compile error

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enza calculli

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Sep 15, 2021, 5:40:09 AM9/15/21

to nimble-users

Dear devs,

I have this message when running nimbleModel function:

compiling... this may take a minute. Use 'showCompilerOutput = TRUE' to see C++ compilation details.

Errore: Failed to create the shared library. Run 'printErrors()' to see the compilation errors.

Any idea about this message?

Thanks a lot,

Enza

Luca

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Sep 15, 2021, 6:16:39 AM9/15/21

to enza calculli, nimble-users

Hi Enza,

can you give the command "printErrors()" and report the output? Which operating system are you using?

Cheers,
Luca

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enza calculli

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Sep 15, 2021, 6:28:36 AM9/15/21

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Hi Luca,

I work with a Windows OS and this is the quite long error:

> printErrors()

P_1_code_dot_MA_MID_1_nfCode.cpp: In member function 'virtual void zlatent_L15_UID_16::simulate(const indexedNodeInfo&) const':

P_1_code_dot_MA_MID_1_nfCode.cpp:2385:52: error: no match for 'operator-' (operand types are 'Eigen::CwiseNullaryOp<seqClass<Eigen::Matrix<double, -1, -1>, int, int, int, (byOrLength)0>, Eigen::Matrix<double, -1, -1> >' and 'int')

