error: in call to ‘sample’

[Angel Berihuete]

Hi everyone!

I am trying to install Stan in the computer cluster of my University. Apparently the installation was done without errors (some warnings). Also the sentence 

bin/stanc --name=bernoulli --o=bernoulli.cpp src/models/basic_estimators/bernoulli.stan

works without errors. But then something wrong happens:

g++ -O3 -Lbin -Isrc -Ilib/boost_1.54.0 -Ilib/eigen_3.2.0 src/models/basic_estimators/bernoulli.cpp -o bernoulli -lstan

In file included from src/stan/model/model_header.hpp:20,

                 from src/models/basic_estimators/bernoulli.cpp:3:

src/stan/mcmc/sample.hpp: In function ‘int stan::gm::command(int, const char**) [with Model = bernoulli_model_namespace::bernoulli_model]’:

src/models/basic_estimators/bernoulli.cpp:273:   instantiated from here

src/stan/mcmc/sample.hpp:11: error: ‘class stan::mcmc::sample’ is not a function,

src/stan/gm/command.hpp:157: error:   conflict with ‘template<class Model, class RNG> void stan::gm::sample(stan::mcmc::base_mcmc*, int, int, int, int, bool, stan::io::mcmc_writer<Model>&, stan::mcmc::sample&, Model&, RNG&)’

src/stan/gm/command.hpp:887: error:   in call to ‘sample’ 

Any help would be welcome

Best regards

Angel

[Bob Carpenter]

On 10/18/13 11:14 AM, Angel Berihuete wrote:
> Hi everyone!
>
> I am trying to install Stan in the computer cluster of my University. Apparently the installation was done without
> errors (some warnings). Also the sentence
>

> /bin/stanc --name=bernoulli --o=bernoulli.cpp src/models/basic_estimators/bernoulli.stan

This writes bernoulli.cpp in the current directory.

> works without errors. But then something wrong happens:

> /g++ -O3 -Lbin -Isrc -Ilib/boost_1.54.0 -Ilib/eigen_3.2.0 src/models/basic_estimators/bernoulli.cpp -o //bernoulli -lstan/

whereas this one looks for the .cpp file here
src/models/basic_estimators/bernoulli.cpp

We just checked the manual, and it looks like the instructions
there are correct.

- Bob

[Jonathan French]

I get the same error messages when I try to compile the bernoulli model.

I've installed stan under Ubuntu with make version 3.81 and g++ version 4.4.3.  I don't seem to have any issues with the installation and the translation to C++ seems fine.  The error is when I compile.  

Was there a solution to this issue?

Thanks

Jonathan

[Daniel Lee]

On Thu, Nov 7, 2013 at 11:07 AM, Jonathan French <jona...@metrumrg.com> wrote:

I get the same error messages when I try to compile the bernoulli model.

I've installed stan under Ubuntu with make version 3.81 and g++ version 4.4.3.  I don't seem to have any issues with the installation and the translation to C++ seems fine.  The error is when I compile.  

Was there a solution to this issue?

Yes, the issue is a user error. Bob explained in his email, but I'll give it another try. If you want to be less error prone, try using the makefiles provided. For help, just type 'make' on the command line and it'll show you an example of how to compile the normal model.

I'll assume that bin/stanc has been built. This line translates from a Stan model 'src/models/basic_estimators/bernoulli.stan' and generates a C++ file in './bernoulli.cpp':

> bin/stanc --name=bernoulli --o=bernoulli.cpp src/models/basic_estimators/bernoulli.stan

This line is incorrect because it is trying to compile the C++ file in './src/models/basic_estimators/bernoulli.cpp'

> g++ -O3 -Lbin -Isrc -Ilib/boost_1.54.0 -Ilib/eigen_3.2.0 src/models/basic_estimators/bernoulli.cpp -o bernoulli -lstan

To fix it, it should be:
> g++ -O3 -Lbin -Isrc -Ilib/boost_1.54.0 -Ilib/eigen_3.2.0 bernoulli.cpp -o bernoulli -lstan

Hopefully that fixes your problem.

On Friday, October 18, 2013 11:14:03 AM UTC-4, Angel Berihuete wrote:

Hi everyone!

