NLMF function mex compile error on Mac

Hello,

I downloaded and am trying to use the non-local means noise filtering.

I learned that I need to complie some of the .c files as follows:

% First Compile c-code!!!!, with :
%   mex vectors_nlmeans_single.c -v
%   mex image2vectors_single.c -v
%   mex vectors_nlmeans_double.c -v
%   mex image2vectors_double.c -v

But I keep failing it with errors.

>> mex vectors_nlmeans_single.c -v
Verbose mode is on.
... Looking for compiler 'Xcode with Clang' ...
... Looking for environment variable 'DEVELOPER_DIR' ...No.
... 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 ('11.0').
... Executing command '
agreed=11.0 
 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 ('11.0').
... Executing command 'xcrun -sdk macosx --show-sdk-path' ...Yes ('/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk').
... Executing command 'xcrun -sdk macosx --show-sdk-version' ...Yes ('10.15.6').
Found installed compiler 'Xcode with Clang'.
Options file details
-------------------------------------------------------------------
	Compiler location: /Applications/Xcode.app/Contents/Developer
	Options file: /Applications/MATLAB_R2017a.app/bin/maci64/mexopts/clang_maci64.xml
	CMDLINE200 : /usr/bin/xcrun -sdk macosx10.15.6 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/MacOSX10.15.sdk -bundle  -Wl,-exported_symbols_list,"/Applications/MATLAB_R2017a.app/extern/lib/maci64/mexFunction.map" /var/folders/30/t_777qwx27zd6z5vdr3hls_80000gn/T/mex_2170662200551954_54357/vectors_nlmeans_single.o /var/folders/30/t_777qwx27zd6z5vdr3hls_80000gn/T/mex_2170662200551954_54357/c_mexapi_version.o  -O -Wl,-exported_symbols_list,"/Applications/MATLAB_R2017a.app/extern/lib/maci64/c_exportsmexfileversion.map"  -L"/Applications/MATLAB_R2017a.app/bin/maci64" -lmx -lmex -lmat -lc++ -o vectors_nlmeans_single.mexmaci64
	CC : /usr/bin/xcrun -sdk macosx10.15.6 clang
	CXX : /usr/bin/xcrun -sdk macosx10.15.6 clang++
	DEFINES : -DTARGET_API_VERSION=700  -DUSE_MEX_CMD   -DMATLAB_MEX_FILE
	MATLABMEX : -DMATLAB_MEX_FILE
	MACOSX_DEPLOYMENT_TARGET : 10.9
	CFLAGS : -fno-common -arch x86_64 -mmacosx-version-min=10.9 -fexceptions -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk
	INCLUDE : -I"/Applications/MATLAB_R2017a.app/extern/include" -I"/Applications/MATLAB_R2017a.app/simulink/include"
	COPTIMFLAGS : -O2 -fwrapv -DNDEBUG
	CDEBUGFLAGS : -g
	LD : /usr/bin/xcrun -sdk macosx10.15.6 clang
	LDXX : /usr/bin/xcrun -sdk macosx10.15.6 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/MacOSX10.15.sdk -bundle  -Wl,-exported_symbols_list,"/Applications/MATLAB_R2017a.app/extern/lib/maci64/mexFunction.map"
	LDBUNDLE : -bundle 
	FUNCTIONMAP : "/Applications/MATLAB_R2017a.app/extern/lib/maci64/mexFunction.map"
	VERSIONMAP : "/Applications/MATLAB_R2017a.app/extern/lib/maci64/c_exportsmexfileversion.map"
	LINKEXPORT : -Wl,-exported_symbols_list,"/Applications/MATLAB_R2017a.app/extern/lib/maci64/mexFunction.map"
	LINKEXPORTVER : -Wl,-exported_symbols_list,"/Applications/MATLAB_R2017a.app/extern/lib/maci64/c_exportsmexfileversion.map"
	LINKLIBS : -L"/Applications/MATLAB_R2017a.app/bin/maci64" -lmx -lmex -lmat -lc++
	LDOPTIMFLAGS : -O
	LDDEBUGFLAGS : -g
	OBJEXT : .o
	LDEXT : .mexmaci64
	SETENV : CC="/usr/bin/xcrun -sdk macosx10.15.6 clang"
                CXX="/usr/bin/xcrun -sdk macosx10.15.6 clang++"
                CFLAGS="-fno-common -arch x86_64 -mmacosx-version-min=10.9 -fexceptions -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DTARGET_API_VERSION=700  -DUSE_MEX_CMD   -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/MacOSX10.15.sdk -fobjc-arc -std=c++11 -stdlib=libc++ -DTARGET_API_VERSION=700  -DUSE_MEX_CMD   -DMATLAB_MEX_FILE"
                COPTIMFLAGS="-O2 -fwrapv -DNDEBUG"
                CXXOPTIMFLAGS="-O2 -fwrapv -DNDEBUG"
                CDEBUGFLAGS="-g"
                CXXDEBUGFLAGS="-g"
                LD="/usr/bin/xcrun -sdk macosx10.15.6 clang"