Interm_56 = (**model_vlatent)[(nimSeqByD(1,1,1,0)) - 1];

~~~~~~~~~~~~~~~~~~~~^~

In file included from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/Eigen/Core:91,

from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/Eigen/Dense:1,

from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/nimble/EigenTypedefs.h:24,

from P_1_code_dot_MA_MID_1_nfCode.cpp:6:

C:/Users/Alessio Pollice/Documents/R/win-library/4.1/nimble/include/Eigen/src/plugins/CommonCwiseBinaryOps.h:19:28: note: candidate: 'template<class OtherDerived> const Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<typename Eigen::internal::traits<T>::Scalar, typename Eigen::internal::traits<OtherDerived>::Scalar>, const Derived, const OtherDerived> Eigen::MatrixBase<Derived>::operator-(const Eigen::MatrixBase<OtherDerived>&) const [with OtherDerived = OtherDerived; Derived = Eigen::CwiseNullaryOp<seqClass<Eigen::Matrix<double, -1, -1>, int, int, int, (byOrLength)0>, Eigen::Matrix<double, -1, -1> >]'

EIGEN_MAKE_CWISE_BINARY_OP(operator-,difference)

^~~~~~~~

C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/Eigen/src/Core/util/Macros.h:952:4: note: in definition of macro 'EIGEN_MAKE_CWISE_BINARY_OP'

(METHOD)(const EIGEN_CURRENT_STORAGE_BASE_CLASS<OtherDerived> &other) const \

^~~~~~

C:/Users/Alessio Pollice/Documents/R/win-library/4.1/nimble/include/Eigen/src/plugins/CommonCwiseBinaryOps.h:19:28: note: template argument deduction/substitution failed:

EIGEN_MAKE_CWISE_BINARY_OP(operator-,difference)

^~~~~~~~

C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/Eigen/src/Core/util/Macros.h:952:4: note: in definition of macro 'EIGEN_MAKE_CWISE_BINARY_OP'

(METHOD)(const EIGEN_CURRENT_STORAGE_BASE_CLASS<OtherDerived> &other) const \

^~~~~~

P_1_code_dot_MA_MID_1_nfCode.cpp:2385:54: note: mismatched types 'const Eigen::MatrixBase<Derived>' and 'int'

Interm_56 = (**model_vlatent)[(nimSeqByD(1,1,1,0)) - 1];

In file included from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/Eigen/src/Core/DenseBase.h:574,

from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/Eigen/Core:459,

from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/Eigen/Dense:1,

from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/nimble/EigenTypedefs.h:24,

from P_1_code_dot_MA_MID_1_nfCode.cpp:6:

C:/Users/Alessio Pollice/Documents/R/win-library/4.1/nimble/include/Eigen/src/plugins/CommonCwiseUnaryOps.h:45:1: note: candidate: 'const NegativeReturnType Eigen::DenseBase<Derived>::operator-() const [with Derived = Eigen::CwiseNullaryOp<seqClass<Eigen::Matrix<double, -1, -1>, int, int, int, (byOrLength)0>, Eigen::Matrix<double, -1, -1> >; Eigen::DenseBase<Derived>::NegativeReturnType = Eigen::CwiseUnaryOp<Eigen::internal::scalar_opposite_op<double>, const Eigen::CwiseNullaryOp<seqClass<Eigen::Matrix<double, -1, -1>, int, int, int, (byOrLength)0>, Eigen::Matrix<double, -1, -1> > >; typename Eigen::internal::traits<T>::Scalar = double]'

operator-() const { return NegativeReturnType(derived()); }

^~~~~~~~

C:/Users/Alessio Pollice/Documents/R/win-library/4.1/nimble/include/Eigen/src/plugins/CommonCwiseUnaryOps.h:45:1: note: candidate expects 0 arguments, 1 provided

In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/stl_algobase.h:67,

from C:/rtools40/mingw64/include/c++/8.3.0/bits/char_traits.h:39,

from C:/rtools40/mingw64/include/c++/8.3.0/ios:40,

from C:/rtools40/mingw64/include/c++/8.3.0/istream:38,

from C:/rtools40/mingw64/include/c++/8.3.0/sstream:38,

from C:/rtools40/mingw64/include/c++/8.3.0/complex:45,

from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/Eigen/Core:99,

from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/Eigen/Dense:1,

from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/nimble/EigenTypedefs.h:24,

from P_1_code_dot_MA_MID_1_nfCode.cpp:6:

C:/rtools40/mingw64/include/c++/8.3.0/bits/stl_iterator.h:392:5: note: candidate: 'template<class IteratorL, class IteratorR> decltype ((_y.base() - _x.base())) std::operator-(const std::reverse_iterator<_Iterator>&, const std::reverse_iterator<_IteratorR>&)'

operator-(const reverse_iterator<_IteratorL>& __x,

^~~~~~~~

C:/rtools40/mingw64/include/c++/8.3.0/bits/stl_iterator.h:392:5: note: template argument deduction/substitution failed:

