[ome-users] Installing OME-perl and MATLAB

[Tom Macura]

Hi Mike,
The OME/MATLAB connector failed because of the following compilation  
error:

>  /usr/local/matlab/extern/include/tmwtypes.h:730: error: two or  
> more data types in declaration specifiers
>  /usr/local/matlab/extern/include/tmwtypes.h:730: warning: useless  
> type name in empty declaration
>
As discussed on the FAQ at the bottom of the OME-MATLAB installer  
instructions on the web-page: (http://www.openmicroscopy.org.uk/ 
install/matlab-connector.html)

You need to add #include <stdbool.h> to tmwtypes.h.

Newer versions of the gcc complier (gcc-4.x) are C99 compliant.  
Previous C standards didn't define the boolean type and so various  
incompatible methods were used to simulate the booleans. In the C99  
standard the bool keyword is defined in its own header (stdbool.h).

Let me know if you continue to have problems. We're glad you're  
trying out OME+MATLAB :)

Best,

Tom



On Oct 26, 2007, at 7:43 PM, McCaughey, Michael J wrote:

> Hey all;
> I'm installing OME 2.6.1 on a new server, and ran into an issue  
> with Matlab.  Installation starts wll, but the tail end of  
> MatlabTask.log looks like
>
> 'Gathering information about your MATLAB installation
> Matlab Vers: 7.5.0.338
> Matlab Arch: glnxa64
> Matlab Root: /usr/local/matlab
> Include: -I/usr/local/matlab/extern/include
> Lib:     -L/usr/local/matlab/bin/glnxa64 -lmx -leng -lut -lmat - 
> lustdio -lz
>
> target dir is /usr/local/matlab/bin/glnxa64
> matlab lib src is /usr/local/matlab/bin/glnxa64
> USING PERL CONFIGURE SCRIPT -- 'perl Makefile.PL -include="-I/usr/ 
> local/matlab/extern/include" -lib="-L/usr/local/matlab/bin/glnxa64 - 
> lmx -leng -lut -lmat -lustdio -lz" -
> version="7.5.0.338"'
> SUCCESS -- OUTPUT: "define is
>
>  Checking if your kit is complete...
>  Looks good
>  Note (probably harmless): No library found for -lustdio
>  Modifying LD_RUN_PATH...
>  Modifying LD_LIBRARY_PATH...
>  Writing Makefile for OME::Matlab
> "
>
> COMPILING MODULE -- 'make'
> FAILURE -- OUTPUT: "cp Matlab.pm blib/lib/OME/Matlab.pm
>  cp Compiled.pm blib/lib/OME/Compiled.pm
>  cp compileDynamicLibraries.pl blib/lib/OME/compileDynamicLibraries.pl
>  cp writeLibraryPackage.pl blib/lib/OME/writeLibraryPackage.pl
>  /usr/bin/perl /usr/lib/perl5/5.8.8/ExtUtils/xsubpp  -typemap /usr/ 
> lib/perl5/5.8.8/ExtUtils/typemap -typemap typemap  Matlab.xs >  
> Matlab.xsc && mv Matlab.xsc Matlab.c
>  Please specify prototyping behavior for Matlab.xs (see perlxs manual)
>  gcc -c  -I/usr/local/matlab/extern/include -D_REENTRANT - 
> D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after- 
> statement -I/usr/local/include -D_LARGEFILE_SOURCE -
> D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall -Wp,- 
> D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp- 
> buffer-size=4 -m64 -mtune=generic   -DVERS
> ION=\"2.007\" -DXS_VERSION=\"2.007\" -fPIC "-I/usr/lib64/ 
> perl5/5.8.8/x86_64-linux-thread-multi/CORE"   Matlab.c
>  In file included from /usr/local/matlab/extern/include/matrix.h:316,
>                   from Matlab.xs:41:
>  /usr/local/matlab/extern/include/tmwtypes.h:730: error: two or  
> more data types in declaration specifiers
>  /usr/local/matlab/extern/include/tmwtypes.h:730: warning: useless  
> type name in empty declaration
>  Matlab.xs: In function ‘XS_OME__Matlab__Array_newNumericScalar’:
>  Matlab.xs:222: warning: ISO C90 forbids mixed declarations and code
>  Matlab.c:451: warning: unused variable ‘package’
>  Matlab.c: In function ‘XS_OME__Matlab__Array_newLogicalScalar’:
>  Matlab.c:530: warning: unused variable ‘package’
>  Matlab.c: In function ‘XS_OME__Matlab__Array_newStringScalar’:
>  Matlab.c:550: warning: unused variable ‘package’
>  Matlab.c: In function ‘XS_OME__Matlab__Array_newDoubleMatrix’:
>  Matlab.c:570: warning: unused variable ‘package’
>  Matlab.c: In function ‘XS_OME__Matlab__Array_newLogicalMatrix’:
>  Matlab.c:598: warning: unused variable ‘package’
>  Matlab.c: In function ‘XS_OME__Matlab__Array_newNumericMatrix’:
>  Matlab.c:619: warning: unused variable ‘package’
>  Matlab.c: In function ‘XS_OME__Matlab__Array_newStructMatrix’:
>  Matlab.c:654: warning: unused variable ‘package’
>  Matlab.c: In function ‘XS_OME__Matlab__Array_newLogicalArray’:
>  Matlab.c:706: warning: unused variable ‘package’
>  Matlab.c: In function ‘XS_OME__Matlab__Array_newStringArray’:
>  Matlab.c:736: warning: unused variable ‘package’
>  Matlab.c: In function ‘XS_OME__Matlab__Array_newNumericArray’:
>  Matlab.c:785: warning: unused variable ‘package’
>  Matlab.xs: In function ‘XS_OME__Matlab__Array_dimensions’:
>  Matlab.xs:480: warning: ISO C90 forbids mixed declarations and code
>  Matlab.xs: In function ‘XS_OME__Matlab__Array_getString’:
>  Matlab.xs:644: warning: ISO C90 forbids mixed declarations and code
>  Matlab.xs: In function ‘XS_OME__Matlab__Array_get’:
>  Matlab.xs:658: warning: ISO C90 forbids mixed declarations and code
>  Matlab.xs:675: warning: format ‘%d’ expects type ‘int’, but  
> argument 4 has type ‘mwSize’
>  Matlab.xs: In function ‘XS_OME__Matlab__Array_set’:
>  Matlab.xs:731: warning: ISO C90 forbids mixed declarations and code
>  Matlab.xs: In function ‘XS_OME__Matlab__Array_getAll’:
>  Matlab.xs:815: warning: ISO C90 forbids mixed declarations and code
>  Matlab.xs: In function ‘XS_OME__Matlab__Array_setAll’:
>  Matlab.xs:874: warning: ISO C90 forbids mixed declarations and code
>  Matlab.c: In function ‘XS_OME__Matlab__Engine_open’:
>  Matlab.c:2107: warning: unused variable ‘package’
>  make: *** [Matlab.o] Error 1
> "
>
>
> Line 730 in /usr/local/matlab/extern/include/tmwtypes.h is:
> typedef boolean_T bool;
>
> Matlab runs fine normally.
>
> Has anyone seen this before?
>
> Thanks, Mike
>
> Michael J. McCaughey, PhD
> Molecular Physiology and Biophysics
> U9203 MRBIII
> 6-6175
>
>
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