[ome-users] Installing OME-perl and MATLAB

[McCaughey, Michael J]

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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