python conda pystan, expects older version of mpfr library?

Question

Sorry if this is not the right place to ask, but it seems to be a general installation question rather than a pystan question...

I am trying to run some simple examples of pystan, a Python Bayesian inference package, and it consistently crashes. So e.g. when I run the "Getting started, Example 1" example at https://pystan.readthedocs.io/en/latest/getting_started.html (except I have added "verbose=True" to the line which gives the error), at the line

sm = pystan.StanModel(model_code=schools_code, verbose=True)

I get a long error trace, which begins with:

INFO:pystan:COMPILING THE C++ CODE FOR MODEL anon_model_19a09b474d1901f191444eaf8a6b8ce2 NOW.
INFO:pystan:OS: darwin, Python: 2.7.14 |Anaconda, Inc.| (default, Oct  5 2017, 02:28:52) 
[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)], Cython 0.26.1
Compiling /var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpQqJaIl/stanfit4anon_model_19a09b474d1901f191444eaf8a6b8ce2_8277449399850120616.pyx because it changed.
[1/1] Cythonizing /var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpQqJaIl/stanfit4anon_model_19a09b474d1901f191444eaf8a6b8ce2_8277449399850120616.pyx
building 'stanfit4anon_model_19a09b474d1901f191444eaf8a6b8ce2_8277449399850120616' extension
creating /var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpQqJaIl/var
creating /var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpQqJaIl/var/folders
creating /var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpQqJaIl/var/folders/6l
creating /var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpQqJaIl/var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp
creating /var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpQqJaIl/var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T
creating /var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpQqJaIl/var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpQqJaIl
gcc -fno-strict-aliasing -I/Users/peter/miniconda2/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -I/var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpQqJaIl -I/Users/peter/miniconda2/lib/python2.7/site-packages/pystan -I/Users/peter/miniconda2/lib/python2.7/site-packages/pystan/stan/src -I/Users/peter/miniconda2/lib/python2.7/site-packages/pystan/stan/lib/stan_math -I/Users/peter/miniconda2/lib/python2.7/site-packages/pystan/stan/lib/stan_math/lib/eigen_3.3.3 -I/Users/peter/miniconda2/lib/python2.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0 -I/Users/peter/miniconda2/lib/python2.7/site-packages/pystan/stan/lib/stan_math/lib/sundials_4.1.0/include -I/Users/peter/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/Users/peter/miniconda2/include/python2.7 -c /var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpQqJaIl/stanfit4anon_model_19a09b474d1901f191444eaf8a6b8ce2_8277449399850120616.cpp -o /var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpQqJaIl/var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpQqJaIl/stanfit4anon_model_19a09b474d1901f191444eaf8a6b8ce2_8277449399850120616.o -O2 -ftemplate-depth-256 -Wno-unused-function -Wno-uninitialized -std=c++1y
dyld: Library not loaded: /usr/local/opt/mpfr/lib/libmpfr.4.dylib
  Referenced from: /usr/local/Cellar/gcc/7.2.0/libexec/gcc/x86_64-apple-darwin16.7.0/7.2.0/cc1plus
  Reason: image not found
gcc: internal compiler error: Abort trap: 6 (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <https://github.com/Homebrew/homebrew-core/issues> for instructions.

I am using miniconda on Mac OS X 10.12.5. I get an identical error whether I run python2 or python3. (Above trace is python2; Python3 is python 3.6.8, installed on July 25).

The key error seems to be that it expects to find the file /usr/local/opt/mpfr/lib/libmpfr.4.dylib . When I look in that directory, I see a file libmpfr.6.dylib , and libmpfr.dylib which is a symbolic link to libmpfr.dylib , but no libmpfr.4.dylib

I wonder if something horrible is going on with assumed library paths, like it is assuming the libraries used by /usr/bin/python rather than ~/miniconda2/bin/python (which is what I use for python, because ~/miniconda2/bin is at the front of my bash shell PATH).

So... do I need to install the older (rev 4) version of libmpfr ? If so, how?

UPDATE: after seeing the reply (below), I updated gcc (to 9.2) and conda. but now it crashes somewhere else...

