[FieldTrip] MEX compilation failure under R2020a on macOS 10.14
Andrew Janke
floss at apjanke.net
Fri May 29 09:30:48 CEST 2020
Hi, FieldTrip folks,
I'm running FieldTrip under Matlab R2020a on macOS 10.14.6 with Xcode
11.3.1.
When I try to recompile all the MEX files, I got some warnings and a
compilation error.
Any ideas? Maybe this MATRIX_DLL_EXPORT_SYM hack is no longer working
under R2020a and recent versions? From src/mxSerialize_cpp.cpp:
// MX_API_VER has unfortunately not changed between R2013b and R2014a,
// so we use the new MATRIX_DLL_EXPORT_SYM as an ugly hack instead
#ifdefined(__cplusplus) &&defined(MATRIX_DLL_EXPORT_SYM)
#defineEXTERN_Cextern
namespacematrix{ namespacedetail{ namespacenoninlined{
namespacemx_array_api{
#endif
This is not urgent – I'm not actually using FieldTrip for work; just
playing around with it after I saw Carlijn Boomen's compilation problems.
Perhaps this is related to the new C++ and interleaved-complex MEX APIs
that Matlab introduced recently?
Details:
>> addpath ~/local/repos/fieldtrip/
>> cd ~/local/repos/fieldtrip/utilities
>> !git log --oneline | head -10
36193a97a updated test scripts, the cfg.sourcemodel should also have a
label if it contains a filter. Select only MEG channels for source
analysis with pre-computed leadfield.
0e3a52de5 fixed bug in selection of optode channels that was intrpduced
with the recent #1377
6325434a6 automatically synchronized identical files to
0fe5399736d832b3206e778603e6427f7bd829fa
0fe539973 fixed multiple regression errors due to PR #1377, mostly
related to sloppy data bookkeeping
6dac9ac18 automatically synchronized identical files to
b79f65a9e7284c0f244f3c52875ba9f7479932fd
b79f65a9e improve ft_sourceanalysis flexbility to work with pre-computed
leadfields (#1377)
b4d569823 Update feature_request.md
49b433569 Update bug_report.md
606c7d67e Update feature_request.md
a48f337db Update bug_report.md
>> ft_compile_mex(true)
Compiling MEX file compat/matlablt2010b/@uint64/abs ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file compat/matlablt2010b/@uint64/min ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file compat/matlablt2010b/@uint64/max ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file compat/matlablt2010b/@uint64/plus ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file compat/matlablt2010b/@uint64/minus ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file compat/matlablt2010b/@uint64/times ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file compat/matlablt2010b/@uint64/rdivide ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file @config/private/deepcopy ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file @config/private/increment ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file @config/private/setzero ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file realtime/online_mri/ft_omri_smooth_volume ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file realtime/src/acquisition/siemens/src/sap2matlab ...
Building with 'Xcode with Clang'.
/Users/janke/local/repos/fieldtrip/realtime/src/acquisition/siemens/src/sap2matlab.c:33:10:
warning: enumeration value 'SAP_ARRAY_SIZE' not handled in switch [-Wswitch]
switch(item->type) {
^
/Users/janke/local/repos/fieldtrip/realtime/src/acquisition/siemens/src/sap2matlab.c:33:10:
note: add missing switch cases
switch(item->type) {
^
1 warning generated.
/Users/janke/local/repos/fieldtrip/realtime/src/acquisition/siemens/src/siemensap.c:323:12:
warning: enumeration value 'SAP_ARRAY_SIZE' not handled in switch [-Wswitch]
switch(typ) {
^
/Users/janke/local/repos/fieldtrip/realtime/src/acquisition/siemens/src/siemensap.c:323:12:
note: add missing switch cases
switch(typ) {
^
/Users/janke/local/repos/fieldtrip/realtime/src/acquisition/siemens/src/siemensap.c:436:20:
warning: enumeration value 'SAP_ARRAY_SIZE' not handled in switch [-Wswitch]
switch(item->type) {
^
/Users/janke/local/repos/fieldtrip/realtime/src/acquisition/siemens/src/siemensap.c:436:20:
note: add missing switch cases
switch(item->type) {
^
2 warnings generated.
MEX completed successfully.
Compiling MEX file src/ft_getopt ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file src/read_16bit ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file src/read_24bit ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file src/lmoutr ...
Building with 'Xcode with Clang'.
/Users/janke/local/repos/fieldtrip/src/geometry.c:176:15: warning:
implicit declaration of function 'mxGetNaN' is invalid in C99
[-Wimplicit-function-declaration]
proj[0] = mxGetNaN();
^
/Users/janke/local/repos/fieldtrip/src/geometry.c:219:11: warning:
implicit declaration of function 'mxGetNaN' is invalid in C99
[-Wimplicit-function-declaration]
*la = mxGetNaN();
^
2 warnings generated.
MEX completed successfully.
Compiling MEX file src/ltrisect ...
Building with 'Xcode with Clang'.
/Users/janke/local/repos/fieldtrip/src/geometry.c:176:15: warning:
implicit declaration of function 'mxGetNaN' is invalid in C99
[-Wimplicit-function-declaration]
proj[0] = mxGetNaN();
^
/Users/janke/local/repos/fieldtrip/src/geometry.c:219:11: warning:
implicit declaration of function 'mxGetNaN' is invalid in C99
[-Wimplicit-function-declaration]
*la = mxGetNaN();
^
2 warnings generated.
