build failures

[Ben Goodrich]

I'm trying to sync rstan up with develop and running into some build failures. With clang++-3.7 or a recent g++, I get

** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/tmp/Rtmp9XgAUX/Rinst40966385420f/rstan/libs/rstan.so':
  /tmp/Rtmp9XgAUX/Rinst40966385420f/rstan/libs/rstan.so: undefined symbol: _ZN4stan4lang15indexes_grammarIN5boost6spirit17line_pos_iteratorINSt3__111__wrap_iterIPKcEEEEEC1ERNS0_12variable_mapERNS5_18basic_stringstreamIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS0_18expression_grammarISA_EE
Error: loading failed

With clang++-3.8, I get an error earlier but that might be related

clang++-3.8 -std=c++11 -stdlib=libc++ -I/usr/share/R/include -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"`"/usr/lib/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/StanHeaders/include"   -fpic  -O2 -D_FORTIFY_SOURCE=2 -Wno-unused-variable -Wno-unused-function -Wno-unused-local-typedefs -c lang__grammars__expression07_grammar_inst.cpp -o lang__grammars__expression07_grammar_inst.o
In file included from chains.cpp:19:
In file included from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/mean.hpp:4:
In file included from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Dense:1:
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:28:
In file included from /usr/include/c++/v1/complex:247:
In file included from /usr/include/c++/v1/sstream:174:
In file included from /usr/include/c++/v1/ostream:138:
In file included from /usr/include/c++/v1/ios:216:
In file included from /usr/include/c++/v1/__locale:15:
/usr/include/c++/v1/string:1938:44: error: 'basic_string<_CharT, _Traits, _Allocator>' is missing exception specification 'noexcept(is_nothrow_copy_constructible<allocator_type>::value)'
basic_string<_CharT, _Traits, _Allocator>::basic_string(const allocator_type& __a)
                                           ^
/usr/include/c++/v1/string:1326:40: note: previous declaration is here
    _LIBCPP_INLINE_VISIBILITY explicit basic_string(const allocator_type& __a)
                                       ^
In file included from lang__ast_def.cpp:18:
In file included from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/lang/ast_def.cpp:5:
In file included from /usr/local/lib/R/site-library/BH/include/boost/variant/recursive_variant.hpp:36:
In file included from /usr/local/lib/R/site-library/BH/include/boost/variant/variant.hpp:21:
In file included from /usr/local/lib/R/site-library/BH/include/boost/type_index.hpp:29:
In file included from /usr/local/lib/R/site-library/BH/include/boost/type_index/stl_type_index.hpp:22:
In file included from /usr/local/lib/R/site-library/BH/include/boost/type_index/type_index_facade.hpp:14:
/usr/include/c++/v1/string:1938:44: error: 'basic_string<_CharT, _Traits, _Allocator>' is missing exception specification 'noexcept(is_nothrow_copy_constructible<allocator_type>::value)'
basic_string<_CharT, _Traits, _Allocator>::basic_string(const allocator_type& __a)
                                           ^
/usr/include/c++/v1/string:1326:40: note: previous declaration is here
    _LIBCPP_INLINE_VISIBILITY explicit basic_string(const allocator_type& __a)
                                       ^
In file included from lang__grammars__expression07_grammar_inst.cpp:18:
In file included from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression07_grammar_inst.cpp:1:
In file included from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression07_grammar_def.hpp:4:
In file included from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast.hpp:32:
In file included from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:26:
/usr/include/c++/v1/string:1938:44: error: 'basic_string<_CharT, _Traits, _Allocator>' is missing exception specification 'noexcept(is_nothrow_copy_constructible<allocator_type>::value)'
basic_string<_CharT, _Traits, _Allocator>::basic_string(const allocator_type& __a)
                                           ^
/usr/include/c++/v1/string:1326:40: note: previous declaration is here
    _LIBCPP_INLINE_VISIBILITY explicit basic_string(const allocator_type& __a)
                                       ^
In file included from lang__grammars__bare_type_grammar_inst.cpp:18:
In file included from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/bare_type_grammar_inst.cpp:1:
In file included from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/bare_type_grammar_def.hpp:4:
In file included from /usr/local/lib/R/site-library/BH/include/boost/spirit/include/qi.hpp:16:
In file included from /usr/local/lib/R/site-library/BH/include/boost/spirit/home/qi.hpp:14:
In file included from /usr/local/lib/R/site-library/BH/include/boost/spirit/home/qi/action.hpp:14:
In file included from /usr/local/lib/R/site-library/BH/include/boost/spirit/home/qi/action/action.hpp:14:
In file included from /usr/local/lib/R/site-library/BH/include/boost/spirit/home/qi/meta_compiler.hpp:14:
In file included from /usr/local/lib/R/site-library/BH/include/boost/spirit/home/support/meta_compiler.hpp:19:
In file included from /usr/local/lib/R/site-library/BH/include/boost/proto/proto.hpp:13:
In file included from /usr/local/lib/R/site-library/BH/include/boost/proto/debug.hpp:12:
In file included from /usr/include/c++/v1/iostream:38:
In file included from /usr/include/c++/v1/ios:216:
In file included from /usr/include/c++/v1/__locale:15:
/usr/include/c++/v1/string:1938:44: error: 'basic_string<_CharT, _Traits, _Allocator>' is missing exception specification 'noexcept(is_nothrow_copy_constructible<allocator_type>::value)'
basic_string<_CharT, _Traits, _Allocator>::basic_string(const allocator_type& __a)
                                           ^
/usr/include/c++/v1/string:1326:40: note: previous declaration is here
    _LIBCPP_INLINE_VISIBILITY explicit basic_string(const allocator_type& __a)
                                       ^
1 error generated.
/usr/lib/R/etc/Makeconf:143: recipe for target 'lang__ast_def.o' failed