INFO:pystan:COMPILING THE C++ CODE FOR MODEL anon_model_19a09b474d1901f191444eaf8a6b8ce2 NOW.
INFO:pystan:OS: darwin, Python: 3.6.8 |Anaconda, Inc.| (default, Dec 29 2018, 19:04:46) 
[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)], Cython 0.28.5
Compiling /var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpw103deo3/stanfit4anon_model_19a09b474d1901f191444eaf8a6b8ce2_6187777314581226416.pyx because it changed.
[1/1] Cythonizing /var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpw103deo3/stanfit4anon_model_19a09b474d1901f191444eaf8a6b8ce2_6187777314581226416.pyx
building 'stanfit4anon_model_19a09b474d1901f191444eaf8a6b8ce2_6187777314581226416' extension
creating /var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpw103deo3/var
creating /var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpw103deo3/var/folders
creating /var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpw103deo3/var/folders/6l
creating /var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpw103deo3/var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp
creating /var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpw103deo3/var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T
creating /var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpw103deo3/var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpw103deo3
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/peter/miniconda3/include -arch x86_64 -I/Users/peter/miniconda3/include -arch x86_64 -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -I/var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpw103deo3 -I/Users/peter/miniconda3/lib/python3.6/site-packages/pystan -I/Users/peter/miniconda3/lib/python3.6/site-packages/pystan/stan/src -I/Users/peter/miniconda3/lib/python3.6/site-packages/pystan/stan/lib/stan_math -I/Users/peter/miniconda3/lib/python3.6/site-packages/pystan/stan/lib/stan_math/lib/eigen_3.3.3 -I/Users/peter/miniconda3/lib/python3.6/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0 -I/Users/peter/miniconda3/lib/python3.6/site-packages/pystan/stan/lib/stan_math/lib/sundials_4.1.0/include -I/Users/peter/miniconda3/lib/python3.6/site-packages/numpy/core/include -I/Users/peter/miniconda3/include/python3.6m -c /var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpw103deo3/stanfit4anon_model_19a09b474d1901f191444eaf8a6b8ce2_6187777314581226416.cpp -o /var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpw103deo3/var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpw103deo3/stanfit4anon_model_19a09b474d1901f191444eaf8a6b8ce2_6187777314581226416.o -O2 -ftemplate-depth-256 -Wno-unused-function -Wno-uninitialized -std=c++1y
In file included from /var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpw103deo3/stanfit4anon_model_19a09b474d1901f191444eaf8a6b8ce2_6187777314581226416.cpp:642:
In file included from /Users/peter/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/peter/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /Users/peter/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1824:
/Users/peter/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
In file included from /var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpw103deo3/stanfit4anon_model_19a09b474d1901f191444eaf8a6b8ce2_6187777314581226416.cpp:646:
In file included from /Users/peter/miniconda3/lib/python3.6/site-packages/pystan/stan_fit.hpp:12:
In file included from /Users/peter/miniconda3/lib/python3.6/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/date_time/posix_time/posix_time_types.hpp:10:
In file included from /Users/peter/miniconda3/lib/python3.6/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/date_time/time_clock.hpp:17:
In file included from /Users/peter/miniconda3/lib/python3.6/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/shared_ptr.hpp:17:
/Users/peter/miniconda3/lib/python3.6/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/smart_ptr/shared_ptr.hpp:370:174: error: no member named 'move' in namespace 'std'
    BOOST_CONSTEXPR shared_ptr( boost::detail::sp_internal_constructor_tag, element_type * px_, boost::detail::shared_count && pn_ ) BOOST_SP_NOEXCEPT : px( px_ ), pn( std::move( pn_ ) )
                                                                                                                                                                        ~~~~~^
/Users/peter/miniconda3/lib/python3.6/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/smart_ptr/shared_ptr.hpp:927:27: error: no member named 'move' in namespace 'std'; did you mean 'modf'?
    return shared_ptr<T>( std::move(r), p );
                          ^~~~~~~~~
                          modf
/usr/include/math.h:407:15: note: 'modf' declared here
extern double modf(double, double *);
              ^
In file included from /var/folders/6l/mw9lfs_51h74dfvg458rrn1c0000gp/T/tmpw103deo3/stanfit4anon_model_19a09b474d1901f191444eaf8a6b8ce2_6187777314581226416.cpp:646:
In file included from /Users/peter/miniconda3/lib/python3.6/site-packages/pystan/stan_fit.hpp:12:
In file included from /Users/peter/miniconda3/lib/python3.6/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/date_time/posix_time/posix_time_types.hpp:10:
In file included from /Users/peter/miniconda3/lib/python3.6/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/date_time/time_clock.hpp:17:
In file included from /Users/peter/miniconda3/lib/python3.6/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/shared_ptr.hpp:17:
/Users/peter/miniconda3/lib/python3.6/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/smart_ptr/shared_ptr.hpp:937:27: error: no member named 'move' in namespace 'std'; did you mean 'modf'?
    return shared_ptr<T>( std::move(r), p );

                          modf
/usr/include/math.h:407:15: note: 'modf' declared here
extern double modf(double, double *);
              ^

score 0 · Answer 1 · answered Sep 24 '19 at 13:34

0

This is not related to python. The error comes from the GCC installed on your machine under /usr/local/Cellar, which expects libmpfr.4.dylib, which corresponds to MPFR 3.x. You need to either install a newer GCC that expects libmpfr.6.dylib (MPFR 4.x), or install MPFR 3.x. But note that MPFR 3.x is old, has unfixed bugs, and is no longer maintained.

answered Sep 24 '19 at 13:34

vinc17

2,829
17
23

(Well, it is python related in the sense that I am having problem with a python package). I updated GCC (to 9.2, and also updated conda) and now get another error. The log is above, if you or anyone else has any idea. . – Peter B Sep 25 '19 at 01:14
@PeterB In the logs you added, I can see that you're still using GCC 4.2.1. The new version of conda probably expects a more recent compiler, thus you now get this error first. – vinc17 Sep 25 '19 at 14:28
And yet GCC 9.2 is installed on my machine. Which is why I think it is something to do with paths. – Peter B Sep 26 '19 at 23:21
Actually, I don't think it is using GCC 4.2.1. I think it is a note about Clang 4.0.1, in which "GCC 4.2.1 Compatible" is an adjective. – Peter B Sep 27 '19 at 02:19
@PeterB Yes, indeed, it is Clang (I got confused by the highlight). And yes, you need to adjust the paths, but I don't know the best way of doing that on your machine (that could be in the `.profile`, but not necessarily). – vinc17 Sep 27 '19 at 07:33

python conda pystan, expects older version of mpfr library?

1 Answers1