Build error in ubuntu 20.04

[FaridTavakol]

Hi Junichi,

I am trying to build this package, and I have followed the instructions on the wiki and corrected the path to the IGTL build and src directories as well as the path to the mex executable. However, I get the following error message when I run make:

/usr/local/MATLAB/R2021a/bin  -I/home/farid/OpenIGTLink/build -I/home/farid/OpenIGTLink/Source -c igtlMexClientSocket.cpp
make: execvp: /usr/local/MATLAB/R2021a/bin: Permission denied
make: *** [Makefile:54: igtlMexClientSocket.o] Error 127

Any idea where this error is coming from?

[FaridTavakol]

So, I have figured out the issue for the permission. In the Makefile in the MEX path I was missing an argument for the mex. So, my previous path was something like: /usr/local/MATLAB/R2021a/bin and I changed it to /usr/local/MATLAB/R2021a/bin/mex and it solved the issue.

[tokjun]

Thanks for reporting the issue and following it up.

[FaridTavakol]

/usr/local/MATLAB/R2021a/bin/mex  -I/home/farid/OpenIGTLink/build -I/home/farid/OpenIGTLink/Source -c igtlMexClientSocket.cpp
Building with 'g++'.
In file included from /home/farid/OpenIGTLink/Source/igtlSmartPointer.h:33,
                 from /home/farid/OpenIGTLink/Source/igtlLightObject.h:33,
                 from /home/farid/OpenIGTLink/Source/igtlObject.h:36,
                 from /home/farid/MatlabIGTL/igtlMexSocket.h:60,
                 from /home/farid/MatlabIGTL/igtlMexClientSocket.h:48,
                 from /home/farid/MatlabIGTL/igtlMexClientSocket.cpp:30:
/home/farid/OpenIGTLink/Source/igtlMacro.h:465:23: error: redeclaration of ‘typedef class igtl::MexSocket igtl::MexSocket::Self’
  465 |     typedef thisClass Self; \
      |                       ^~~~
/home/farid/MatlabIGTL/igtlMexSocket.h:84:3: note: in expansion of macro ‘igtlTypeMacro’
   84 |   igtlTypeMacro(igtl::MexSocket, igtl::Object)
      |   ^~~~~~~~~~~~~
In file included from /home/farid/MatlabIGTL/igtlMexClientSocket.h:48,
                 from /home/farid/MatlabIGTL/igtlMexClientSocket.cpp:30:
/home/farid/MatlabIGTL/igtlMexSocket.h:79:34: note: previous declaration ‘typedef class igtl::MexSocket igtl::MexSocket::Self’
   79 |   typedef MexSocket              Self;
      |                                  ^~~~
In file included from /home/farid/OpenIGTLink/Source/igtlSmartPointer.h:33,
                 from /home/farid/OpenIGTLink/Source/igtlLightObject.h:33,
                 from /home/farid/OpenIGTLink/Source/igtlObject.h:36,
                 from /home/farid/MatlabIGTL/igtlMexSocket.h:60,
                 from /home/farid/MatlabIGTL/igtlMexClientSocket.h:48,
                 from /home/farid/MatlabIGTL/igtlMexClientSocket.cpp:30:
/home/farid/OpenIGTLink/Source/igtlMacro.h:466:24: error: redeclaration of ‘typedef class igtl::Object igtl::MexSocket::Superclass’
  466 |     typedef superclass Superclass; \
      |                        ^~~~~~~~~~
/home/farid/MatlabIGTL/igtlMexSocket.h:84:3: note: in expansion of macro ‘igtlTypeMacro’
   84 |   igtlTypeMacro(igtl::MexSocket, igtl::Object)
      |   ^~~~~~~~~~~~~
In file included from /home/farid/MatlabIGTL/igtlMexClientSocket.h:48,
                 from /home/farid/MatlabIGTL/igtlMexClientSocket.cpp:30:
/home/farid/MatlabIGTL/igtlMexSocket.h:80:19: note: previous declaration ‘typedef class igtl::Object igtl::MexSocket::Superclass’
   80 |   typedef Object  Superclass;
      |                   ^~~~~~~~~~
In file included from /home/farid/OpenIGTLink/Source/igtlSmartPointer.h:33,
                 from /home/farid/OpenIGTLink/Source/igtlLightObject.h:33,
                 from /home/farid/OpenIGTLink/Source/igtlObject.h:36,
                 from /home/farid/MatlabIGTL/igtlMexSocket.h:60,
                 from /home/farid/MatlabIGTL/igtlMexClientSocket.h:48,
                 from /home/farid/MatlabIGTL/igtlMexClientSocket.cpp:30:
