/lang/grammars/term_grammar_inst.o
stan/lang/grammars/term_grammar_inst.cpp:1:0: warning: -fPIC ignored for target (all code is position independent)
#include <stan/lang/grammars/term_grammar_def.hpp>
^

cc1plus.exe: out of memory allocating 65536 bytes
make: *** [stan/lang/grammars/term_grammar_inst.o] Error 1
ERROR: compilation failed for package 'rstan'

• removing 'D:/Personal_folders/user1/Test_Torsten/Work/R_project/packrat/lib/x86_64-w64-mingw32/3.5.1/rstan'
  In R CMD INSTALL
  Error: Failed to install 'rstan' from GitHub

Error is the same if Rstan is preinstalled or not installed.
Is there any chance for allocating more memory or other way?
Thank you.

[BUG] CMT doesn't accept negative value

Description

in pmx_solve_xxx functions cmt is not allowed to be negative.

Example

Negative compartment id gives

Exception: xxxx_model_namespace::xxxx_model: cmt[i_0__] is -1, but must be greater than or equal to 1

Expected Output

Follow NONMEM behavior:

When CMT specifies the output compartment, it is allowed to have a negative sign (e.g., with the One-compartment model, CMT may be -2). This signals that after the prediction is computed the out- put compartment is to be turned off, i.e. the amount in the compartment is to be set to zero. The amount remains zero until the compartment is subsequently turned on. This is quite useful with urine observations

Current Version:

v0.87.1

Installation issue

Refer from original issue message #2

I had to reinstall Torsten on a different computer (windows 10). The Makevars file were uncommented in skeleton folder in RcppArmadillo and RcppEigen packages so that
CXX_STD = CXX11

However installation problems similar to above except the following error message

make: *** [C:/PROGRA1/R/R-351.0/etc/x64/Makeconf:215: stanc.o] Error 1
ERROR: compilation failed for package 'rstan'

Can you help me figure out what could be the problem?

[BUG] failure to build example models

From https://discourse.mc-stan.org/t/problem-installing-torsten-0-90/27585/5?u=yizhang
by Casey Davis.

Description

On new macbook pro with M3 chip:

48 warnings and 14 errors generated.
make: *** [src/cmdstan/main.o] Error 1

Is this something going on with a Torsten incompatibility with the M3 chip?

Expected Output

Build success.

Current Version:

v0.90.0

Full error msg

[FEATURE] MPI dynamic load balancing for pmx_solve_group solvers

Description

Support dynamic load balancing for population solvers pmx_solver_group_xxx.

Example

• With TORSTEN_MPI=2, group solvers solve population models with dynamic load balancing.
• Improved performance when load distribution is highly uneven among the population.

Expected Output

Same as static load balancing MPI solvers.

Current Version:

v0.87.1

[BUG] MacOS compiling failure

Hello,

Description

Describe the issue as clearly as possible. Issues are meant for feature requests. The issue should contain enough information for a developer to put together a solution.
I recently chose to install Torsten for PK modeling on my computer. I followed the installation instructions and did not get any errors. I tried following the test step below

library("cmdstanr")
set_cmdstan_path("Torsten/cmdstan")
file.dir <- file.path("Torsten", "example-models", "pk2cpt")
file <- file.path(file.dir, "pk2cpt.stan")

But I get an error when I run the next step: model <- cmdstan_model(file)

I have added a screenshot of some of the error and pasted all the error message below.

ERROR MESSAGE

Compiling Stan program...
In file included from src/cmdstan/main.cpp:1:
In file included from src/cmdstan/command.hpp:4:
In file included from src/cmdstan/arguments/arg_data.hpp:4:
In file included from src/cmdstan/arguments/categorical_argument.hpp:4:
In file included from src/cmdstan/arguments/argument.hpp:4:
In file included from stan/src/stan/callbacks/writer.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/fun/Eigen.hpp:22:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/Dense:1:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/Core:19:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/src/Core/util/Macros.h:679:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:320:5: error: tried including <math.h> but didn't find libc++'s <math.h> header. This usually means that your header search paths are not configured properly. The header search paths should contain the C++ Standard Library headers before any C Standard Library, and you are probably using compiler flags that make that not be the case.

error tried including <math.h> but didn't find libc++'s <math.h> header. \

^

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:587:17: error: expected unqualified-id
return std::isnan(__lcpp_x);
^
/usr/local/include/math.h:166:5: note: expanded from macro 'isnan'
( sizeof(x) == sizeof(float) ? __inline_isnanf((float)(x))
^
In file included from src/cmdstan/main.cpp:1:
In file included from src/cmdstan/command.hpp:4:
In file included from src/cmdstan/arguments/arg_data.hpp:4:
In file included from src/cmdstan/arguments/categorical_argument.hpp:4:
In file included from src/cmdstan/arguments/argument.hpp:4:
In file included from stan/src/stan/callbacks/writer.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/fun/Eigen.hpp:22:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/Dense:1:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/Core:19:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/src/Core/util/Macros.h:679:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:607:17: error: expected unqualified-id
return std::isinf(__lcpp_x);
^
/usr/local/include/math.h:161:5: note: expanded from macro 'isinf'
( sizeof(x) == sizeof(float) ? __inline_isinff((float)(x))
^
In file included from src/cmdstan/main.cpp:1:
In file included from src/cmdstan/command.hpp:4:
In file included from src/cmdstan/arguments/arg_data.hpp:4:
In file included from src/cmdstan/arguments/categorical_argument.hpp:4:
In file included from src/cmdstan/arguments/argument.hpp:4:
In file included from stan/src/stan/callbacks/writer.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/fun/Eigen.hpp:22:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/Dense:1:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/Core:19:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/
src/Core/util/Macros.h:679:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:646:38: error: no member named '__promote' in namespace 'std'

                            std::__promote<_A1, _A2> >::type
                            ~~~~~^

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:646:48: error: '_A1' does not refer to a value
std::__promote<_A1, _A2> >::type
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:643:17: note: declared here
template <class _A1, class _A2>
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:646:58: error: expected unqualified-id
std::__promote<_A1, _A2> >::type
^

In file included from src/cmdstan/main.cpp:1:
In file included from src/cmdstan/command.hpp:4:
In file included from src/cmdstan/arguments/arg_data.hpp:4:
In file included from src/cmdstan/arguments/categorical_argument.hpp:4:
In file included from src/cmdstan/arguments/argument.hpp:4:
In file included from stan/src/stan/callbacks/writer.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/fun/Eigen.hpp:22:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/Dense:1:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/Core:19:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/src/Core/util/Macros.h:679:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:833:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/type_traits:421:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/invoke.h:15:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__type_traits/apply_cv.h:15:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__type_traits/remove_reference.h:13:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cstddef:46:5: error: tried including <stddef.h> but didn't find libc++'s <stddef.h> header. This usually means that your header search paths are not configured properly. The header search paths should contain the C++ Standard Library headers before any C Standard Library, and you are probably using compiler flags that make that not be the case.

error tried includi

ng <stddef.h> but didn't find libc++'s <stddef.h> header.
^

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cstddef:59:9: error: no member named 'nullptr_t' in the global namespace
using ::nullptr_t;
~~^

In file included from src/cmdstan/main.cpp:1:
In file included from src/cmdstan/command.hpp:4:
In file included from src/cmdstan/arguments/arg_data.hpp:4:
In file included from src/cmdstan/arguments/categorical_argument.hpp:4:
In file included from src/cmdstan/arguments/argument.hpp:4:
In file included from stan/src/stan/callbacks/writer.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/fun/Eigen.hpp:22:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/Dense:1:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/Core:19:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/src/Core/util/Macros.h:679:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:833:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/type_traits:456:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__type_traits/is_compound.h:14:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__type_traits/is_fundamental.h:14:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:24:49: error: use of undeclared identifier 'nullptr_t'; did you mean 'nullptr'?
template <> struct __is_nullptr_t_impl<nullptr_t> : public true_type {};
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:24:49: error: template argument for template type parameter must be a type
template <> struct __is_nullptr_t_impl<nullptr_t> : public true_type {};

^~~~~~~~~

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:23:17: note: template parameter is declared here
template struct __is_nullptr_t_impl : public false_type {};
^