MEX completed successfully.
Compiling MEX file src/plinproj ...
Building with 'Xcode with Clang'.
/Users/janke/local/repos/fieldtrip/src/geometry.c:176:15: warning:
implicit declaration of function 'mxGetNaN' is invalid in C99
[-Wimplicit-function-declaration]
proj[0] = mxGetNaN();
^
/Users/janke/local/repos/fieldtrip/src/geometry.c:219:11: warning:
implicit declaration of function 'mxGetNaN' is invalid in C99
[-Wimplicit-function-declaration]
*la = mxGetNaN();
^
2 warnings generated.
MEX completed successfully.
Compiling MEX file src/ptriproj ...
Building with 'Xcode with Clang'.
/Users/janke/local/repos/fieldtrip/src/geometry.c:176:15: warning:
implicit declaration of function 'mxGetNaN' is invalid in C99
[-Wimplicit-function-declaration]
proj[0] = mxGetNaN();
^
/Users/janke/local/repos/fieldtrip/src/geometry.c:219:11: warning:
implicit declaration of function 'mxGetNaN' is invalid in C99
[-Wimplicit-function-declaration]
*la = mxGetNaN();
^
2 warnings generated.
MEX completed successfully.
Compiling MEX file src/routlm ...
Building with 'Xcode with Clang'.
/Users/janke/local/repos/fieldtrip/src/geometry.c:176:15: warning:
implicit declaration of function 'mxGetNaN' is invalid in C99
[-Wimplicit-function-declaration]
proj[0] = mxGetNaN();
^
/Users/janke/local/repos/fieldtrip/src/geometry.c:219:11: warning:
implicit declaration of function 'mxGetNaN' is invalid in C99
[-Wimplicit-function-declaration]
*la = mxGetNaN();
^
2 warnings generated.
MEX completed successfully.
Compiling MEX file src/solid_angle ...
Building with 'Xcode with Clang'.
/Users/janke/local/repos/fieldtrip/src/geometry.c:176:15: warning:
implicit declaration of function 'mxGetNaN' is invalid in C99
[-Wimplicit-function-declaration]
proj[0] = mxGetNaN();
^
/Users/janke/local/repos/fieldtrip/src/geometry.c:219:11: warning:
implicit declaration of function 'mxGetNaN' is invalid in C99
[-Wimplicit-function-declaration]
*la = mxGetNaN();
^
2 warnings generated.
MEX completed successfully.
Compiling MEX file src/rfbevent ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file src/meg_leadfield1 ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file src/splint_gh ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file src/plgndr ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file src/ft_spike_sub_crossx ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file src/rename ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file src/getpid ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file src/nanmean ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file src/nanstd ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file src/nanvar ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file src/nansum ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file src/nanstd ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file src/det2x2 ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file src/inv2x2 ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file src/mtimes2x2 ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file src/sandwich2x2 ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file src/combineClusters ...
Building with 'Xcode Clang++'.
MEX completed successfully.
Compiling MEX file external/fileexchange/CalcMD5 ...
Building with 'Xcode with Clang'.
MEX completed successfully.
Compiling MEX file src/mxSerialize_cpp ...
Building with 'Xcode Clang++'.
Error using mex
/Users/janke/local/repos/fieldtrip/src/mxSerialize_cpp.cpp:10:1: error:
unknown type name 'EXTERN_C'
EXTERN_C mxArray* mxSerialize(mxArray const *);
^
/Users/janke/local/repos/fieldtrip/src/mxSerialize_cpp.cpp:10:17: error:
expected ';' after top level declarator
EXTERN_C mxArray* mxSerialize(mxArray const *);
^
;
/Users/janke/local/repos/fieldtrip/src/mxSerialize_cpp.cpp:11:1: error:
unknown type name 'EXTERN_C'
EXTERN_C mxArray* mxDeserialize(const void *, size_t);
^
/Users/janke/local/repos/fieldtrip/src/mxSerialize_cpp.cpp:11:17: error:
expected ';' after top level declarator
EXTERN_C mxArray* mxDeserialize(const void *, size_t);
^
;
/Users/janke/local/repos/fieldtrip/src/mxSerialize_cpp.cpp:22:31: error:
use of undeclared identifier 'mxSerialize'
plhs[0] = (mxArray *) mxSerialize(prhs[0]);
^
5 errors generated.
Error in ft_compile_mex>compile_mex_list (line 217)
eval(cmd);
Error in ft_compile_mex (line 114)
compile_mex_list(L, ftpath, force);
>> ver
-----------------------------------------------------------------------------------------------------
MATLAB Version: 9.8.0.1323502 (R2020a)
MATLAB License Number: 973906
Operating System: Mac OS X Version: 10.14.6 Build: 18G4032
Java Version: Java 1.8.0_202-b08 with Oracle Corporation Java
HotSpot(TM) 64-Bit Server VM mixed mode
-----------------------------------------------------------------------------------------------------
MATLAB Version
9.8 (R2020a)
Database Toolbox Version
9.2.1 (R2020a)
FieldTrip Version
unknown www.fieldtriptoolbox.org
Financial Toolbox Version
5.15 (R2020a)
Optimization Toolbox Version
8.5 (R2020a)
Statistics and Machine Learning Toolbox Version
11.7 (R2020a)
>>
Cheers,
Andrew
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