/home/farid/OpenIGTLink/Source/igtlMacro.h:467:38: error: redeclaration of ‘typedef class igtl::SmartPointer<igtl::MexSocket> igtl::MexSocket::Pointer’
  467 |     typedef igtl::SmartPointer<Self> Pointer; \
      |                                      ^~~~~~~
/home/farid/MatlabIGTL/igtlMexSocket.h:84:3: note: in expansion of macro ‘igtlTypeMacro’
   84 |   igtlTypeMacro(igtl::MexSocket, igtl::Object)
      |   ^~~~~~~~~~~~~
In file included from /home/farid/MatlabIGTL/igtlMexClientSocket.h:48,
                 from /home/farid/MatlabIGTL/igtlMexClientSocket.cpp:30:
/home/farid/MatlabIGTL/igtlMexSocket.h:81:37: note: previous declaration ‘typedef class igtl::SmartPointer<igtl::MexSocket> igtl::MexSocket::Pointer’
   81 |   typedef SmartPointer<Self>        Pointer;
      |                                     ^~~~~~~
In file included from /home/farid/OpenIGTLink/Source/igtlSmartPointer.h:33,
                 from /home/farid/OpenIGTLink/Source/igtlLightObject.h:33,
                 from /home/farid/OpenIGTLink/Source/igtlObject.h:36,
                 from /home/farid/MatlabIGTL/igtlMexSocket.h:60,
                 from /home/farid/MatlabIGTL/igtlMexClientSocket.h:48,
                 from /home/farid/MatlabIGTL/igtlMexClientSocket.cpp:30:
/home/farid/OpenIGTLink/Source/igtlMacro.h:468:44: error: redeclaration of ‘typedef class igtl::SmartPointer<const igtl::MexSocket> igtl::MexSocket::ConstPointer’
  468 |     typedef igtl::SmartPointer<const Self> ConstPointer;
      |                                            ^~~~~~~~~~~~
/home/farid/MatlabIGTL/igtlMexSocket.h:84:3: note: in expansion of macro ‘igtlTypeMacro’
   84 |   igtlTypeMacro(igtl::MexSocket, igtl::Object)
      |   ^~~~~~~~~~~~~
In file included from /home/farid/MatlabIGTL/igtlMexClientSocket.h:48,
                 from /home/farid/MatlabIGTL/igtlMexClientSocket.cpp:30:
/home/farid/MatlabIGTL/igtlMexSocket.h:82:37: note: previous declaration ‘typedef class igtl::SmartPointer<const igtl::MexSocket> igtl::MexSocket::ConstPointer’
   82 |   typedef SmartPointer<const Self>  ConstPointer;
      |                                     ^~~~~~~~~~~~
In file included from /home/farid/OpenIGTLink/Source/igtlSmartPointer.h:33,
                 from /home/farid/OpenIGTLink/Source/igtlLightObject.h:33,
                 from /home/farid/OpenIGTLink/Source/igtlObject.h:36,
                 from /home/farid/MatlabIGTL/igtlMexSocket.h:60,
                 from /home/farid/MatlabIGTL/igtlMexClientSocket.h:48,
                 from /home/farid/MatlabIGTL/igtlMexClientSocket.cpp:30:
/home/farid/OpenIGTLink/Source/igtlMacro.h:465:23: error: redeclaration of ‘typedef class igtl::MexClientSocket igtl::MexClientSocket::Self’
  465 |     typedef thisClass Self; \
      |                       ^~~~
/home/farid/MatlabIGTL/igtlMexClientSocket.h:64:3: note: in expansion of macro ‘igtlTypeMacro’
   64 |   igtlTypeMacro(igtl::MexClientSocket, igtl::MexSocket)
      |   ^~~~~~~~~~~~~
In file included from /home/farid/MatlabIGTL/igtlMexClientSocket.cpp:30:
/home/farid/MatlabIGTL/igtlMexClientSocket.h:59:40: note: previous declaration ‘typedef class igtl::MexClientSocket igtl::MexClientSocket::Self’
   59 |   typedef MexClientSocket              Self;
      |                                        ^~~~
In file included from /home/farid/OpenIGTLink/Source/igtlSmartPointer.h:33,
                 from /home/farid/OpenIGTLink/Source/igtlLightObject.h:33,
                 from /home/farid/OpenIGTLink/Source/igtlObject.h:36,
                 from /home/farid/MatlabIGTL/igtlMexSocket.h:60,
                 from /home/farid/MatlabIGTL/igtlMexClientSocket.h:48,
                 from /home/farid/MatlabIGTL/igtlMexClientSocket.cpp:30:
/home/farid/OpenIGTLink/Source/igtlMacro.h:466:24: error: redeclaration of ‘typedef class igtl::MexSocket igtl::MexClientSocket::Superclass’
  466 |     typedef superclass Superclass; \