                LDXX="/usr/bin/xcrun -sdk macosx10.15.6 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/MacOSX10.15.sdk -bundle  -Wl,-exported_symbols_list,"/Applications/MATLAB_R2017a.app/extern/lib/maci64/mexFunction.map" -L"/Applications/MATLAB_R2017a.app/bin/maci64" -lmx -lmex -lmat -lc++ -Wl,-exported_symbols_list,"/Applications/MATLAB_R2017a.app/extern/lib/maci64/mexFunction.map""
                LDDEBUGFLAGS="-g"
	DEVELOPER_DIR_CHECK : 
	XCODE_DIR : /Applications/Xcode.app/Contents/Developer
	XCRUN_DIR : /usr/bin
	XCODE_AGREED_VERSION : 11.0
	ISYSROOT : /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk
	SDKVER : 10.15.6
	MATLABROOT : /Applications/MATLAB_R2017a.app
	ARCH : maci64
	SRC : /Users/stlee/Dropbox/SharedFolders/SeongtaekDocs/Manuscripts/ASL-FAIR/Data/FAIR-EPIv2-injured-AllinOne/SCIDTI258_1dpi_test/vectors_nlmeans_single.c;/Applications/MATLAB_R2017a.app/extern/version/c_mexapi_version.c
	OBJ : /var/folders/30/t_777qwx27zd6z5vdr3hls_80000gn/T/mex_2170662200551954_54357/vectors_nlmeans_single.o;/var/folders/30/t_777qwx27zd6z5vdr3hls_80000gn/T/mex_2170662200551954_54357/c_mexapi_version.o
	OBJS : /var/folders/30/t_777qwx27zd6z5vdr3hls_80000gn/T/mex_2170662200551954_54357/vectors_nlmeans_single.o /var/folders/30/t_777qwx27zd6z5vdr3hls_80000gn/T/mex_2170662200551954_54357/c_mexapi_version.o 
	SRCROOT : /Users/stlee/Dropbox/SharedFolders/SeongtaekDocs/Manuscripts/ASL-FAIR/Data/FAIR-EPIv2-injured-AllinOne/SCIDTI258_1dpi_test/vectors_nlmeans_single
	DEF : /var/folders/30/t_777qwx27zd6z5vdr3hls_80000gn/T/mex_2170662200551954_54357/vectors_nlmeans_single.def
	EXP : vectors_nlmeans_single.exp
	LIB : vectors_nlmeans_single.lib
	EXE : vectors_nlmeans_single.mexmaci64
	ILK : vectors_nlmeans_single.ilk
	MANIFEST : vectors_nlmeans_single.mexmaci64.manifest
	TEMPNAME : vectors_nlmeans_single
	EXEDIR : 
	EXENAME : vectors_nlmeans_single
	OPTIM : -O2 -fwrapv -DNDEBUG
	LINKOPTIM : -O
	CMDLINE100_0 : /usr/bin/xcrun -sdk macosx10.15.6 clang -c -DTARGET_API_VERSION=700  -DUSE_MEX_CMD   -DMATLAB_MEX_FILE -I"/Applications/MATLAB_R2017a.app/extern/include" -I"/Applications/MATLAB_R2017a.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/MacOSX10.15.sdk -O2 -fwrapv -DNDEBUG /Users/stlee/Dropbox/SharedFolders/SeongtaekDocs/Manuscripts/ASL-FAIR/Data/FAIR-EPIv2-injured-AllinOne/SCIDTI258_1dpi_test/vectors_nlmeans_single.c -o /var/folders/30/t_777qwx27zd6z5vdr3hls_80000gn/T/mex_2170662200551954_54357/vectors_nlmeans_single.o
	CMDLINE100_1 : /usr/bin/xcrun -sdk macosx10.15.6 clang -c -DTARGET_API_VERSION=700  -DUSE_MEX_CMD   -DMATLAB_MEX_FILE -I"/Applications/MATLAB_R2017a.app/extern/include" -I"/Applications/MATLAB_R2017a.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/MacOSX10.15.sdk -O2 -fwrapv -DNDEBUG /Applications/MATLAB_R2017a.app/extern/version/c_mexapi_version.c -o /var/folders/30/t_777qwx27zd6z5vdr3hls_80000gn/T/mex_2170662200551954_54357/c_mexapi_version.o
-------------------------------------------------------------------
Building with 'Xcode with Clang'.
/usr/bin/xcrun -sdk macosx10.15.6 clang -c -DTARGET_API_VERSION=700  -DUSE_MEX_CMD   -DMATLAB_MEX_FILE -I"/Applications/MATLAB_R2017a.app/extern/include" -I"/Applications/MATLAB_R2017a.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/MacOSX10.15.sdk -O2 -fwrapv -DNDEBUG /Users/stlee/Dropbox/SharedFolders/SeongtaekDocs/Manuscripts/ASL-FAIR/Data/FAIR-EPIv2-injured-AllinOne/SCIDTI258_1dpi_test/vectors_nlmeans_single.c -o /var/folders/30/t_777qwx27zd6z5vdr3hls_80000gn/T/mex_2170662200551954_54357/vectors_nlmeans_single.o
Error using mex
xcodebuild: error: SDK "macosx10.15.6" cannot be located.
xcrun: error: sh -c '/Applications/Xcode.app/Contents/Developer/usr/bin/xcodebuild -sdk macosx10.15.6 -find
clang 2> /dev/null' failed with exit code 16384: (null) (errno=No such file or directory)
xcrun: error: unable to find utility "clang", not a developer tool or in PATH