P_1_code_dot_MA_MID_1_nfCode.cpp:2385:54: note: 'Eigen::CwiseNullaryOp<seqClass<Eigen::Matrix<double, -1, -1>, int, int, int, (byOrLength)0>, Eigen::Matrix<double, -1, -1> >' is not derived from 'const std::reverse_iterator<_Iterator>'

Interm_56 = (**model_vlatent)[(nimSeqByD(1,1,1,0)) - 1];

In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/stl_algobase.h:67,

from C:/rtools40/mingw64/include/c++/8.3.0/bits/char_traits.h:39,

from C:/rtools40/mingw64/include/c++/8.3.0/ios:40,

from C:/rtools40/mingw64/include/c++/8.3.0/istream:38,

from C:/rtools40/mingw64/include/c++/8.3.0/sstream:38,

from C:/rtools40/mingw64/include/c++/8.3.0/complex:45,

from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/Eigen/Core:99,

from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/Eigen/Dense:1,

from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/nimble/EigenTypedefs.h:24,

from P_1_code_dot_MA_MID_1_nfCode.cpp:6:

C:/rtools40/mingw64/include/c++/8.3.0/bits/stl_iterator.h:1188:5: note: candidate: 'template<class IteratorL, class IteratorR> decltype ((_x.base() - _y.base())) std::operator-(const std::move_iterator<_IteratorL>&, const std::move_iterator<_IteratorR>&)'

operator-(const move_iterator<_IteratorL>& __x,

^~~~~~~~

C:/rtools40/mingw64/include/c++/8.3.0/bits/stl_iterator.h:1188:5: note: template argument deduction/substitution failed:

Interm_56 = (**model_vlatent)[(nimSeqByD(1,1,1,0)) - 1];

In file included from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/Eigen/Core:99,

from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/Eigen/Dense:1,

from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/nimble/EigenTypedefs.h:24,

from P_1_code_dot_MA_MID_1_nfCode.cpp:6:

C:/rtools40/mingw64/include/c++/8.3.0/complex:356:5: note: candidate: 'template<class _Tp> std::complex<_Tp> std::operator-(const std::complex<_Tp>&, const std::complex<_Tp>&)'

operator-(const complex<_Tp>& _x, const complex<_Tp>& _y)

^~~~~~~~

C:/rtools40/mingw64/include/c++/8.3.0/complex:356:5: note: template argument deduction/substitution failed:

Interm_56 = (**model_vlatent)[(nimSeqByD(1,1,1,0)) - 1];

In file included from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/Eigen/Core:99,

from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/Eigen/Dense:1,

from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/nimble/EigenTypedefs.h:24,

from P_1_code_dot_MA_MID_1_nfCode.cpp:6:

C:/rtools40/mingw64/include/c++/8.3.0/complex:365:5: note: candidate: 'template<class Tp> std::complex<_Tp> std::operator-(const std::complex<_Tp>&, const Tp&)'

operator-(const complex<_Tp>& _x, const Tp& __y)

^~~~~~~~

C:/rtools40/mingw64/include/c++/8.3.0/complex:365:5: note: template argument deduction/substitution failed:

Interm_56 = (**model_vlatent)[(nimSeqByD(1,1,1,0)) - 1];

In file included from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/Eigen/Core:99,

from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/Eigen/Dense:1,

from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/nimble/EigenTypedefs.h:24,

from P_1_code_dot_MA_MID_1_nfCode.cpp:6:

C:/rtools40/mingw64/include/c++/8.3.0/complex:374:5: note: candidate: 'template<class Tp> std::complex<_Tp> std::operator-(const Tp&, const std::complex<_Tp>&)'

operator-(const Tp& _x, const complex<_Tp>& __y)

^~~~~~~~

C:/rtools40/mingw64/include/c++/8.3.0/complex:374:5: note: template argument deduction/substitution failed:

P_1_code_dot_MA_MID_1_nfCode.cpp:2385:54: note: mismatched types 'const std::complex<_Tp>' and 'int'

Interm_56 = (**model_vlatent)[(nimSeqByD(1,1,1,0)) - 1];

In file included from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/Eigen/Core:99,

from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/Eigen/Dense:1,

from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/nimble/EigenTypedefs.h:24,

from P_1_code_dot_MA_MID_1_nfCode.cpp:6:

C:/rtools40/mingw64/include/c++/8.3.0/complex:451:5: note: candidate: 'template<class _Tp> std::complex<_Tp> std::operator-(const std::complex<_Tp>&)'

operator-(const complex<_Tp>& __x)

^~~~~~~~

C:/rtools40/mingw64/include/c++/8.3.0/complex:451:5: note: template argument deduction/substitution failed:

Interm_56 = (**model_vlatent)[(nimSeqByD(1,1,1,0)) - 1];

In file included from C:/rtools40/mingw64/include/c++/8.3.0/vector:65,