      |                        ^~~~~~~~~~
/home/farid/MatlabIGTL/igtlMexClientSocket.h:64:3: note: in expansion of macro ‘igtlTypeMacro’
   64 |   igtlTypeMacro(igtl::MexClientSocket, igtl::MexSocket)
      |   ^~~~~~~~~~~~~
In file included from /home/farid/MatlabIGTL/igtlMexClientSocket.cpp:30:
/home/farid/MatlabIGTL/igtlMexClientSocket.h:60:40: note: previous declaration ‘typedef class igtl::MexSocket igtl::MexClientSocket::Superclass’
   60 |   typedef MexSocket                    Superclass;
      |                                        ^~~~~~~~~~
In file included from /home/farid/OpenIGTLink/Source/igtlSmartPointer.h:33,
                 from /home/farid/OpenIGTLink/Source/igtlLightObject.h:33,
                 from /home/farid/OpenIGTLink/Source/igtlObject.h:36,
                 from /home/farid/MatlabIGTL/igtlMexSocket.h:60,
                 from /home/farid/MatlabIGTL/igtlMexClientSocket.h:48,
                 from /home/farid/MatlabIGTL/igtlMexClientSocket.cpp:30:
/home/farid/OpenIGTLink/Source/igtlMacro.h:467:38: error: redeclaration of ‘typedef class igtl::SmartPointer<igtl::MexClientSocket> igtl::MexClientSocket::Pointer’
  467 |     typedef igtl::SmartPointer<Self> Pointer; \
      |                                      ^~~~~~~
/home/farid/MatlabIGTL/igtlMexClientSocket.h:64:3: note: in expansion of macro ‘igtlTypeMacro’
   64 |   igtlTypeMacro(igtl::MexClientSocket, igtl::MexSocket)
      |   ^~~~~~~~~~~~~
In file included from /home/farid/MatlabIGTL/igtlMexClientSocket.cpp:30:
/home/farid/MatlabIGTL/igtlMexClientSocket.h:61:37: note: previous declaration ‘typedef class igtl::SmartPointer<igtl::MexClientSocket> igtl::MexClientSocket::Pointer’
   61 |   typedef SmartPointer<Self>        Pointer;
      |                                     ^~~~~~~
In file included from /home/farid/OpenIGTLink/Source/igtlSmartPointer.h:33,
                 from /home/farid/OpenIGTLink/Source/igtlLightObject.h:33,
                 from /home/farid/OpenIGTLink/Source/igtlObject.h:36,
                 from /home/farid/MatlabIGTL/igtlMexSocket.h:60,
                 from /home/farid/MatlabIGTL/igtlMexClientSocket.h:48,
                 from /home/farid/MatlabIGTL/igtlMexClientSocket.cpp:30:
/home/farid/OpenIGTLink/Source/igtlMacro.h:468:44: error: redeclaration of ‘typedef class igtl::SmartPointer<const igtl::MexClientSocket> igtl::MexClientSocket::ConstPointer’
  468 |     typedef igtl::SmartPointer<const Self> ConstPointer;
      |                                            ^~~~~~~~~~~~
/home/farid/MatlabIGTL/igtlMexClientSocket.h:64:3: note: in expansion of macro ‘igtlTypeMacro’
   64 |   igtlTypeMacro(igtl::MexClientSocket, igtl::MexSocket)
      |   ^~~~~~~~~~~~~
In file included from /home/farid/MatlabIGTL/igtlMexClientSocket.cpp:30:
/home/farid/MatlabIGTL/igtlMexClientSocket.h:62:37: note: previous declaration ‘typedef class igtl::SmartPointer<const igtl::MexClientSocket> igtl::MexClientSocket::ConstPointer’
   62 |   typedef SmartPointer<const Self>  ConstPointer;
      |                                     ^~~~~~~~~~~~

make: *** [Makefile:54: igtlMexClientSocket.o] Error 255

I am encountering a new error while building. It seems like a Typedef is being declared twice. I tried commenting out line 465 of igtlMacro.h and it seemed to proceed to some extent.

However, it was once again stopped building due to a missing file/ directory for the header file iglt_header.h. I was wondering if this module has been previously tested on an Ubuntu system before?

[tokjun]

It was tested before but with much older versions.

There is also Matlab OpenIGTLink interface developed at Queen's, and it has been part of MatlabBridge for 3D Slicer (https://www.slicer.org/wiki/Documentation/Nightly/Extensions/MatlabBridge). It used to be an independent interface, but I'm not sure if it's still the case, or it only works with 3D Slicer.