In file included from src/cmdstan/main.cpp:1:
In file included from src/cmdstan/command.hpp:4:
In file included from src/cmdstan/arguments/arg_data.hpp:4:
In file included from src/cmdstan/arguments/categorical_argument.hpp:4:
In file included from src/cmdstan/arguments/argument.hpp:4:
In file included from stan/src/stan/callbacks/writer.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/fun/Eigen.hpp:22:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/Dense:1:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/Core:19:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/src/Core/util/Macros.h:679:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:833:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/type_traits:538:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cstdint:149:5: error: tried including <stdint.h> but didn't find libc++'s <stdint.h> header. This usually means that your header search paths are not configured properly. The header search paths should contain the C++ Standard Library headers before any C Standard Library, and you are probably using compiler flags that make that not be the case.

error tried including <stdint.h> but didn't find libc++'s <stdint.h> header. \

^

In file included from src/cmdstan/main.cpp:1:
In file included from src/cmdstan/command.hpp:4:
In file included from src/cmdstan/arguments/arg_data.hpp:4:
In file included from src/cmdstan/arguments/categorical_argument.hpp:4:
In file included from src/cmdstan/arguments/argument.hpp:4:
In file included from stan/src/stan/callbacks/writer.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/fun/Eigen.hpp:22:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/Dense:1:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/Core:34:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/new:96:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cstdlib:90:5: error: tried including <stdlib.h> but didn't find libc++'s <stdlib.h> header. This usually means that your header search paths are not configured properly. The header search paths should contain the C++ Standard Library headers before any C Standard Library, and you are probably using compiler flags that make that not be the case.

error tried including <stdlib.h> but didn't find libc++'s <stdlib.h> header. \

^

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cstdlib:132:9: error: target of using declaration conflicts with declaration already in scope
using ::abs _LIBCPP_USING_IF_EXISTS;
^
/usr/local/include/stdlib.h:132:6: note: target of using declaration
int abs(int) __pure2;
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:353:1: note: conflicting declaration
using ::abs _LIBCPP_USING_IF_EXISTS;
^

In file included from src/cmdstan/main.cpp:1:
In file included from src/cmdstan/command.hpp:4:
In file included from src/cmdstan/arguments/arg_data.hpp:4:
In file included from src/cmdstan/arguments/categorical_argument.hpp:4:
In file included from src/cmdstan/arguments/argument.hpp:4:
In file included from stan/src/stan/callbacks/writer.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/fun/Eigen.hpp:22:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/Dense:1:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/Core:34:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/new:97:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/exception:199:45: error: field has incomplete type 'exception_ptr'
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : _ptr() {}
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/exception:194:24: note: definition of 'std::exception_ptr' is not complete until the closing '}'
class _LIBCPP_TYPE_VIS exception_ptr
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/exception:199:5: error: 'abi_tag' attribute only applies to structs, variables, functions, and namespaces
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : _ptr() {}
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:709:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY'

define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI

                                ^

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config
:688:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
attribute((abi_tag(_LIBCPP_TOSTRING(_LIBCPP_VERSIONED_IDENTIFIER))))
^
In file included from src/cmdstan/main.cpp:1:
In file included from src/cmdstan/command.hpp:4:
In file included from src/cmdstan/arguments/arg_data.hpp:4:
In file included from src/cmdstan/arguments/categorical_argument.hpp:4:
In file included from src/cmdstan/arguments/argument.hpp:4:
In file included from stan/src/stan/callbacks/writer.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/fun/Eigen.hpp:22:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/Dense:1:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/Core:34:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/new:97:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/exception:199:55: error: expected ';' at end of declaration list
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : _ptr() {}
^

In file included from src/cmdstan/main.cpp:1:
In file included from src/cmdstan/command.hpp:4:
In file included from src/cmdstan/arguments/arg_data.hpp:4:
In file included from src/cmdstan/arguments/categorical_argument.hpp:4:
In file included from src/cmdstan/arguments/argument.hpp:4:
In file included from stan/src/stan/callbacks/writer.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/fun/Eigen.hpp:22:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/Dense:1:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/Core:50:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:243:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/sstream:191:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/istream:165:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/ostream:168:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/shared_ptr.h:31:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h:17:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/hash.h:28:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cstring:66:5: error: tried including <string.h> but didn't find libc++'s <string.h> header. This usually means that your header search paths are not configured properly. The header search paths should contain th
e C++ Standard Library headers before any C Standard Library, and you are probably using compiler flags that make that not be the case.

error tried including <string.h> but didn't find libc++'s <string.h> header. \

^

In file included from src/cmdstan/main.cpp:1:
In file included from src/cmdstan/command.hpp:4:
In file included from src/cmdstan/arguments/arg_data.hpp:4:
In file included from src/cmdstan/arguments/categorical_argument.hpp:4:
In file included from src/cmdstan/arguments/argument.hpp:4:
In file included from stan/src/stan/callbacks/writer.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/fun/Eigen.hpp:22:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/Dense:1:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/Core:50:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:243:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/sstream:191:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/istream:165:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/ostream:168:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/shared_ptr.h:31:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h:188:3: error: non-static data member cannot be constexpr; did you intend to make it const?
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : _ptr(__value_init_tag(), __value_init_tag()) {}
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:465:31: note: expanded from macro '_LIBCPP_CONSTEXPR'

define _LIBCPP_CONSTEXPR constexpr

                          ^

In file included from src/cmdstan/main.cpp:1:
In file included from src/cmdstan/command.hpp:4
:
In file included from src/cmdstan/arguments/arg_data.hpp:4:
In file included from src/cmdstan/arguments/categorical_argument.hpp:4:
In file included from src/cmdstan/arguments/argument.hpp:4:
In file included from stan/src/stan/callbacks/writer.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/fun/Eigen.hpp:22:
In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/Dense:1:

In file included from stan/lib/stan_math/lib/eigen_3.4.0/Eigen/Core:50:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:243:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/sstream:191:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/istream:165:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/ostream:168:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/shared_ptr.h:31:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h:188:32: error: member 'nullptr_t' declared as a template
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : _ptr(__value_init_tag(), __value_init_tag()) {}
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]

20 errors generated.

make: *** [src/cmdstan/main.o] Error 1

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

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

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

• CmdStanR documentation and vignettes: mc-stan.org/cmdstanr
• Use set_cmdstan_path() to set the path to CmdStan
• Use install_cmdstan() to install CmdStan

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<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
180 | : public boost::functional::detail::unary_function<typename unary_traits::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<class _Arg1, class _Arg2, class _Result> 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<class _Arg, class _Result> 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<class _Arg, class _Result> 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<boost::SinglePassRangeConcept<const boost::iterator_range<__gnu_cxx::__normal_iterator<char*, std::__cxx11::basic_string > > > >::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<boost::SinglePassRangeConcept<const boost::iterator_range<__gnu_cxx::__normal_iterator<char*, std::__cxx11::basic_string > > > >'
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<boost::algorithm::detail::copy_iterator_rangeF<std::__cxx11::basic_string, __gnu_cxx::__normal_iterator<char*, std::__cxx11::basic_string > >, boost::algorithm::split_iterator<__gnu_cxx::__normal_iterator<char*, std::__cxx11::basic_string > >, boost::use_default, boost::use_default>; = void; _Tp = std::__cxx11::basic_string; _Alloc = std::allocator<std::__cxx11::basic_string >; allocator_type = std::allocator<std::__cxx11::basic_string >]'
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<std::__cxx11::basic_string >; RangeT = std::__cxx11::basic_string&; FinderT = detail::token_finderF<detail::is_any_ofF >]'
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<std::__cxx11::basic_string >; 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::__cxx11::basic_string >&, 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<double, -1, -1>]'
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<char*, std::__cxx11::basic_string > >]'
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!

[BUG] cHat is always 0 for `pmx_solve_twocpt`

Description

I'm trying to fit a 2-compartment pop-pk model and have found that pmx_solve_twocpt always return 0. Also, likely for this reason, the example-model pk2cpt.stan fails to initialize. This occurs with the develop branch, master branch, and v0.91.0rc2.

I'm on an M3 mac with empty Makevars file.

