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Per the instructions here I should post a question on this forum with my bug. Essentially I have an error when compiling mengine. I'm trying to run a mathematica notebook on a linux server which needs to call matlab, so I'm in the process of installing MATLink. See log messages at the end of this post for the error. Things I've checked:

  • I've made sure both math and matlab are in PATH.
  • Mathematica can call matlab from within.
  • I have MATLAB 9.5.0.1265761 (R2018b) Update 6, which as seen here (very last page) requires gcc 6.3.x. I have tried both with gcc9 and gcc6 and it doesn't work. Current version is gcc (Ubuntu 6.5.0-2ubuntu1~16.04) 6.5.0 20181026.
  • I've run apt-get install uuid-dev and installed it without problems.
  • I've installed csh without problems.

Thank you for the time.

Linux version:

   Static hostname: ecb22
         Icon name: computer-vm
           Chassis: vm
        Machine ID: 31e79e4e754145a2aea3fec8b9baabef
           Boot ID: 2fc0465ca7764389a2bc7f1938bdf4a4
    Virtualization: kvm
  Operating System: Ubuntu 16.04.6 LTS
            Kernel: Linux 4.4.0-119-generic
      Architecture: x86-64

Developer info:

In[2]:= MATLink`Developer`GetInfo[]
MATLink 1.1 for Unix (Fri 15 Aug 2014)12.1.0 for Linux x86 (64-bit) (March 18, 2020)
>   csh:    g++:        MATLAB:
    /bin/csh/usr/bin/g++/home/ubuntu/MATLAB18/bin
>   libuuid:
        libuuid.so.1 (libc6,x86-64) => /lib/x86_64-linux-gnu/libuuid.so.1
        libuuid.so (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libuuid.so
>   System PATH:
    /home/ubuntu/bin
    /home/ubuntu/.local/bin
    /home/ubuntu/anaconda3/bin
    /home/ubuntu/anaconda3/condabin
    /usr/local/sbin
    /usr/local/bin
    /usr/sbin
    /usr/bin
    /sbin
    /bin
    /usr/games
    /usr/local/games
    /home/ubuntu/mosek/9.1/tools/platform/linux64x86/bin
    /home/ubuntu/mosek/mosek.lic
    /home/ubuntu/MATLAB18/bin/

Compiling engine from within Mathematica:

In[3]:= MATLink`Developer`CompileMEngine[]
Compiling the MATLink Engine from source...

g++ -O -Wall -I/usr/local/Wolfram/Mathematica/12.1/Executables/../SystemFiles/Links/MathLink/DeveloperKit/Linux-x86-64/CompilerAdditions -I/home/ubuntu/MATLAB18/bin/../extern/include -L/usr/local/Wolfram/Mathematica/12.1/Executables/../SystemFiles/Links/MathLink/DeveloperKit/Linux-x86-64/CompilerAdditions -L/home/ubuntu/MATLAB18/bin/../bin/glnxa64 menginetm.cpp mengine.cpp set.cpp get.cpp main.cpp -Wl,-rpath-link,/home/ubuntu/MATLAB18/bin/../bin/glnxa64/ -DMLINTERFACE=3 -lML64i3 -luuid -lmx -leng -o mengine
set.cpp: In function 'void eng_make_ComplexArray(double*, int, double*, int, int*, int ':
set.cpp:95:43: error: 'mxGetPiIsDeprecated' was not declared in this scope
     std::copy(imag, imag+ilen, mxGetPi(var));
                                           ^
set.cpp: In function 'void eng_make_SparseComplex(int*, int, int*, int, double*, int, double*, int, int, int)':
set.cpp:116:43: error: 'mxGetPiIsDeprecated' was not declared in this scope
     std::copy(imag, imag+ilen, mxGetPi(var));
                                           ^
set.cpp: In function 'void eng_make_String(const short unsigned int*, int)':
set.cpp:160:31: warning: narrowing conversion of 'len' from 'int' to 'mwSize {aka long unsigned int}' inside { } [-Wnarrowing]
     mwSize mbDims[2] = {1, len};
                               ^
In file included from /usr/include/c++/6/cassert:44:0,
                 from set.cpp:13:
set.cpp: In function 'void eng_make_Struct()':
set.cpp:192:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     assert(mxGetNumberOfElements(var) == len);