I am trying to install Stan in the computer cluster of my University. Apparently the installation was done without errors (some warnings). Also the sentence 

bin/stanc --name=bernoulli --o=bernoulli.cpp src/models/basic_estimators/bernoulli.stan

works without errors. But then something wrong happens:

g++ -O3 -Lbin -Isrc -Ilib/boost_1.54.0 -Ilib/eigen_3.2.0 src/models/basic_estimators/bernoulli.cpp -o bernoulli -lstan

In file included from src/stan/model/model_header.hpp:20,

                 from src/models/basic_estimators/bernoulli.cpp:3:

src/stan/mcmc/sample.hpp: In function ‘int stan::gm::command(int, const char**) [with Model = bernoulli_model_namespace::bernoulli_model]’:

src/models/basic_estimators/bernoulli.cpp:273:   instantiated from here

src/stan/mcmc/sample.hpp:11: error: ‘class stan::mcmc::sample’ is not a function,

src/stan/gm/command.hpp:157: error:   conflict with ‘template<class Model, class RNG> void stan::gm::sample(stan::mcmc::base_mcmc*, int, int, int, int, bool, stan::io::mcmc_writer<Model>&, stan::mcmc::sample&, Model&, RNG&)’

src/stan/gm/command.hpp:887: error:   in call to ‘sample’ 

Any help would be welcome

Best regards

Angel

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[Jonathan French]

Daniel,

Thanks for the reply.  It probably is an error on my part, but I get the same errors when I run directly using make.  Using the example in make help, I get:

/data/stan# make src/models/basic_distributions/normal


--- Translating Stan model to C++ code ---
bin/stanc src/models/basic_distributions/normal.stan --o=src/models/basic_distributions/normal.cpp
Model name=normal_model
Input file=src/models/basic_distributions/normal.stan
Output file=src/models/basic_distributions/normal.cpp
g++ -I src -isystem lib/eigen_3.2.0 -isystem lib/boost_1.54.0 -Wall -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -c -O3 -o src/models/basic_distributions/normal.o src/models/basic_distributions/normal.cpp

In file included from src/stan/model/model_header.hpp:20,

from src/models/basic_distributions/normal.cpp:3:
src/stan/mcmc/sample.hpp: In function ‘int stan::gm::command(int, const char**) [with Model = normal_model_namespace::normal_model]’:
src/models/basic_distributions/normal.cpp:241: instantiated from here

src/stan/mcmc/sample.hpp:11: error: ‘class stan::mcmc::sample’ is not a function,
src/stan/gm/command.hpp:157: error: conflict with ‘template<class Model, class RNG> void stan::gm::sample(stan::mcmc::base_mcmc*, int, int, int, int, bool, stan::io::mcmc_writer<Model>&, stan::mcmc::sample&, Model&, RNG&)’

src/stan/gm/command.hpp:904: error: in call to ‘sample’
src/stan/math/constants.hpp: At global scope:
src/stan/math/constants.hpp:63: warning: ‘stan::math::NEGATIVE_EPSILON’ defined but not used
src/stan/agrad/rev/var_stack.hpp:49: warning: ‘void stan::agrad::free_memory()’ defined but not used
make: *** [src/models/basic_distributions/normal.o] Error 1

[Daniel Lee]

Ok. There's definitely a problem. The g++ line is missing the options specifying the stan library. The g++ line above should be:
g++ -I src -isystem lib/eigen_3.2.0 -isystem lib/boost_1.54.0 -Wall -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -c -O3 -o src/models/basic_distributions/normal.o src/models/basic_distributions/normal.cpp -Lbin -lstan

Would you mind trying that from the command line and seeing if that succeeds?

Just to double check, you're still on:

Ubuntu with make version 3.81 and g++ version 4.4.3

Can you type "make" on the command line and paste the top portion? The LDLIBS variable should be set to "-Lbin -lstan", but it looks like that has been erased somehow.

Daniel

On Thu, Nov 7, 2013 at 12:38 PM, Jonathan French <jona...@metrumrg.com> wrote:

Daniel,

Thanks for the reply.  It probably is an error on my part, but I get the same errors when I run directly using make.  Using the example in make help, I get:

/data/stan# make src/models/basic_distributions/normal


--- Translating Stan model to C++ code ---
bin/stanc src/models/basic_distributions/normal.stan --o=src/models/basic_distributions/normal.cpp
Model name=normal_model
Input file=src/models/basic_distributions/normal.stan
Output file=src/models/basic_distributions/normal.cpp
g++ -I src -isystem lib/eigen_3.2.0 -isystem lib/boost_1.54.0 -Wall -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -c -O3 -o src/models/basic_distributions/normal.o src/models/basic_distributions/normal.cpp

In file included from src/stan/model/model_header.hpp:20,

from src/models/basic_distributions/normal.cpp:3:
src/stan/mcmc/sample.hpp: In function ‘int stan::gm::command(int, const char**) [with Model = normal_model_namespace::normal_model]’:
src/models/basic_distributions/normal.cpp:241: instantiated from here

src/stan/mcmc/sample.hpp:11: error: ‘class stan::mcmc::sample’ is not a function,
src/stan/gm/command.hpp:157: error: conflict with ‘template<class Model, class RNG> void stan::gm::sample(stan::mcmc::base_mcmc*, int, int, int, int, bool, stan::io::mcmc_writer<Model>&, stan::mcmc::sample&, Model&, RNG&)’

src/stan/gm/command.hpp:904: error: in call to ‘sample’
src/stan/math/constants.hpp: At global scope:
src/stan/math/constants.hpp:63: warning: ‘stan::math::NEGATIVE_EPSILON’ defined but not used
src/stan/agrad/rev/var_stack.hpp:49: warning: ‘void stan::agrad::free_memory()’ defined but not used
make: *** [src/models/basic_distributions/normal.o] Error 1

On Thursday, November 7, 2013 11:56:01 AM UTC-5, Daniel Lee wrote:

On Thu, Nov 7, 2013 at 11:07 AM, Jonathan French <jona...@metrumrg.com> wrote:

I get the same error messages when I try to compile the bernoulli model.