Example

First, the code I used to run the example model:

ref <- 'develop'
system(glue::glue("git clone -b {ref} https://github.com/metrumresearchgroup/Torsten.git ~/testing/Torsten_{ref}"))
torsten_dir <- glue::glue("~/testing/Torsten_{ref}")

# set cmdstanr to use torsten flavor of cmdstan
# Note: this can also be done with ENV vars
cmdstanr::set_cmdstan_path(fs::path(torsten_dir, "cmdstan"))
cmdstanr::check_cmdstan_toolchain()
cmdstanr::rebuild_cmdstan()

model_dir <- fs::path(torsten_dir, "example-models", "pk2cpt")
model_src <- fs::path_expand(fs::path(model_dir, "pk2cpt.stan"))
model <- cmdstanr::cmdstan_model(model_src)

# does not initialize
model_fit <- model$sample(data = file.path(model_dir, "pk2cpt.data.R"),
                          init = file.path(model_dir, "pk2cpt.init.R"),
                          seed = 1229453,
                          chains = 4,
                          parallel_chains = 2,
                          refresh = 500)

I tested this with a local version of pk2cpt.stan with a print statement after line 54:

model2_dir <- here::here()
model2_src <- fs::path_expand(fs::path(model2_dir, "pk2cpt.stan"))
model2 <- cmdstanr::cmdstan_model(model2_src)

model2_fit <- model2$sample(data = file.path(model_dir, "pk2cpt.data.R"),
                          init = file.path(model_dir, "pk2cpt.init.R"),
                          seed = 1229453,
                          chains = 1,
                          parallel_chains = 1,
                          refresh = 1)                     

I see:

Running MCMC with 1 chain...

Chain 1 cHatObs: [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0] 
Chain 1 Rejecting initial value:
Chain 1   Error evaluating the log probability at the initial value.
Chain 1 Exception: normal_lpdf: Location parameter[1] is -inf, but must be finite! (in '/var/folders/6r/tqtyyh5x67s_cjlvmm_lmm040000gn/T/RtmpwEkfLn/model-98381647a45e.stan', line 67, column 2 to column 40)
Chain 1 Exception: normal_lpdf: Location parameter[1] is -inf, but must be finite! (in '/var/folders/6r/tqtyyh5x67s_cjlvmm_lmm040000gn/T/RtmpwEkfLn/model-98381647a45e.stan', line 67, column 2 to column 40)
Chain 1 Warning: file '/Users/jacquelineburos/testing/Torsten_v0.91.0rc2/example-models/pk2cpt/pk2cpt.data.R' is being read as an 'RDump' file.
Chain 1 	This format is deprecated and will not receive new features.
Chain 1 	Consider saving your data in JSON format instead.
Chain 1 Warning: file '/Users/jacquelineburos/testing/Torsten_v0.91.0rc2/example-models/pk2cpt/pk2cpt.init.R' is being read as an 'RDump' file.
Chain 1 	This format is deprecated and will not receive new features.
Chain 1 	Consider saving your data in JSON format instead.
Chain 1 Initialization between (-2, 2) failed after 1 attempts. 
Chain 1  Try specifying initial values, reducing ranges of constrained values, or reparameterizing the model.
Chain 1 Initialization failed.
Warning: Chain 1 finished unexpectedly!

Warning message:
No chains finished successfully. Unable to retrieve the fit. 

Expected Output

It's possible there is something wrong with my setup, but at least right now I'm not able to use this analytic solution while pmx_solve_linode works fine.

Current Version:

v0.91.0, develop, master, v0.89.0rc2

I would note, I tried to use v0.89.0 but I was not able to build cmdstan+torsten from this version.

../tbb_2020.3/src/tbbmalloc/frontend.cpp:779:8: error: invalid instruction, any one of the following would fix this:
       "clz %0, %1\n"
       ^
<inline asm>:1:2: note: instantiated into assembly here
        clz r2, r1
        ^
../tbb_2020.3/src/tbbmalloc/frontend.cpp:779:8: note: instruction requires: armv5t
       "clz %0, %1\n"
       ^
<inline asm>:1:2: note: instantiated into assembly here
        clz r2, r1
        ^
../tbb_2020.3/src/tbbmalloc/frontend.cpp:779:8: note: instruction requires: thumb2
       "clz %0, %1\n"

[BUG] Wrong results when some of parameters are passed in functor as real data

Description

Adaptor implementation is based on original packing & unpacking of theta & x_r, and it doesn't consider the possibility when base functor could be using x_r to pass in some of the ODE parameters.

Example

The following one-cpt functor passes absorption rate ka through real data argument x_r

struct OneCptODEDebug {
  template <typename T0, typename T1, typename T2, typename T3>
  inline
  std::vector<typename stan::return_type<T0, T1, T2, T3>::type>
  operator()(const T0& t,
             const std::vector<T1>& x,
             const std::vector<T2>& parms,
             const std::vector<T3>& x_r,
             const std::vector<int>& x_i,
             std::ostream* pstream__) const {
    typedef typename stan::return_type<T0, T1, T2, T3>::type scalar;

    double ka = x_r[0];
    scalar CL = parms.at(0), V1 = parms.at(1), k10 = CL / V1;
    std::vector<scalar> y(2, 0);

    y.at(0) = -ka * x.at(0);
    y.at(1) = ka * x.at(0) - k10 * x.at(1);

    return y;
  }
};

and it triggers error in one-cpt unit test

TEST_F(TorstenOneCptTest, multiple_bolus) {
  ii[0] = 12;
  addl[0] = 14;

  double rel_tol = 1e-8, abs_tol = 1e-8;
  long int max_num_steps = 1e8;
  MatrixXd x_rk45 = torsten::pmx_solve_rk45(f_onecpt, nCmt,
                                time, amt, rate, ii, evid, cmt, addl, ss,
                                pMatrix, biovar, tlag,
                                0,
                                rel_tol, abs_tol, max_num_steps);
  MatrixXd x(10, nCmt);
  x << 1000.0, 0.0,
    740.8182, 254.97490,
    548.8116, 436.02020,
    406.5697, 562.53846,
    301.1942, 648.89603,
    223.1302, 705.72856,
    165.2989, 740.90816,
    122.4564, 760.25988,
    90.71795, 768.09246,
    8.229747, 667.87079;
  MatrixXd xt = x.transpose();

  torsten::test::test_val(x_rk45, xt, 1e-5, 1e-5);
}

as it gives

bash-3.2$ test/unit/math/torsten/debug_test
Running main() from lib/gtest_1.8.1/src/gtest_main.cc
[==========] Running 1 test from 1 test case.
[----------] Global test environment set-up.
[----------] 1 test from TorstenOneCptTest
[ RUN      ] TorstenOneCptTest.multiple_bolus
./test/unit/math/torsten/test_util.hpp:156: Failure
The difference between y1_i and y2_i is 259.18179999999995, which exceeds std::max(abs(y1_i), abs(y2_i)) * rtol, where
y1_i evaluates to 1000,
y2_i evaluates to 740.81820000000005, and
std::max(abs(y1_i), abs(y2_i)) * rtol evaluates to 0.01.
./test/unit/math/torsten/test_util.hpp:156: Failure
The difference between y1_i and y2_i is 254.97489999999999, which exceeds std::max(abs(y1_i), abs(y2_i)) * rtol, where
y1_i evaluates to 0,
y2_i evaluates to 254.97489999999999, and
std::max(abs(y1_i), abs(y2_i)) * rtol evaluates to 0.002549749.

Expected Output

pass test

Current Version:

v0.87.1

pmx_integrate_ode_ functions not available [BUG]

Description

The family of function pmx_integrate_ode_ is described in the documentation but does not appear to be found by STAN during the compilation process.

Example

Compiling Stan program...
Semantic error in '/tmp/Rtmpch722Q/model-14e2926ff4481.stan', line 93, column 38 to column 124:
   -------------------------------------------------
    91:      ii[:j24], evid[:j24], cmt[:j24], addl[:j24], ss[:j24], K, biovar, tlag);
    92:    int n_cmt_pd = 3;
    93:    matrix [n_cmt_pd, n_t - j24] x_pd = pmx_integrate_ode_rk45(f_ode, x_init[:, j24], 24.0, time[j24 + 1:], prm_i, {0.0}, {0});   
                                               ^
    94:    return  {y_hat_p, y_hat_l, y_hat_pd};
    95:   }
   -------------------------------------------------

A returning function was expected but an undeclared identifier 'pmx_integrate_ode_rk45' was supplied.

