DrugowitschLab / dm

C++ Diffusion model toolset with Python and Matlab interfaces
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Unable to compile new c++ commit #1

Closed ummd closed 9 years ago

ummd commented 9 years ago

mex -v CFLAGS='$CFLAGS -std=c++11' ddm_fpt.cpp ../src/ddm_fpt_lib.cpp Verbose mode is on. Neither -compatibleArrayDims nor -largeArrayDims is selected. Using -compatibleArrayDims. In the future, MATLAB will require the use of -largeArrayDims and remove the -compatibleArrayDims option. For more information: http://www.mathworks.com/help/matlab/matlab_external/upgrading-mex-files-to-use-64-bit-api.html. No MEX options file identified; looking for an implicit selection. ... Looking for compiler 'Xcode Clang++' ... ... Executing command 'xcode-select -print-path' ...Yes ('/Applications/Xcode.app/Contents/Developer'). ... Looking for folder '/Applications/Xcode.app/Contents/Developer' ...Yes. ... Executing command 'which xcrun' ...Yes ('/usr/bin/xcrun'). ... Looking for folder '/usr/bin' ...Yes. ... Executing command 'defaults read com.apple.dt.Xcode IDEXcodeVersionForAgreedToGMLicense' ...No. ... Executing command 'defaults read /Library/Preferences/com.apple.dt.Xcode IDEXcodeVersionForAgreedToGMLicense' ...Yes ('6.1'). ... Executing command ' agreed=6.1 if echo $agreed | grep -E '[.\"]' >/dev/null; then lhs=expr "$agreed" : '\([0-9]*\)[\.].*' rhs=expr "$agreed" : '[0-9]*[\.]\(.*\)$' if echo $rhs | grep -E '[."]' >/dev/null; then rhs=expr "$rhs" : '\([0-9]*\)[\.].*' fi if [ $lhs -gt 4 ] || ( [ $lhs -eq 4 ] && [ $rhs -ge 3 ] ); then echo $agreed else exit 1 fi fi' ...Yes ('6.1'). ... Executing command 'xcode-select -print-path' ...Yes ('/Applications/Xcode.app/Contents/Developer'). ... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk' ...No. ... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk' ...No. ... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk' ...Yes. ... Executing command 'xcode-select -print-path' ...Yes ('/Applications/Xcode.app/Contents/Developer'). ... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk' ...No. ... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk' ...No. ... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk' ...Yes. ... Executing command 'echo /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk | rev | cut -c1-10 | rev | egrep -oh '[0-9]+.[0-9]+'' ...Yes ('10.9'). Found installed compiler 'Xcode Clang++'.