I've installed stan under Ubuntu with make version 3.81 and g++ version 4.4.3.  I don't seem to have any issues with the installation and the translation to C++ seems fine.  The error is when I compile.  

Was there a solution to this issue?

Yes, the issue is a user error. Bob explained in his email, but I'll give it another try. If you want to be less error prone, try using the makefiles provided. For help, just type 'make' on the command line and it'll show you an example of how to compile the normal model.

I'll assume that bin/stanc has been built. This line translates from a Stan model 'src/models/basic_estimators/bernoulli.stan' and generates a C++ file in './bernoulli.cpp':

> bin/stanc --name=bernoulli --o=bernoulli.cpp src/models/basic_estimators/bernoulli.stan

This line is incorrect because it is trying to compile the C++ file in './src/models/basic_estimators/bernoulli.cpp'
> g++ -O3 -Lbin -Isrc -Ilib/boost_1.54.0 -Ilib/eigen_3.2.0 src/models/basic_estimators/bernoulli.cpp -o bernoulli -lstan

To fix it, it should be:
> g++ -O3 -Lbin -Isrc -Ilib/boost_1.54.0 -Ilib/eigen_3.2.0 bernoulli.cpp -o bernoulli -lstan

Hopefully that fixes your problem.

[Daniel Lee]

Hang on -- that wasn't quite right. Could you paste the result of "make" from the command line?

[Jonathan French]

Yes, I'm still on the same system.  The top portion of the make output is

Stan makefile:

  Current configuration:

  - OS (Operating System):    linux

  - CC (Compiler):            g++

  - Compiler version:         4.4

  - O (Optimization Level):   3

  - O_STANC (Opt for stanc):  0

  - STAN_HOME                 ./

  Library configuration:

  - EIGEN                     lib/eigen_3.2.0

  - BOOST                     lib/boost_1.54.0

  - GTEST                     lib/gtest_1.7.0

The g++ line still returns the same errors as before:

/data/stan# g++ -I src -isystem lib/eigen_3.2.0 -isystem lib/boost_1.54.0 -Wall -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -c -O3 -o src/models/basic_distributions/normal.o src/models/basic_distributions/normal.cpp -Lbin -lstan

In file included from src/stan/model/model_header.hpp:20,

                 from src/models/basic_distributions/normal.cpp:3:

src/stan/mcmc/sample.hpp: In function ‘int stan::gm::command(int, const char**) [with Model = normal_model_namespace::normal_model]’:

src/models/basic_distributions/normal.cpp:241:   instantiated from here

src/stan/mcmc/sample.hpp:11: error: ‘class stan::mcmc::sample’ is not a function,

src/stan/gm/command.hpp:157: error:   conflict with ‘template<class Model, class RNG> void stan::gm::sample(stan::mcmc::base_mcmc*, int, int, int, int, bool, stan::io::mcmc_writer<Model>&, stan::mcmc::sample&, Model&, RNG&)’

src/stan/gm/command.hpp:904: error:   in call to ‘sample’

src/stan/math/constants.hpp: At global scope:

src/stan/math/constants.hpp:63: warning: ‘stan::math::NEGATIVE_EPSILON’ defined but not used

src/stan/agrad/rev/var_stack.hpp:49: warning: ‘void stan::agrad::free_memory()’ defined but not used

Thanks,

Jonathan

[Daniel Lee]

Do you happen to have another compiler installed? I'm trying to install g++ 4.4 on my Mac (hopefully they're compatible). That error message looks like the compiler is having some trouble -- I'll do what I can to reproduce the issue on my end.

Daniel

[Daniel Lee]

I just verified that it doesn't compile using g++ v4.4.

I get the same error novel. Do you have access to a different compiler? I don't have time to hunt down what is incompatible with g++ 4.4 right now, but hopefully one of us can get to it soon.

Daniel

[Daniel Lee]

I just created an issue for it, if you wanted to track progress. #375: https://github.com/stan-dev/stan/issues/375

[Jonathan French]

Thanks, Daniel.  We can update our compiler to a newer version.  That sounds like it will probably solve the issue.

Thanks again

Jonathan