Expected Output

Model should compile without errors

Current Version:

v0.90.0

[BUG] Indexing error when infusion events end close to start of another event

Description

This bug tends to happen (but not always) when an infusion event (evid=1) has a rate that make it such that the infusion ends very close to the time of the next event. For example if amt=0.5 and rate=0.5 and the infusion starts at time=6 then it will end at time=7 and the bug will occur when you have another event that occurs close to time=7.

This only happens when I compile with MPI.

Specifically, the error I get is about an index being out of range somewhere:

Chain 1 test: stan/lib/stan_math/lib/eigen_3.3.9/Eigen/src/Core/DenseCoeffsBase.h:425: Eigen::DenseCoeffsBase<Derived, 1>::Scalar& Eigen::DenseCoeffsBase<Derived, 1>::operator()(Eigen::Index) [with Derived = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; Eigen::DenseCoeffsBase<Derived, 1>::Scalar = stan::math::var_value<double>; Eigen::Index = long int]: Assertion `index >= 0 && index < size()' failed.
Warning: Chain 1 finished unexpectedly!

Example

I tried to simplify the model and provide a few cases to best illustrate the bug. For some of these I don't get the error and for some I do. Below is the Stan model and the R code to run the different cases.

Simple Example Stan Model

functions{
  vector pk(real t, vector x, array[] real parms, array[] real rate, array[] int dummy){
			  
    // Parameters
    real CL = parms[1];
    real Q = parms[2];
    real V1 = parms[3];
    real V2 = parms[4];
    real ka = parms[5];
    
    real lambda1 = parms[6];
    real lambda2 = parms[7];
    
    // Re-parametrization
    real k10 = CL / V1;
    real k12 = Q / V1;
    real k21 = Q / V2;
    
    // Return object (derivative)
    vector[3] y;

    // PK component of the ODE system
    y[1] = -ka*x[1];
    y[2] = ka*x[1] - (k10 + k12)*x[2] + k21*x[3];
    y[3] = k12*x[2] - k21*x[3];

    return y;
  }
}

data {
  // Count data
  int<lower = 1> nt;  // number of events
  int<lower = 1> nSbj; // number of subjects
  array[nSbj] int<lower = 1> len; // Number of events per subject

  // NONMEM data
  array[nt] real<lower = 0> amt;
  array[nt] int<lower = 1> cmt;
  array[nt] int<lower = 0> evid;
  array[nt] real<lower = 0> time;
  array[nt] real<lower = 0> ii;
  array[nt] int<lower = 0> addl;
  array[nt] int<lower = 0> ss;
  array[nt] real<lower = 0> rate;
}

transformed data{
  int nCmt = 3;
  int nTheta = 7;
  real rtol = 1e-3;
  real atol = 1e-3;
  int max_step = 10000;
}

parameters {
  real<lower = 0> sigma;
}

transformed parameters{
  array[nSbj, nTheta] real theta;
  matrix[nCmt, nt] x;
  
  // Set individual parameters
  for(j in 1:nSbj) {
    theta[j] = {1.03, 1.27, 3.57, 1.61, 0.0, 0.0, 0.0};
  }

  x = pmx_solve_group_bdf(pk, nCmt,
                           len,
                           time, amt, rate, ii, evid, cmt, addl, ss,
                           theta,
                           rtol, atol, max_step);
}

model {
  
}

Simple R Script illustrating

library(tidyverse)
cmdstanr::set_cmdstan_path("/data/home/apourzan/Torsten/cmdstan")
library(cmdstanr)

# Compile
model <- cmdstan_model("Stan/test.stan")

# Case 1
# End of first infusion gets close to start of second
dat_stan <-
  list(nt = 3,
       nSbj = 1,
       len = 3,
       amt = c(0.4, 0.4, 0.0),
       cmt = c(2, 2, 2),
       evid = c(1, 1, 0),
       time = c(18.55555555555555358183,
                19.53125000000000000000,
                33.52430555555555713454),
       ii = c(0, 0, 0),
       addl = c(0, 0, 0),
       ss = c(0, 0, 0),
       rate = c(0.4099644128113879015807,
                0.4000000000000000222045,
                0.0000000000000000000000))

dat_stan$time[2] - (dat_stan$time[1] + dat_stan$amt[1]/dat_stan$rate[1])

fit <-
  model$sample(
    data = dat_stan,
    seed = 2022,
    chains = 1,
    iter_warmup = 1e0,
    iter_sampling = 1e0,
    parallel_chains = 1
  )

# Case 2
# If we round the time, then end of first doesn't get AS close to start of second and it works
dat_stan$time[1] <- 18.55556

dat_stan$time[2] - (dat_stan$time[1] + dat_stan$amt[1]/dat_stan$rate[1])

fit <-
  model$sample(
    data = dat_stan,
    seed = 2022,
    chains = 1,
    iter_warmup = 1e0,
    iter_sampling = 1e0,
    parallel_chains = 1
  )

# Case 3
# If we take out the third event it also works despite the same problem of end of infusion being close to start of next. Maybe only breaks if there's an observation event?
dat_stan <-
  list(nt = 2,
       nSbj = 1,
       len = 2,
       amt = c(0.4, 0.4),
       cmt = c(2, 2),
       evid = c(1, 1),
       time = c(18.55555555555555358183,
                19.53125000000000000000),
       ii = c(0, 0),
       addl = c(0, 0),
       ss = c(0, 0),
       rate = c(0.4099644128113879015807,
                0.4000000000000000222045))

dat_stan$time[2] - (dat_stan$time[1] + dat_stan$amt[1]/dat_stan$rate[1])

fit <-
  model$sample(
    data = dat_stan,
    seed = 2022,
    chains = 1,
    iter_warmup = 1e0,
    iter_sampling = 1e0,
    parallel_chains = 1
  )

# Case 4
# Different times, still 3 events, but end of infusion still gets close to start of next event, yet it doesn't break
dat_stan <-
  list(nt = 3,
       nSbj = 1,
       len = 3,
       amt = c(0.4, 0.4, 0.0),
       cmt = c(2, 2, 2),
       evid = c(1, 1, 0),
       time = c(18.0,
                19.0,
                33.52430555555555713454),
       ii = c(0, 0, 0),
       addl = c(0, 0, 0),
       ss = c(0, 0, 0),
       rate = c(0.4,
                0.4,
                0.0000000000000000000000))

dat_stan$time[2] - (dat_stan$time[1] + dat_stan$amt[1]/dat_stan$rate[1])

fit <-
  model$sample(
    data = dat_stan,
    seed = 2022,
    chains = 1,
    iter_warmup = 1e0,
    iter_sampling = 1e0,
    parallel_chains = 1
  )
# Case 5
# Another case where it breaks and the end time of infusion is exactly at the start time of next event
dat_stan <-
  list(nt = 2,
       nSbj = 1,
       len = 2,
       amt = c(0.8, 0.0),
       cmt = c(2, 2),
       evid = c(1, 0),
       time = c(32.45833333333333570181,
                32.52430555555555713454),
       ii = c(0, 0),
       addl = c(0, 0),
       ss = c(0, 0),
       rate = c(12.12631578947368460319,
                0.00000000000000000000))

dat_stan$time[2] - (dat_stan$time[1] + dat_stan$amt[1]/dat_stan$rate[1])

fit <-
  model$sample(
    data = dat_stan,
    seed = 2022,
    chains = 1,
    iter_warmup = 1e0,
    iter_sampling = 1e0,
    parallel_chains = 1
  )

Expected Output

When it works the chains finish. Otherwise, I get the indexing error above.

Current Version:

Using the latest version of Torsten, v0.90.

Function PKModelTwoCpt not found

Hi, I am just starting with torsten and have a problem. I tried to run the twoCptModel example but got the following error. I can run simple stan code such as the 8school example. I can also find the PKModelTwoCpt.hpp file in the folder. But it just cannot compile.