Options file details

Compiler location: /Applications/Xcode.app/Contents/Developer
Options file: /Applications/MATLAB_R2014a.app/bin/maci64/mexopts/clang++_maci64.xml
CMDLINE200 : /usr/bin/xcrun -sdk macosx10.9 clang++ -Wl,-twolevel_namespace -undefined error -arch x86_64 -mmacosx-version-min=10.9 -Wl,-syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -framework Cocoa -bundle  -Wl,-exported_symbols_list,"/Applications/MATLAB_R2014a.app/extern/lib/maci64/mexFunction.map" -O -Wl,-exported_symbols_list,"/Applications/MATLAB_R2014a.app/extern/lib/maci64/mexFunction.map" /var/folders/ft/5mf41vp15hs6pft80kk3k9m80000gr/T//mex_930007819564959_2685/ddm_fpt.o /var/folders/ft/5mf41vp15hs6pft80kk3k9m80000gr/T//mex_930007819564959_2685/ddm_fpt_lib.o   -L"/Applications/MATLAB_R2014a.app/bin/maci64" -lmx -lmex -lmat -o ddm_fpt.mexmaci64
CXX : /usr/bin/xcrun -sdk macosx10.9 clang++
DEFINES : -DMX_COMPAT_32   -DMATLAB_MEX_FILE 
MATLABMEX : -DMATLAB_MEX_FILE 
CXXFLAGS : -fno-common -arch x86_64 -mmacosx-version-min=10.9 -fexceptions -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -fobjc-arc
INCLUDE : -I"/Applications/MATLAB_R2014a.app/extern/include" -I"/Applications/MATLAB_R2014a.app/simulink/include"
CXXOPTIMFLAGS : -O2 -DNDEBUG
CXXDEBUGFLAGS : -g
LDXX : /usr/bin/xcrun -sdk macosx10.9 clang++
LDFLAGS : -Wl,-twolevel_namespace -undefined error -arch x86_64 -mmacosx-version-min=10.9 -Wl,-syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -framework Cocoa -bundle  -Wl,-exported_symbols_list,"/Applications/MATLAB_R2014a.app/extern/lib/maci64/mexFunction.map"
LDBUNDLE : -bundle 
LINKEXPORT : -Wl,-exported_symbols_list,"/Applications/MATLAB_R2014a.app/extern/lib/maci64/mexFunction.map"
LINKLIBS : -L"/Applications/MATLAB_R2014a.app/bin/maci64" -lmx -lmex -lmat
LDOPTIMFLAGS : -O
LDDEBUGFLAGS : -g
OBJEXT : .o
LDEXT : .mexmaci64
XCODE_DIR : /Applications/Xcode.app/Contents/Developer
XCRUN_DIR : /usr/bin
XCODE_AGREED_VERSION : 6.1
ISYSROOT : /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk
SDKVER : 10.9
MATLABROOT : /Applications/MATLAB_R2014a.app
ARCH : maci64
SRC : /Users/ryanwebb/Documents/MATLAB/routines/dm-master/matlab/ddm_fpt.cpp;/Users/ryanwebb/Documents/MATLAB/routines/dm-master/src/ddm_fpt_lib.cpp
OBJ : /var/folders/ft/5mf41vp15hs6pft80kk3k9m80000gr/T//mex_930007819564959_2685/ddm_fpt.o;/var/folders/ft/5mf41vp15hs6pft80kk3k9m80000gr/T//mex_930007819564959_2685/ddm_fpt_lib.o
OBJS : /var/folders/ft/5mf41vp15hs6pft80kk3k9m80000gr/T//mex_930007819564959_2685/ddm_fpt.o /var/folders/ft/5mf41vp15hs6pft80kk3k9m80000gr/T//mex_930007819564959_2685/ddm_fpt_lib.o 
SRCROOT : /Users/ryanwebb/Documents/MATLAB/routines/dm-master/matlab/ddm_fpt
DEF : /var/folders/ft/5mf41vp15hs6pft80kk3k9m80000gr/T//mex_930007819564959_2685/ddm_fpt.def
EXP : ddm_fpt.exp
LIB : ddm_fpt.lib
EXE : ddm_fpt.mexmaci64
ILK : ddm_fpt.ilk
MANIFEST : ddm_fpt.mexmaci64.manifest
TEMPNAME : ddm_fpt
EXEDIR : 
EXENAME : ddm_fpt
CFLAGS :  -std=c++11
OPTIM : -O2 -DNDEBUG
LINKOPTIM : -O
CMDLINE100_0 : /usr/bin/xcrun -sdk macosx10.9 clang++ -c -DMX_COMPAT_32   -DMATLAB_MEX_FILE  -I"/Applications/MATLAB_R2014a.app/extern/include" -I"/Applications/MATLAB_R2014a.app/simulink/include" -fno-common -arch x86_64 -mmacosx-version-min=10.9 -fexceptions -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -fobjc-arc -O2 -DNDEBUG /Users/ryanwebb/Documents/MATLAB/routines/dm-master/matlab/ddm_fpt.cpp -o /var/folders/ft/5mf41vp15hs6pft80kk3k9m80000gr/T//mex_930007819564959_2685/ddm_fpt.o
CMDLINE100_1 : /usr/bin/xcrun -sdk macosx10.9 clang++ -c -DMX_COMPAT_32   -DMATLAB_MEX_FILE  -I"/Applications/MATLAB_R2014a.app/extern/include" -I"/Applications/MATLAB_R2014a.app/simulink/include" -fno-common -arch x86_64 -mmacosx-version-min=10.9 -fexceptions -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -fobjc-arc -O2 -DNDEBUG /Users/ryanwebb/Documents/MATLAB/routines/dm-master/src/ddm_fpt_lib.cpp -o /var/folders/ft/5mf41vp15hs6pft80kk3k9m80000gr/T//mex_930007819564959_2685/ddm_fpt_lib.o
CMDLINE300_0 : rm -f /var/folders/ft/5mf41vp15hs6pft80kk3k9m80000gr/T//mex_930007819564959_2685/ddm_fpt.o
CMDLINE300_1 : rm -f /var/folders/ft/5mf41vp15hs6pft80kk3k9m80000gr/T//mex_930007819564959_2685/ddm_fpt_lib.o

Building with 'Xcode Clang++'. /usr/bin/xcrun -sdk macosx10.9 clang++ -c -DMX_COMPAT_32 -DMATLAB_MEX_FILE -I"/Applications/MATLAB_R2014a.app/extern/include" -I"/Applications/MATLAB_R2014a.app/simulink/include" -fno-common -arch x86_64 -mmacosx-version-min=10.9 -fexceptions -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -fobjc-arc -O2 -DNDEBUG /Users/ryanwebb/Documents/MATLAB/routines/dm-master/matlab/ddm_fpt.cpp -o /var/folders/ft/5mf41vp15hs6pft80kk3k9m80000gr/T//mex_930007819564959_2685/ddm_fpt.o Error using mex In file included from /Users/ryanwebb/Documents/MATLAB/routines/dm-master/matlab/ddm_fpt.cpp:54: /Users/ryanwebb/Documents/MATLAB/routines/dm-master/matlab/../src/ddm_fpt_lib.h:42:24: error: expected expression { return data_t(x, [](value_t p) { delete[] p; }); } ^ /Users/ryanwebb/Documents/MATLAB/routines/dm-master/matlab/../src/ddm_fpt_lib.h:46:24: error: expected expression { return data_t(x, [](value_t p) { }); } ^ /Users/ryanwebb/Documents/MATLAB/routines/dm-master/matlab/../src/ddm_fpt_lib.h:97:12: error: unknown type name 'constexpr' static constexpr double PI = 3.14159265358979323846; ^ /Users/ryanwebb/Documents/MATLAB/routines/dm-master/matlab/../src/ddm_fpt_lib.h:97:22: error: expected member name or ';' after declaration specifiers static constexpr double PI = 3.14159265358979323846;