Any ideas what could have changed in the past few months that would cause osmething like this?

Ben

[Daniel Lee]

This looks like the same error Allen has been patiently tracking down. My guess is that it's with Bob's indexing. How do I recreate this locally?

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[Ben Goodrich]

On Monday, November 30, 2015 at 5:00:03 PM UTC-5, Daniel Lee wrote:

This looks like the same error Allen has been patiently tracking down. My guess is that it's with Bob's indexing. How do I recreate this locally?

Pull from https://github.com/stan-dev/rstan/pull/213 and try R CMD build /path/to/rstan/package

Ben

[Daniel Lee]

How do I change compilers for the build? It's working fine with the current version of clang++ for Mac.

[Ben Goodrich]

On Monday, November 30, 2015 at 5:18:31 PM UTC-5, Daniel Lee wrote:

How do I change compilers for the build? It's working fine with the current version of clang++ for Mac.

Specify CXX as something other than clang++ in the Makevars file described at

https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started#configuration

Ben

[Daniel Lee]

What version of g++ doesn't work?

Do older versions of g++, say 4.6, 4.7, 4.8, work?

[Ben Goodrich]

On Monday, November 30, 2015 at 5:38:36 PM UTC-5, Daniel Lee wrote:

What version of g++ doesn't work?

Do older versions of g++, say 4.6, 4.7, 4.8, work?

For me it fails with all versions of g++, but only if I use the binary version of R. For my self-compiled R, I can build rstan. So, it may be a Debian bug.

Ben
 

On Mon, Nov 30, 2015 at 5:20 PM, Ben Goodrich <goodri...@gmail.com> wrote:

On Monday, November 30, 2015 at 5:18:31 PM UTC-5, Daniel Lee wrote:

How do I change compilers for the build? It's working fine with the current version of clang++ for Mac.

Specify CXX as something other than clang++ in the Makevars file described at

https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started#configuration

Ben

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[Jiqiang Guo]

I am taking a look.  It might be just that there are files not complied into rstan.so. 

Jiqiang 

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[Jiqiang Guo]

I fixed the problem with https://github.com/stan-dev/rstan/commit/d2b24a9113894b7d4c4148bd13c9bb9ef9e180cd so now stanc in rstan can be built. 

But still the package cannot be built due to the refactor in writer.  @syclik, is there more refactor after your initial pull request?

Jiqiang 

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[Daniel Lee]

Thanks for find that! Wow.

Allen, I think this was the root cause of the problem with Pystan too.

Yes, there was. I'll update the pull request tonight.

On Mon, Nov 30, 2015 at 8:47 PM, Jiqiang Guo <guo...@gmail.com> wrote:

I fixed the problem with https://github.com/stan-dev/rstan/commit/d2b24a9113894b7d4c4148bd13c9bb9ef9e180cd so now stanc in rstan can be built. 