SYNTAX ERROR, MESSAGE(S) FROM PARSER:

No matches for:

PKModelTwoCpt(real[], real[], real[], real[], int[], int[], int[], int[], real[], real[], real[])

Function PKModelTwoCpt not found.
error in 'model283c556e597_twoCptModel' at line 69, column 40

67:   // compartment at each event.
68:   x = PKModelTwoCpt(time, amt, rate, ii, evid, cmt, addl, ss,
69:                    theta, biovar, tlag);
                                           ^
70: 

---

Error in stanc(file = file, model_code = model_code, model_name = model_name, :
failed to parse Stan model 'twoCptModel' due to the above error.
In addition: Warning message:
In readLines(file, warn = TRUE) :
incomplete final line found on

Example cannot run using torsten

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

• CmdStanR documentation and vignettes: mc-stan.org/cmdstanr

• Use set_cmdstan_path() to set the path to CmdStan

• Use install_cmdstan() to install CmdStan

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 -D__TBBMALLOC_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 -D__TBBMALLOC_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 -D__TBBMALLOC_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 -D__TBBMALLOC_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 -D__TBBMALLOC_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 -D__TBBMALLOC_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 -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/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 -D__TBBMALLOC_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 -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/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 -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/concurrent_queue.cpp
g++ -o concurrent_vector.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/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 -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/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 -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/cache_aligned_allocator.cpp
g++ -o pipeline.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/pipeline.cpp
g++ -o queuing_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_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 -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/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 -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/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 -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/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 -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/spin_mutex.cpp
g++ -o critical_section.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/critical_section.cpp
g++ -o 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/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 -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/condition_variable.cpp
g++ -o tbb_thread.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_thread.cpp
g++ -o concurrent_monitor.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/concurrent_monitor.cpp
g++ -o semaphore.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/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 -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/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 -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 -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 -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_misc_ex.cpp
g++ -o task.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.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 -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/governor.cpp
g++ -o market.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/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 -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/scheduler.cpp
g++ -o observer_proxy.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/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 -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_main.cpp
g++ -o concurrent_vector_v2.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/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 -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/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 -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/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 -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/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 ---

[BUG] Incorrect gradient w.r.t. dosing interval "II"

Description

Gradient wrt II is incorrect when ss=1.

Example

In one-cpt test fixture, setup

  time[0] = 0.0;
  time[1] = 5.0;
  resize(2);

  amt[0] = 1200;
  amt[1] = 800;
  rate[0] = 0;
  rate[1] = 0;
  addl[0] = 2;
  addl[1] = 0;
  ii[0] = 1.4;
  ii[1] = 0.7;
  ss[0] = 1;
  ss[1] = 0;

gives wrong gradient compare to finite difference result

g[i] evaluates to 110.33698404186646,
g_fd(i) evaluates to -2807.6201142782033

Expected Output

Consistent gradient within error tolerance.

Current Version:

v0.87.1

Installation error: version '2.18.1.10' is invalid for package 'StanHeaders'

All,

I am trying to torsten within a docker image on an AWS ubuntu instance. I am getting an error regarding download issues for 'StanHeader'. Seems like version "2.18.1.10" is explicitly mentioned during installation. 2.18.1.10 seems to be a perfectly valid version for StanHeaders.

Not sure what is going on.

Thanks
ayeerr

install_torsten()
Error in download_version_url(package, version, repos, type) :
version '2.18.1.10' is invalid for package 'StanHeaders'
Calls: source ... install_torsten -> -> -> download_version_url
Execution halted
Warning message:
1 components of ... were not used.

We detected these problematic arguments:

• lib

[BUG]

I am using macOS Mojave system version 10.14.6. I am using R version 3.6.3 and cmdstan_version (2.25.0).

I have compiled and excute the Torsten examples before with no issues early today, however, now I have started receiving error massages as below:

suppressMessages(library(tidyverse))
suppressMessages(library(bayesplot))
suppressMessages(library(parallel))
library(cmdstanr)

setwd("~/Desktop/Torsten-master/example-models/pk2cpt")
set_cmdstan_path(path = file.path("..", "..", "cmdstan"))
CmdStan path set to: /Users/mg/Desktop/Torsten-master/example-models/pk2cpt/../../cmdstan

nChains <- 4
nPost <- 500 ## Number of post-burn-in samples per chain after thinning
nBurn <- 500 ## Number of burn-in samples per chain after thinning
nThin <- 1

nIter <- (nPost + nBurn) * nThin
nBurnin <- nBurn * nThin
nsample = nIter - nBurnin

file <- file.path(cmdstan_path(), "..", "example-models", "pk2cpt", "pk2cpt.stan")
model <- cmdstan_model(file)

Compiling Stan program...

Semantic error in '/var/folders/bd/xq4sxv9j3bl_j6rt1hggt3ch0000gn/T/Rtmpp29l70/model-31fb39d93132.stan', line 53, column 6 to column 65:

51:    // arrays abd returns a matrix with the predicted amount in each 
52:    // compartment at each event.
53:    x = pmx_solve_twocpt(time, amt, ii, evid, cmt, addl, ss, theta);
           ^
54:  
55:    cHat = x[2, :] ./ V1; // we're interested in the amount in the second compartment

---

Ill-typed arguments supplied to function 'pmx_solve_twocpt'. Available signatures:
(real[], real[], real[], real[], data int[], data int[], data int[], data int[], real[]) => matrix
(real[], real[], real[], real[], data int[], data int[], data int[], data int[], real[], real[]) => matrix
(real[], real[], real[], real[], data int[], data int[], data int[], data int[], real[], real[], real[]) => matrix
(real[], real[], real[], real[], data int[], data int[], data int[], data int[], real[], real[], real[,]) => matrix
(real[], real[], real[], real[], data int[], data int[], data int[], data int[], real[], real[,]) => matrix
(real[], real[], real[], real[], data int[], data int[], data int[], data int[], real[], real[,], real[]) => matrix
(real[], real[], real[], real[], data int[], data int[], data int[], data int[], real[], real[,], real[,]) => matrix
(real[], real[], real[], real[], data int[], data int[], data int[], data int[], real[,]) => matrix
(real[], real[], real[], real[], data int[], data int[], data int[], data int[], real[,], real[]) => matrix
(real[], real[], real[], real[], data int[], data int[], data int[], data int[], real[,], real[], real[]) => matrix
(real[], real[], real[], real[], data int[], data int[], data int[], data int[], real[,], real[], real[,]) => matrix
(real[], real[], real[], real[], data int[], data int[], data int[], data int[], real[,], real[,]) => matrix
(real[], real[], real[], real[], data int[], data int[], data int[], data int[], real[,], real[,], real[]) => matrix
(real[], real[], real[], real[], data int[], data int[], data int[], data int[], real[,], real[,], real[,]) => matrix
Instead supplied arguments of incompatible type: real[], real[], real[], int[], int[], int[], int[], real[].

make: *** [/var/folders/bd/xq4sxv9j3bl_j6rt1hggt3ch0000gn/T/Rtmpp29l70/model-31fb39d93132.hpp] Error 1
Error: An error occured during compilation! See the message above for more information.

I had an issue compiling mrgsolve model to simulate the data using R script in "pk2cpt" folder "pk2cpt_sim.R" but the compilation of mrgsolve model failed ,so I have reinstall mrgsolve package again and managed to simulate the data, but Torsten failed.

Unfortunately I have not saved the whole error massage from mrgsolve run but this is one line I used to search for solution for the problem:

In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:

Thank you in advance for your help.

[BUG] installation issues

I am trying to install Torsten on macOS Mojave system version 10.14.6. I am using R version 3.6.3 and rstan_2.21.2.

After downloading the folder from:
https://github.com/metrumresearchgroup/Torsten

I also tried to install Torsten by running R script “install_torsten” found in folder downloaded from https://github.com/metrumresearchgroup/TorstenHeaders
but now success and got following massages

library(rstan)
library(devtools)
devtools::load_all('TorstenHeaders')
Error in normalizePath(path, winslash = "/", mustWork = TRUE) :
path[1]="TorstenHeaders": No such file or directory
install_torsten()
Error in find.package("torstenHeaders") :
there is no package called ‘torstenHeaders’

I would be grateful if you give me some instruction on how to successfully install Torsten.

Best redards

Example run using updated torsten

@sundav05 According to error msg you've likely downloaded an old version of Torsten. To use cmdstanr as Torsten's R interface, you need the latest version. You can either re-download

git clone -b develop [email protected]:metrumresearchgroup/Torsten.git; cd Torsten

or update

cd Torsten
git checkout develop
git pull

It may also help if you can share the platform & compiler information.