/Users/ryanwebb/Documents/MATLAB/routines/dm-master/matlab/../src/ddm_fpt_lib.h:111:33: error: use of undeclared identifier
'PI'
       fourmu2pi_ = (4 \* mu2_ + PI \* PI) / 8;
                                ^
/Users/ryanwebb/Documents/MATLAB/routines/dm-master/matlab/../src/ddm_fpt_lib.h:111:38: error: use of undeclared identifier
'PI'
       fourmu2pi_ = (4 \* mu2_ + PI \* PI) / 8;
                                     ^
/Users/ryanwebb/Documents/MATLAB/routines/dm-master/matlab/../src/ddm_fpt_lib.h:113:16: error: use of undeclared identifier
'PI'
       Cf1l_ = PI / (4 \* fourmu2pi_);
               ^
/Users/ryanwebb/Documents/MATLAB/routines/dm-master/matlab/../src/ddm_fpt_lib.h:211:12: error: unknown type name
'constexpr'
    static constexpr double PI = 3.14159265358979323846;
           ^
/Users/ryanwebb/Documents/MATLAB/routines/dm-master/matlab/../src/ddm_fpt_lib.h:211:22: error: expected member name or ';'
after declaration specifiers
    static constexpr double PI = 3.14159265358979323846;
    ~~~~~~~~~~~~~~~~ ^
/Users/ryanwebb/Documents/MATLAB/routines/dm-master/matlab/../src/ddm_fpt_lib.h:212:12: error: unknown type name
'constexpr'
    static constexpr double TWOPI = 2 \* PI;
           ^
/Users/ryanwebb/Documents/MATLAB/routines/dm-master/matlab/../src/ddm_fpt_lib.h:212:22: error: expected member name or ';'
after declaration specifiers
    static constexpr double TWOPI = 2 \* PI;
    ~~~~~~~~~~~~~~~~ ^
/Users/ryanwebb/Documents/MATLAB/routines/dm-master/matlab/../src/ddm_fpt_lib.h:213:12: error: unknown type name
'constexpr'
    static constexpr double PISQR = PI \* PI;
           ^
/Users/ryanwebb/Documents/MATLAB/routines/dm-master/matlab/../src/ddm_fpt_lib.h:213:22: error: expected member name or ';'
after declaration specifiers
    static constexpr double PISQR = PI \* PI;
    ~~~~~~~~~~~~~~~~ ^
/Users/ryanwebb/Documents/MATLAB/routines/dm-master/matlab/../src/ddm_fpt_lib.h:233:12: error: unknown type name
'constexpr'
    static constexpr double SERIES_ACC = 1e-29;
           ^
/Users/ryanwebb/Documents/MATLAB/routines/dm-master/matlab/../src/ddm_fpt_lib.h:233:22: error: expected member name or ';'
after declaration specifiers
    static constexpr double SERIES_ACC = 1e-29;
    ~~~~~~~~~~~~~~~~ ^
/Users/ryanwebb/Documents/MATLAB/routines/dm-master/matlab/../src/ddm_fpt_lib.h:237:54: error: use of undeclared identifier
'TWOPI'
    { return (2.0 + sqrt(-2 \* t \* log(2 \* tol \* sqrt(TWOPI \* t))) <
                                                     ^
/Users/ryanwebb/Documents/MATLAB/routines/dm-master/matlab/../src/ddm_fpt_lib.h:238:29: error: use of undeclared identifier
'PI'
             sqrt(- 2 \* log(PI \* t \* tol) / (t \* PISQR))) ? 1 : 0; }
                            ^
/Users/ryanwebb/Documents/MATLAB/routines/dm-master/matlab/../src/ddm_fpt_lib.h:238:50: error: use of undeclared identifier
'PISQR'
             sqrt(- 2 \* log(PI \* t \* tol) / (t \* PISQR))) ? 1 : 0; }
                                                 ^
/Users/ryanwebb/Documents/MATLAB/routines/dm-master/matlab/../src/ddm_fpt_lib.h:298:64: error: use of undeclared identifier
'SERIES_ACC'
    { return exp(c3 - c2 \* t) / c1 \* fpt_symfastseries(t / c1, SERIES_ACC); }
                                                               ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
jdrugo commented 9 years ago

MATLAB seems to have changed compiler flags syntax. I have updated matlab/README.md accordingly.