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<TITLE>Installing OME-perl and MATLAB</TITLE>
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<P><FONT SIZE=2>Hey all;<BR>
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<BR>
<BR>
'Gathering information about your MATLAB installation<BR>
Matlab Vers: 7.5.0.338<BR>
Matlab Arch: glnxa64<BR>
Matlab Root: /usr/local/matlab<BR>
Include: -I/usr/local/matlab/extern/include<BR>
Lib: -L/usr/local/matlab/bin/glnxa64 -lmx -leng -lut -lmat -lustdio -lz<BR>
<BR>
target dir is /usr/local/matlab/bin/glnxa64<BR>
matlab lib src is /usr/local/matlab/bin/glnxa64<BR>
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" -<BR>
version="7.5.0.338"'<BR>
SUCCESS -- OUTPUT: "define is<BR>
<BR>
Checking if your kit is complete...<BR>
Looks good<BR>
Note (probably harmless): No library found for -lustdio<BR>
Modifying LD_RUN_PATH...<BR>
Modifying LD_LIBRARY_PATH...<BR>
Writing Makefile for OME::Matlab<BR>
"<BR>
<BR>
COMPILING MODULE -- 'make'<BR>
FAILURE -- OUTPUT: "cp Matlab.pm blib/lib/OME/Matlab.pm<BR>
cp Compiled.pm blib/lib/OME/Compiled.pm<BR>
cp compileDynamicLibraries.pl blib/lib/OME/compileDynamicLibraries.pl<BR>
cp writeLibraryPackage.pl blib/lib/OME/writeLibraryPackage.pl<BR>
/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<BR>
Please specify prototyping behavior for Matlab.xs (see perlxs manual)<BR>
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 -<BR>
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<BR>
ION=\"2.007\" -DXS_VERSION=\"2.007\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" Matlab.c<BR>
In file included from /usr/local/matlab/extern/include/matrix.h:316,<BR>
from Matlab.xs:41:<BR>
/usr/local/matlab/extern/include/tmwtypes.h:730: error: two or more data types in declaration specifiers<BR>
/usr/local/matlab/extern/include/tmwtypes.h:730: warning: useless type name in empty declaration<BR>
Matlab.xs: In function ‘XS_OME__Matlab__Array_newNumericScalar’:<BR>
Matlab.xs:222: warning: ISO C90 forbids mixed declarations and code<BR>
Matlab.c:451: warning: unused variable ‘package’<BR>
Matlab.c: In function ‘XS_OME__Matlab__Array_newLogicalScalar’:<BR>
Matlab.c:530: warning: unused variable ‘package’<BR>
Matlab.c: In function ‘XS_OME__Matlab__Array_newStringScalar’:<BR>
Matlab.c:550: warning: unused variable ‘package’<BR>
Matlab.c: In function ‘XS_OME__Matlab__Array_newDoubleMatrix’:<BR>
Matlab.c:570: warning: unused variable ‘package’<BR>
Matlab.c: In function ‘XS_OME__Matlab__Array_newLogicalMatrix’:<BR>
Matlab.c:598: warning: unused variable ‘package’<BR>
Matlab.c: In function ‘XS_OME__Matlab__Array_newNumericMatrix’:<BR>
Matlab.c:619: warning: unused variable ‘package’<BR>
Matlab.c: In function ‘XS_OME__Matlab__Array_newStructMatrix’:<BR>
Matlab.c:654: warning: unused variable ‘package’<BR>
Matlab.c: In function ‘XS_OME__Matlab__Array_newLogicalArray’:<BR>
Matlab.c:706: warning: unused variable ‘package’<BR>
Matlab.c: In function ‘XS_OME__Matlab__Array_newStringArray’:<BR>
Matlab.c:736: warning: unused variable ‘package’<BR>
Matlab.c: In function ‘XS_OME__Matlab__Array_newNumericArray’:<BR>
Matlab.c:785: warning: unused variable ‘package’<BR>
Matlab.xs: In function ‘XS_OME__Matlab__Array_dimensions’:<BR>
Matlab.xs:480: warning: ISO C90 forbids mixed declarations and code<BR>
Matlab.xs: In function ‘XS_OME__Matlab__Array_getString’:<BR>
Matlab.xs:644: warning: ISO C90 forbids mixed declarations and code<BR>
Matlab.xs: In function ‘XS_OME__Matlab__Array_get’:<BR>
Matlab.xs:658: warning: ISO C90 forbids mixed declarations and code<BR>
Matlab.xs:675: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘mwSize’<BR>
Matlab.xs: In function ‘XS_OME__Matlab__Array_set’:<BR>
Matlab.xs:731: warning: ISO C90 forbids mixed declarations and code<BR>
Matlab.xs: In function ‘XS_OME__Matlab__Array_getAll’:<BR>
Matlab.xs:815: warning: ISO C90 forbids mixed declarations and code<BR>
Matlab.xs: In function ‘XS_OME__Matlab__Array_setAll’:<BR>
Matlab.xs:874: warning: ISO C90 forbids mixed declarations and code<BR>
Matlab.c: In function ‘XS_OME__Matlab__Engine_open’:<BR>
Matlab.c:2107: warning: unused variable ‘package’<BR>
make: *** [Matlab.o] Error 1<BR>
"<BR>
<BR>
<BR>
Line 730 in /usr/local/matlab/extern/include/tmwtypes.h is:<BR>
typedef boolean_T bool;<BR>
<BR>
Matlab runs fine normally.<BR>
<BR>
Has anyone seen this before?<BR>
<BR>
Thanks, Mike<BR>
<BR>
Michael J. McCaughey, PhD<BR>
Molecular Physiology and Biophysics<BR>
U9203 MRBIII<BR>
6-6175<BR>
<BR>
</FONT>
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