Guessing that you are providing a customized cmdstan wrapper that uses libraries from a system installation of cmdstan?

cmdstanr is Stan's to-be-released R interface, and yes it's a light-weight wrapper of cmdstan. Torsten provides customized version of the following libraries in the Stan family:

• Stan Math: math kernel
• Stan: sampler
• cmdstan: command line interface
• stanc3: Stan-to-c++ transpiler.

User will be able to find these components in Torsten folder after download. cmdstanr is installed from official Stan repo. So if a Torsten can be built by cmdstan, so should it be by cmdstanr.

Originally posted by @yizhang-yiz in #26 (comment)

error in fitting one compartment model with oral dose

I tried to fit a one compartment population PK model using clinical data but I kept having warning massage. I have tried to run the two compartments population PK examples provided in this github and experienced the problem as following:

// poppk2cpt example

fit
variable mean median sd mad q5 q95 rhat ess_bulk ess_tail
lp__ 883.90 884.27 7.31 7.34 871.43 895.30 1.01 505 792
CLHat 5.03 5.03 0.04 0.04 4.96 5.10 1.00 1773 1677
QHat 8.41 8.40 0.34 0.33 7.88 9.00 1.01 1387 988
V1Hat 20.76 20.97 1.59 1.35 17.85 22.92 1.01 1245 573
V2Hat 72.27 72.16 2.16 1.92 68.86 75.85 1.00 1518 934
kaHat 1.25 1.27 0.11 0.09 1.07 1.41 1.00 1239 599
sigma 0.10 0.10 0.00 0.00 0.10 0.11 1.00 4544 1472
L[1,1] 1.00 1.00 0.00 0.00 1.00 1.00 NA NA NA
L[2,1] -0.04 -0.05 0.39 0.44 -0.65 0.62 1.00 3146 1674
L[3,1] -0.01 -0.02 0.42 0.47 -0.69 0.68 1.00 4244 1832

showing 10 of 6187 rows (change via 'max_rows' argument)

Warning messages:
1: In .subset2(x, "print")(...) : NAs introduced by coercion
2: In .subset2(x, "print")(...) : NAs introduced by coercion

I think this issue generate error massage when plotting some diagnostic plots as following:

Error: Some 'pars' don't match parameter names: CL, Q, V1, V2, ka FALSE
Run rlang::last_error() to see where the error occurred.

ggsave(file.path(figDir, "density.pdf"))
Saving 13.6 x 5.89 in image
p <- mcmc_pairs(fit$draws(), pars = c("CL", "Q", "V1", "V2", "ka", "sigma"),

•             off_diag_args = list(size = 1, alpha = 0.5))
  

Error: Some 'pars' don't match parameter names: CL, Q, V1, V2, ka FALSE
Run rlang::last_error() to see where the error occurred.

ggsave(file.path(figDir, "pair.pdf"), p, width = 10, height = 8)
Error in grid.draw(plot) : object 'p' not found

I am using Mac Pro macOS Mojave V. 10.14.6 (18G6032).

Your help appreciated.

[FEATURE] Passing fixed data as ODE parameters in pmx_solve_xxx functions

Description

Referenced in
metrumresearchgroup/math#5

Example

Quote @charlesm93 in above issue

Sometimes we want to fit a PK/PD model with fixed PK parameters. Currently however, users must pass both PK and PD parameters in the array theta. We should relax this, and allow users to pass variables in the ODE system using x_r and x_i (i.e. real and integer data). This should lead to an appreciable speed-up.

Even more so, in fact, with the mixed solver (for the Friberg-Karlsson model, the theoretical speed-up would be around 70 - 80 %). The coding shouldn't be too bad; we need to make sure we promote variables only when necessary.

The only major drawback I see (other than development effort) is that this would make the function signature heavier. It might be worth thinking about ways around it.

Expected Output

Allow users to pass variables in the ODE system using x_r and x_i (i.e. real and integer data). An example can be found at #17.

Current Version:

v0.87.1

usage of EVID

Hi,
I could not fully understand how should EVID be used when using the pmx_solve_group function family. I see from the example (twocpt_population/twocpt_population.stan) that when EVID=1 and time=0 and the output from that time is an output to x. What would happen with other EVID, for example an EVID to reset a compartment? And is it possible to use the same EVID options that in mrgsolve or is limited to NONMEM? The problem at hand that I have requires to reset some (not necessary all) compartments and add some "amt" to a few compartments, I was usign EVID=8 in mrgsolve but I could not find that solution in NONMEM manual, so step by step is there EVID=8 option available in pmx_solve_group?

Just to clarify I can "implement" EVID=8 type solution by hand using pmx_integrate_ode. But it would be nice and neat (and fast) to have an implementation of EVID=8 in pmx_solve_group so it would be easy to use also with that family of functions.

Just also linking the doc of mrgsolve for this specific usage case:
https://mrgsolve.github.io/user_guide/input-data-sets.html

[BUG] steady state functor uses default integrator controls params

Description

Currently integrators within SS adaptor uses default constructor, so the effect of ODE controls do not propagate into steady state functor definition.

Example

In PMXOdeFunctorSSAdaptor definition there's

    operator()(const Eigen::Matrix<T0, Eigen::Dynamic, 1>& x,
               const Eigen::Matrix<T1, Eigen::Dynamic, 1>& y,
               const std::vector<double>& x_r,
               const std::vector<int>& x_i,
               std::ostream* msgs) const {
//....
      const PMXOdeIntegrator<It> integrator_;

Expected Output

The integrator_ should use pmx_solve_xxx's ODE control param for construction.

Current Version:

v0.87.1

Problem Running MPI on Metworx

I'm currently running Torsten v0.90.0 on Metrum's Metworx platform on a cluster, but I'm not sure if MPI is working. I've adding the following to Torsten/cmdstan/make/local

TORSTEN_MPI=1
TBB_CXX_TYPE=gcc
CXXFLAGS += -isystem /usr/local/include
CXXFLAGS += -isystem /usr/local/mpich3/include

I'm able to compile and run the twocpt_population.stan example using mod$sample_mpi() in cmdstanr, but I don't get any speedup from increasing n in the mpi_args = list("n" = 1) argument. Furthermore, when I set n=8 I get the following error:

Chain 1 Fatal error in PMPI_Test: Other MPI error, error stack:
Chain 1 PMPI_Test(174).................: MPI_Test(request=0x564c49888a60, flag=0x7ffe48c9b8bc, status=0x1) failed
Chain 1 MPIR_Test_impl(67).............: 
Chain 1 MPIDU_Sched_progress_state(961): Invalid communicator
Chain 1 Fatal error in PMPI_Test: Other MPI error, error stack:
Chain 1 PMPI_Test(174).................: MPI_Test(request=0x556df4feedd0, flag=0x7ffe7597d47c, status=0x1) failed
Chain 1 MPIR_Test_impl(67).............: 
Chain 1 MPIDU_Sched_progress_state(961): Invalid communicator
Warning: Chain 1 finished unexpectedly!

Warning messages:
1: In mod$sample_mpi(data = file.path(file.dir, "twocpt_population.data.R"),  :
  'validate_csv' is deprecated. Please use 'diagnostics' instead.
2: No chains finished successfully. Unable to retrieve the fit. 

Any ideas what could be going wrong? @yizhang-yiz

installation issue

My Rtools40 is missing mingw32-make. I tried to run the following check_cmdstan commands and it didn't work.

check_cmdstan_toolchain()
Error:
RTools installation found but PATH was not properly set.
Run check_cmdstan_toolchain(fix = TRUE) to fix the issue.
check_cmdstan_toolchain(fix = TRUE)
Installing mingw32-make and writing RTools path to ~/.Renviron ...
Error in processx::run("pacman", args = c("-Syu", "mingw-w64-x86_64-make", :
System command 'pacman' failed, exit status: 1, stderr (last 10 lines):
E> error: failed to update mingw32 (download library error)
E> error: failed retrieving file 'mingw64.db' from cloud.r-project.org : SSL certificate problem: unable to get local issuer certificate
E> error: failed retrieving file 'mingw64.db' from cran.r-project.org : SSL certificate problem: unable to get local issuer certificate
E> error: failed retrieving file 'mingw64.db' from r-windows.github.io : SSL certificate problem: unable to get local issuer certificate
E> error: failed to update mingw64 (download library error)
E> error: failed retrieving file 'ucrt64.db' from cloud.r-project.org : SSL certificate problem: unable to get local issuer certificate
E> error: failed retrieving file 'ucrt64.db' from cran.r-project.org : SSL certificate problem: unable to get local issuer certificate
E> error: failed retrieving file 'ucrt64.db' from r-windo

I realized it may be due to the computer being company restricted. Therefore I called IT and asked them to sign in as admin. As R-studio was installed under my account and wouldn't run in admin account, I used Rtools bash to run the following command to install mingw32-make

pacman -Syu mingw-w64-X86_64-make.