Does anyone please teach me how to resolve this?

The installed version of iOS is macOS Catalina ver 10.15.6, and Xcode ver 12.0.1.

Thanks in advance.

[Walter Roberson]

Did you install the command line tools?

https://www.ics.uci.edu/~pattis/common/handouts/macmingweclipse/allexperimental/macxcodecommandlinetools.html

[Jason]

Hi. I ran the following on terminal.

xcode-select --install

It says comand line tools are already installed.

[Joseph Bellevue]

I am having a similar error. Did you get this resolved by chance? If so could you tell me how you fixed it?

[Jason]

Unfortunately, I haven't solved this error yet. Still don't know how to fix it ugh.

Answer 1

[Christoph]

Dear all,

I had the same problem and propose the following soltuion:

$xcrun -sdk macosx --show-sdk-version

10.15.6

In

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs

you see that a version with the number 10.15 is installed.

I usually changed the mexopts file in the home directory ~/.matlab/R2017b/ but this does not work. The reason is that the SDKVER Variable has the version number 10.15.6.

IF you do not want to change SETVER globally I can provide the follwing workaround (for the C-Compiler).

Copy from

/Applications/MATLAB_R2017b.app/bin/maci64/mexopts/clang_maci64.xml

to your home directory

~/.matlab/R2017b

in <var I changed

        CC="$XCRUN_DIR/xcrun -sdk macosx10.15 clang"
        CXX="$XCRUN_DIR/xcrun -sdk macosx10.15 clang++"

start Matlab und run

        mex -f ~/.matlab/R2017b/clang_maci64.xml *.c

Good luck!

Cheeers

Christoph

[Shuyi Zhang]

Finally! problem solved for Catalina 10.15.7, Thank you so much!

[William Ruppenthal]

I couldn't get Matlab to read that local options file after creating it, and couldn't find anything easily online about making sure it read the local options, but when I made the global change it worked!

[Yaelan Jung]

When I ran the last step (mex -f ~...), there is an error saying 'not enough input arguments', which is weird because I'm giving the file name as input. Would you have any ideas why there's an error? Thank you so much!

Answer 2

[Srinivas Gorur Shandilya]

I have written a tool to automatically fix this from within MATLAB. Find it here:

https://github.com/sg-s/matlab-catalina-compiler-fix