get.cpp: In function 'void toMma(const mxArray*, MLINK)':
get.cpp:95:54: error: 'mxGetPiIsDeprecated' was not declared in this scope
                     MLPutReal64List(link, mxGetPi(var), nnz); break;
                                                      ^
get.cpp:97:70: error: 'mxGetImagDataIsDeprecated' was not declared in this scope
                     MLPutReal32List(link, (float *) mxGetImagData(var), nnz); break;
                                                                      ^
get.cpp:133:55: error: 'mxGetPiIsDeprecated' was not declared in this scope
                     MLPutReal64Array(link, mxGetPi(var), mmDims, NULL, depth); break;
                                                       ^
get.cpp:135:71: error: 'mxGetImagDataIsDeprecated' was not declared in this scope
                     MLPutReal32Array(link, (float *) mxGetImagData(var), mmDims, NULL, depth); break;
                                                                       ^
Makefile.lin64:21: recipe for target 'mengine' failed
make: *** [mengine] Error 1

MATLink`Developer`CompileMEngine::failed:
   Automatically compiling the MATLink Engine has failed. See
    http://matlink.org/troubleshooting/, then try to compile it manually and ensure
    that the path to the MATLAB directory is set correctly in the makefile.

Out[3]= $Aborted

Compiling manually, basically the same error:

(base) $ make -f Makefile.lin64
g++ -O -Wall -I/usr/local/Wolfram/Mathematica/12.1/Executables/../SystemFiles/Links/MathLink/DeveloperKit/Linux-x86-64/CompilerAdditions -I/home/ubuntu/MATLAB18/bin/../extern/include -L/usr/local/Wolfram/Mathematica/12.1/Executables/../SystemFiles/Links/MathLink/DeveloperKit/Linux-x86-64/CompilerAdditions -L/home/ubuntu/MATLAB18/bin/../bin/glnxa64 menginetm.cpp mengine.cpp set.cpp get.cpp main.cpp -Wl,-rpath-link,/home/ubuntu/MATLAB18/bin/../bin/glnxa64/ -DMLINTERFACE=3 -lML64i3 -luuid -lmx -leng -o mengine
set.cpp: In function 'void eng_make_ComplexArray(double*, int, double*, int, int*, int ':
set.cpp:95:43: error: 'mxGetPiIsDeprecated' was not declared in this scope
     std::copy(imag, imag+ilen, mxGetPi(var));
                                           ^
set.cpp: In function 'void eng_make_SparseComplex(int*, int, int*, int, double*, int, double*, int, int, int)':
set.cpp:116:43: error: 'mxGetPiIsDeprecated' was not declared in this scope
     std::copy(imag, imag+ilen, mxGetPi(var));
                                           ^
set.cpp: In function 'void eng_make_String(const short unsigned int*, int)':
set.cpp:160:31: warning: narrowing conversion of 'len' from 'int' to 'mwSize {aka long unsigned int}' inside { } [-Wnarrowing]
     mwSize mbDims[2] = {1, len};
                               ^
In file included from /usr/include/c++/6/cassert:44:0,
                 from set.cpp:13:
set.cpp: In function 'void eng_make_Struct()':
set.cpp:192:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     assert(mxGetNumberOfElements(var) == len);

get.cpp: In function 'void toMma(const mxArray*, MLINK)':
get.cpp:95:54: error: 'mxGetPiIsDeprecated' was not declared in this scope
                     MLPutReal64List(link, mxGetPi(var), nnz); break;
                                                      ^
get.cpp:97:70: error: 'mxGetImagDataIsDeprecated' was not declared in this scope
                     MLPutReal32List(link, (float *) mxGetImagData(var), nnz); break;
                                                                      ^
get.cpp:133:55: error: 'mxGetPiIsDeprecated' was not declared in this scope
                     MLPutReal64Array(link, mxGetPi(var), mmDims, NULL, depth); break;
                                                       ^
get.cpp:135:71: error: 'mxGetImagDataIsDeprecated' was not declared in this scope
                     MLPutReal32Array(link, (float *) mxGetImagData(var), mmDims, NULL, depth); break;
                                                                       ^
Makefile.lin64:21: recipe for target 'mengine' failed
make: *** [mengine] Error 1
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1 Answer 1

Reset to default
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This is an incompatibility between MATLink on Linux and recent versions of MATLAB.

Please open Makefile.lin64 and change the CFLAGS line to read

CFLAGS = -Wall -DMX_COMPAT_32

This will fix it until a new MATLink version becomes available.

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