It seems to be installing all right, all process reporting 100% installation. However after IT logged off, I came back to my own account, the same issue persisted. and I couldn't find where the ingw32-make was installed.

I tried the following command which showed that it still can't find mingw32-make. Now what should I do? Should I ask IT to log in as admin, reinstall Rtools40 and Rstudio as admin then set up the toolchain using "check_cmdstan_toolchain(fix = TRUE)" in R?
Is there a quick fix to find out why the installation for mingw32-make under admin didn't work when I logged back into my account? Many thanks.

Sys.which("make")
make
"C:\Users\zhup3107\DOCUME1\rtools40\rtools40\usr\bin\make.exe"
system('mingw32-make -v')
[1] 127
system('g++ -v')
Using built-in specs.
COLLECT_GCC=C:\Users\zhup3107\DOCUME1\rtools40\rtools40\mingw64\bin\G__1.EXE
COLLECT_LTO_WRAPPER=C:/Users/zhup3107/DOCUME1/rtools40/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/lto-wrapper.exe
Target: x86_64-w64-mingw32
Configured with: ../gcc-8.3.0/configure --prefix=/mingw64 --with-local-prefix=/mingw64/local --build=x86_64-w64-mingw32 --host=x86_64-w64-mingw32 --target=x86_64-w64-mingw32 --with-native-system-header-dir=/mingw64/x86_64-w64-mingw32/include --libexecdir=/mingw64/lib --enable-bootstrap --with-arch=x86-64 --with-tune=generic --enable-languages=c,lto,c++,fortran --disable-shared --enable-static --enable-libatomic --enable-threads=posix --enable-graphite --enable-fully-dynamic-string --enable-libstdcxx-filesystem-ts=yes --enable-libstdcxx-time=yes --disable-libstdcxx-pch --disable-libstdcxx-debug --disable-isl-version-check --enable-lto --enable-libgomp --disable-multilib --enable-checking=release --disable-rpath --disable-win32-registry --disable-nls --disable-werror --disable-symvers --with-libiconv --with-system-zlib --with-gmp=/mingw64 --with-mpfr=/mingw64 --with-mpc=/mingw64 --with-isl=/mingw64 --with-pkgversion='Built by Jeroen for the R-project' --with-bugurl=https://github.com/r-windows --with-gnu-as --with-gnu-ld
Thread model: posix
gcc version 8.3.0 (Built by Jeroen for the R-project)
[1] 0

cmdstanr cannot load Torsten path from the user guide

I have attempted to install Torsten, but I am having trouble. Can you please help?

I have successfully installed cmdstan:
cmdstan_path()
[1] "C:/Users/Cathrine Leonowens/Documents/.cmdstan/cmdstan-2.29.2"

check_cmdstan_toolchain()
The C++ toolchain required for CmdStan is setup properly!

And RStan is correctly installed (tested using the code here: )

When I run the following code from your installation instructions ():
cmdstanr::set_cmdstan_path("Torsten/cmdstan")
I get the following error:
Warning message:
Path not set. Can't find directory: Torsten/cmdstan

When I re-check the path for cmdstan, I get the correct path:
cmdstan_path()
[1] "C:/Users/Cathrine Leonowens/Documents/.cmdstan/cmdstan-2.29.2"

Current Version:

R: 4.1.3
RStudio: 2022.02.1 Build 461, "Prairie Trillium" Release (8aaa5d47, 2022-03-17) for Windows
cmdstan:2.29.2
Rstan: 2.21.0
rtools: 4.0.3.0

Am I missing a step?

OpenSSL: error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version[BUG]

Description

Executing source(install.R) from R console to install torsten resulted with SSL error.
Our SUSE 11.4 does not support this due to outdated version may be.

Example

source('install.R')
Loading required package: usethis
Loading torstenHeaders
Error in open.connection(x, "rb") :
error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version

The above error is reported while trying to install. by checking the files inside the TorstenHeaders folder, noticed that https://github.com are used in the script.

Just manually trying to call this site result same error.

wget https://github.com/metrumresearchgroup/TorstenHeaders/tree/master/inst
--2019-09-04 11:44:11-- https://github.com/metrumresearchgroup/TorstenHeaders/tree/master/inst
Resolving github.com... 140.82.118.3
Connecting to github.com|140.82.118.3|:443... connected.
OpenSSL: error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
Unable to establish SSL connection.

Expected Output

Other site, example CRAN works well.

wget http://cran.r-project.org/web/packages/
--2019-09-04 11:44:49-- http://cran.r-project.org/web/packages/
Resolving cran.r-project.org... 137.208.57.37
Connecting to cran.r-project.org|137.208.57.37|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3070 (3.0K) [text/html]
Saving to: `index.html'

100%[===============================================================================================>] 3,070 --.-K/s in 0s

2019-09-04 11:44:50 (118 MB/s) - `index.html' saved [3070/3070].

Troubleshooting:
We have upgraded to openssl version to latest 1.1.1c & git 2.9.5

Can you kindly let us know what binary needs upgrade OR please provide an offline installation package

Current Version:

v0.87.1

[BUG] installation failed

Description

Hi there! I'm trying to use Torsten since I want to do a PKPD project.
I got the idea that Torsten needs cmdstan and then cmdstandr to work. And i suppose i need the stan that's inside Torsten's repository and I install from there. So i go:
cd C:\Torsten\cmdstan

However, I failed to install the Stan with mingw32:

Information:

Before this, I installed MinGW for mingw32 to work.

Current Version:

v0.87.1

Error in Instalation

I tried to install Torsten. Then I download Git by zipn file from https://github.com/metrumresearchgroup/Torsten.git.
and unfreeze by Lhaplus.
After unfreezing, I excused following code on Rstudio.

devtools::load_all('Torsten_master/TorstenHeaders')

but next error come out

"
Error in utils::unzip(file.path(td, "math.zip"), exdir = td) :
cannot open file 'C:/Users/kano/AppData/Local/Temp/RtmpSqZq6g/torsten/math-157f5f950191216a860817b5fa5696c54288c14d/lib/boost_1.69.0/doc/html/boost_asio/reference/async_result_lt__std__packaged_task_lt__Result_lp_Args_ellipsis__rp__gt__comma__Signature__gt_/completion_handler_type.html': No such file or directory
5. utils::unzip(file.path(td, "math.zip"), exdir = td) at zzz.R#35
4. nsenv[[f_name]](dirname(ns_path), package)
3. run_pkg_hook(package, "load")
2. pkgload::load_all(path = path, reset = reset, recompile = recompile,
export_all = export_all, helpers = helpers, quiet = quiet,
...)

1. devtools::load_all("Torsten_master/TorstenHeaders")
   "

Actually, I cant find "completion_handler_type.html" in the folder but find "async_result.html" in that folder.

What can I do to install torsten?

I use windows10, gcc 4.9.3, rstan 2.19.2, R x64 3.5.3 and Rstudio1.1.453

thank you.

[BUG] Function pmx_solve_twocpt not found.

First I should mention that I really do not know if this is really a bug of the code. Probably it is not.