from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/nimble/NimArrBase.h:38,

from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/nimble/RcppNimbleUtils.h:24,

from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/nimble/NamedObjects.h:28,

from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/nimble/EigenTypedefs.h:26,

from P_1_code_dot_MA_MID_1_nfCode.cpp:6:

C:/rtools40/mingw64/include/c++/8.3.0/bits/stl_bvector.h:210:3: note: candidate: 'std::ptrdiff_t std::operator-(const std::_Bit_iterator_base&, const std::_Bit_iterator_base&)'

operator-(const Bit_iterator_base& _x, const Bit_iterator_base& _y)

^~~~~~~~

C:/rtools40/mingw64/include/c++/8.3.0/bits/stl_bvector.h:210:3: note: no known conversion for argument 1 from 'Eigen::CwiseNullaryOp<seqClass<Eigen::Matrix<double, -1, -1>, int, int, int, (byOrLength)0>, Eigen::Matrix<double, -1, -1> >' to 'const std::_Bit_iterator_base&'

P_1_code_dot_MA_MID_1_nfCode.cpp:2387:27: error: cannot bind non-const lvalue reference of type 'NimArr<1, double>&' to an rvalue of type 'NimArr<1, double>'

Interm_57 = rcFun_nimble3(Interm_56, 0);

^~~~~~~~~

In file included from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/nimble/RcppNimbleUtils.h:25,

from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/nimble/NamedObjects.h:28,

from C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/nimble/EigenTypedefs.h:26,

from P_1_code_dot_MA_MID_1_nfCode.cpp:6:

C:\Users\Alessio Pollice\Documents\R\win-library\4.1\nimble\include/nimble/NimArr.h:276:3: note: after user-defined conversion: 'NimArr<1, T>::NimArr(int) [with T = double]'

NimArr<1, T>(int is1) : NimArrBase<T>() { setSize(is1); }

^~~~~~~~~~~~

P_1_code_dot_MA_MID_1_nfCode.cpp:2313:20: note: initializing argument 1 of 'NimArr<1, double> rcFun_nimble3(NimArr<1, double>&, int)'

NimArr<1, double> rcFun_nimble3 ( NimArr<1, double> & ARG1_z, int ARG2_log ) {

^~~~~~~~~~~~~

make: *** [C:/PROGRA~1/R/R-4.1.0/etc/x64/Makeconf:245: P_1_code_dot_MA_MID_1_nfCode.o] Error 1

Thank you for helping.

Luca

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Sep 15, 2021, 6:35:38 AM9/15/21

to enza calculli, nimble-users

Hi Enza,

I could have helped if the problem had been with the Rtools installation, but that seems to work fine. I suspect that you'll have to share the Nimble code that you're trying to compile – if it's possible for you to share it, of course.

Cheers,
Luca

> > To view this discussion on the web visit https://groups.google.com/d/msgid/nimble-users/567db56b-8417-4c6d-b480-a03b12de201bn%40googlegroups.com <https://groups.google.com/d/msgid/nimble-users/567db56b-8417-4c6d-b480-a03b12de201bn%40googlegroups.com> <https://groups.google.com/d/msgid/nimble-users/567db56b-8417-4c6d-b480-a03b12de201bn%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/nimble-users/567db56b-8417-4c6d-b480-a03b12de201bn%40googlegroups.com?utm_medium=email&utm_source=footer>>.

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enza calculli

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Sep 15, 2021, 7:04:12 AM9/15/21

to nimble-users

Sure Luca!

My script is attached.

Thanks,

Enza

model_nimble.R

Chris Paciorek

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Sep 15, 2021, 8:46:36 PM9/15/21

to enza calculli, nimble-users

Hi Enza,

You're getting errors because you have K=2, which means you are passing only one probability into the stick_breaking function. In your case, this produces code that

looks like:

zlatent[1:2] <- stick_breaking_fixed(vlatent[1:1])

and the nimble compiler is having trouble with the [1:1] syntax as it's not syntax that would usually be used.

Fortunately if you have K=2 there is an easy work-around because you don't actually need the stick_breaking function. Try this:

zlatent[1:2] <- c(vlatent[1], 1-vlatent[1])

I'll also file an issue for us to fix the compiler so it works for the [1:1] special case, as it would be useful to be able to use different values of K with the same

model code and have it work for the K=2 case.

A secondary issue is that our stick_breaking function needs to be fixed to allow the case of a single input probability instead of multiple input probabilities.

We'll fix that in our upcoming release.

-Chris

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