But still the package cannot be built due to the refactor in writer.  @syclik, is there more refactor after your initial pull request?

Jiqiang 

On Nov 30, 2015, at 5:59 PM, Ben Goodrich <goodri...@gmail.com> wrote:

On Monday, November 30, 2015 at 5:38:36 PM UTC-5, Daniel Lee wrote:

What version of g++ doesn't work?

Do older versions of g++, say 4.6, 4.7, 4.8, work?

For me it fails with all versions of g++, but only if I use the binary version of R. For my self-compiled R, I can build rstan. So, it may be a Debian bug.

Ben
 

On Mon, Nov 30, 2015 at 5:20 PM, Ben Goodrich <goodri...@gmail.com> wrote:

On Monday, November 30, 2015 at 5:18:31 PM UTC-5, Daniel Lee wrote:

How do I change compilers for the build? It's working fine with the current version of clang++ for Mac.

Specify CXX as something other than clang++ in the Makevars file described at

https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started#configuration

Ben

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[Bob Carpenter]

Awesome! I was really worried about this one.

- Bob

> On Nov 30, 2015, at 8:47 PM, Jiqiang Guo <guo...@gmail.com> wrote:
>
> I fixed the problem with https://github.com/stan-dev/rstan/commit/d2b24a9113894b7d4c4148bd13c9bb9ef9e180cd so now stanc in rstan can be built.
>
> But still the package cannot be built due to the refactor in writer. @syclik, is there more refactor after your initial pull request?
>
> Jiqiang
>> On Nov 30, 2015, at 5:59 PM, Ben Goodrich <goodri...@gmail.com> wrote:
>>
>> On Monday, November 30, 2015 at 5:38:36 PM UTC-5, Daniel Lee wrote:
>> What version of g++ doesn't work?
>>
>> Do older versions of g++, say 4.6, 4.7, 4.8, work?
>>
>> For me it fails with all versions of g++, but only if I use the binary version of R. For my self-compiled R, I can build rstan. So, it may be a Debian bug.
>>
>> Ben
>>
>> On Mon, Nov 30, 2015 at 5:20 PM, Ben Goodrich <goodri...@gmail.com> wrote:
>> On Monday, November 30, 2015 at 5:18:31 PM UTC-5, Daniel Lee wrote:
>> How do I change compilers for the build? It's working fine with the current version of clang++ for Mac.
>>
>> Specify CXX as something other than clang++ in the Makevars file described at
>>
>> https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started#configuration
>>
>> Ben
>>
>> --
>> You received this message because you are subscribed to the Google Groups "stan development mailing list" group.

[Daniel Lee]

I'm going to bed now. I'll try to have it done in the morning before the meeting.

Daniel

[Ben Goodrich]

On Monday, November 30, 2015 at 11:01:48 PM UTC-5, Daniel Lee wrote:

I'm going to bed now. I'll try to have it done in the morning before the meeting.

I got it a little bit farther, but it still does not build any models.

[Daniel Lee]

Ben, I got it working! But I had to comment out the advi stuff. I had to pull it out cause there's a new argument and I'm not quite sure how to do it easily.

Hopefully the pull request gets us close: https://github.com/stan-dev/rstan/pull/213

[Ben Goodrich]

On Tuesday, December 1, 2015 at 11:49:25 AM UTC-5, Daniel Lee wrote:

Ben, I got it working! But I had to comment out the advi stuff. I had to pull it out cause there's a new argument and I'm not quite sure how to do it easily.

Hopefully the pull request gets us close: https://github.com/stan-dev/rstan/pull/213

OK, I can probably manage from here.

Ben

[Daniel Lee]

I think Travis has changed their default git submodule behavior. We need to update the submodule.

[Daniel Lee]

Or... this one could be because the StanHeaders package is out of date.

[Ben Goodrich]

On Tuesday, December 1, 2015 at 1:41:37 PM UTC-5, Daniel Lee wrote:

Or... this one could be because the StanHeaders package is out of date.

I think it is going to be fine once I merge this PR into develop. Your last commit makes it build and run MCMC for me locally. I have another old branch that supported adaptive ADVI as of September.

Ben

[Daniel Lee]

The advi code is inside stan_fit.hpp, it's just commented out. (I don't know how it got there, but it wasn't compiling... I figured out that the argument order was changed, but there were other things that I didn't have the patience for at the moment.)