After installation, I am trying to run the example "https://github.com/metrumresearchgroup/torsten_stancon_2019_tutorial/blob/master/RScripts/twoCptPopModel.r" but when I do that, I am getting the following error when run the fit <- stan(file = ...):

SYNTAX ERROR, MESSAGE(S) FROM PARSER:
No matches for:

pmx_solve_twocpt(real[ ], real[ ], real[ ], real[ ], int[ ], int[ ], int[ ], int[ ], real[ ], real[ ], real[ ])

Function pmx_solve_twocpt not found.
error in 'model1a9761637faef_twoCptPopulationModel' at line 64, column 72

62:                                                addl[start[j]:end[j]],
63:                                                ss[start[j]:end[j]],
64:                                                theta[j, ], biovar, tlag);
                                                                           ^
65: 

---

I am using RStudio 2021.9.1 in Ubuntu 20.04. I have installed rstan, cmdstan and I also downloaded Torsten via git clone. I have performed the steps bellow, and in it everything looks fine.

cd Torsten/cmdstan/
make build
make ../example-models/pk2cpt/pk2cpt

Many thanks for your support.

example-models: format and inconsistency with User Manual

Currently the examples in Torsten/example-models vary in format and the examples intended to match with the User Manual are not fully consistent with the manual text.

I propose that the examples be more self-contained within their respective folders rather than spread between the example folder and the R folder (with the exception of shared function scripts like stanTools.R). The User Manual text and the corresponding examples should also be realigned to match.

[BUG]

Hello,
It is me again with the same error encountered the running
“ GenTwoCptModel.stan” and “LinTwoCptModel.stan"

Hello it is me again with the same error encountered the running
Semantic error in “ GenTwoCptModel.stan” and “LinTwoCptModel.stan"

'/var/folders/bd/xq4sxv9j3bl_j6rt1hggt3ch0000gn/T/Rtmpp29l70/model-31fb794415be.stan', line 106, column 7 to line 109, column 43:

104: // 1e-8, 1e-8, 1e8);
105:
106: x = generalOdeModel_rk45(twoCptModelODE, 3,
^
107: time, amt, rate, ii, evid, cmt, addl, ss,
108: theta, biovar, tlag,

A returning function was expected but an undeclared identifier 'generalOdeModel_rk45' was supplied.

Semantic error in '/var/folders/bd/xq4sxv9j3bl_j6rt1hggt3ch0000gn/T/Rtmpp29l70/model-31fb794415be.stan', line 106, column 7 to line 109, column 43:

104: // 1e-8, 1e-8, 1e8);
105:
106: x = generalOdeModel_rk45(twoCptModelODE, 3,
^
107: time, amt, rate, ii, evid, cmt, addl, ss,
108: theta, biovar, tlag,

A returning function was expected but an undeclared identifier 'generalOdeModel_rk45' was supplied.

make: *** [/var/folders/bd/xq4sxv9j3bl_j6rt1hggt3ch0000gn/T/Rtmpp29l70/model-31fb794415be.hpp] Error 1
make: *** [/var/folders/bd/xq4sxv9j3bl_j6rt1hggt3ch0000gn/T/Rtmpp29l70/model-31fb794415be.hpp] Error 1
Error: An error occured during compilation! See the message above for more information.

Semantic error in '/var/folders/bd/xq4sxv9j3bl_j6rt1hggt3ch0000gn/T/Rtmpp29l70/model-31fb4f99fc66.stan', line 68, column 6 to line 69, column 34:

66:    // contains the biovariability fraction and the lag time of each compartment,
67:    // and the NONMEM data.
68:    x = linOdeModel(time, amt, rate, ii, evid, cmt, addl, ss,
           ^
69:                    K, biovar, tlag);
70:    cHat = col(x, 2) ./ V1;

---

A returning function was expected but an undeclared identifier 'linOdeModel' was supplied.

make: *** [/var/folders/bd/xq4sxv9j3bl_j6rt1hggt3ch0000gn/T/Rtmpp29l70/model-31fb4f99fc66.hpp] Error 1

Semantic error in '/var/folders/bd/xq4sxv9j3bl_j6rt1hggt3ch0000gn/T/Rtmpp29l70/model-31fb4f99fc66.stan', line 68, column 6 to line 69, column 34:

66:    // contains the biovariability fraction and the lag time of each compartment,
67:    // and the NONMEM data.
68:    x = linOdeModel(time, amt, rate, ii, evid, cmt, addl, ss,
           ^
69:                    K, biovar, tlag);
70:    cHat = col(x, 2) ./ V1;

---

A returning function was expected but an undeclared identifier 'linOdeModel' was supplied.

make: *** [/var/folders/bd/xq4sxv9j3bl_j6rt1hggt3ch0000gn/T/Rtmpp29l70/model-31fb4f99fc66.hpp] Error 1
Error: An error occured during compilation! See the message above for more information.

Semantic error in '/var/folders/bd/xq4sxv9j3bl_j6rt1hggt3ch0000gn/T/Rtmpp29l70/model-31fb689b55e.stan', line 106, column 7 to line 109, column 43:

104: // 1e-8, 1e-8, 1e8);
105:
106: x = generalOdeModel_rk45(twoCptModelODE, 3,
^
107: time, amt, rate, ii, evid, cmt, addl, ss,
108: theta, biovar, tlag,

A returning function was expected but an undeclared identifier 'generalOdeModel_rk45' was supplied.

Semantic error in '/var/folders/bd/xq4sxv9j3bl_j6rt1hggt3ch0000gn/T/Rtmpp29l70/model-31fb689b55e.stan', line 106, column 7 to line 109, column 43:

104: // 1e-8, 1e-8, 1e8);
105:
106: x = generalOdeModel_rk45(twoCptModelODE, 3,
^
107: time, amt, rate, ii, evid, cmt, addl, ss,
108: theta, biovar, tlag,

A returning function was expected but an undeclared identifier 'generalOdeModel_rk45' was supplied.

make: *** [/var/folders/bd/xq4sxv9j3bl_j6rt1hggt3ch0000gn/T/Rtmpp29l70/model-31fb689b55e.hpp] Error 1
make: *** [/var/folders/bd/xq4sxv9j3bl_j6rt1hggt3ch0000gn/T/Rtmpp29l70/model-31fb689b55e.hpp] Error 1
Error: An error occured during compilation! See the message above for more information.

Change in README to link MPICH installation page[DOC]

Description

The first look into MPI might be a bit challenging.

Expected documentation

I found this tutorial https://mpitutorial.com/tutorials/ very enlightening.

I would recommend to link in README the MPICH download page.
https://www.mpich.org/downloads/

Current Version:

v0.87.1

Manual: correct function signatures

Main issues

The signature of Torsten functions is inaccurate. Torsten functions return a matrix, not a 2-d or 1-d array, as indicated in the user manual.

Also the user manual under the example-models directory is different from the user manual in the doc directory. I propose to remove the former, and only keep the latter.

Other issues

I'll also proofread the manual, correct minor typos, and add certain missing references.

Another issue is the examples: they do not take advantage of new syntax features which would make the code significantly shorter. Based on @yizhang-cae 's comment in issue #4 this problem can be addressed by directly modifying the examples. I'm happy to do it, using the code I developed for the Torsten workshop at U. Buffalo. That said, I'd rather avoid interfering with some of the restructuring @billgillespie may be working on.

Finally, there is the technical appendix (for a draft, see https://github.com/charlesm93/presentations/blob/master/TorstenAppendix/Torsten_appendix.pdf), but this is less an issue than a milestone for releasing Torsten v1.0.

How to verify

Whoever reviews the pull request will need to:

• proofread the user manual.
• rerun the example code.

Installation problems

Hi

I am trying to install the torsten and followed the procedure outlined in the torsten manual. I downloaded the torsten_master as a zip file. In R, I setwd-ed to the Torsten-master folder and tried to install torsten using source('install.R').

I am getting a following error. Anyone has an idea of how I can circumvent this.

Thanks
rajavenks

Torsten_Error_051818.txt

TAD time after dose

Description

Hi, I wanted to know if it is possible to implement an example of how to use time after dose (TAD) in the ODE function with the pmx_solve utilities in Stan/Torsten.

Example

If I need to calculate a parameter that is a function of TAD for example:

FOO = 1 + FOO0 * exp(-BETA * TAD)

Expected Output

Something like the self.tad that can be used in mrgsolve would be just what's needed:

2.3.20 in https://mrgsolve.org/user_guide/model-specification.html

$MAIN

double TAD = self.tad();

Current Version:

v0.87.1

Thanks

Installation test fails on one occation

I was able to install torsten and it all went well. However when testing the installation there one test that fails (line 78 shows the error). Is there some configuration that could be changed to make this error free ?

Thanks in advance.
ri

result_model.txt