[ome-users] matlab version

Anh Vu anh.q.vu at gmail.com
Wed Aug 3 20:20:28 BST 2005 

I did as you instructed, however, I had to su then do make clean
because the blib folder is owned by root because I previously did an
installation using sudo.
And these are the results. It looks like it works. The user name that
I have matlab license for is avu.
------------------------------------------------------------------------------------------------------------------------
[avu at batch2112b Matlab]$ su
Password:
[root at batch2112b Matlab]# make clean
rm -rf Matlab.c ../blib ./blib Makefile.aperl
blib/arch/auto/OME/Matlab/extralibs.all
blib/arch/auto/OME/Matlab/extralibs.ld perlmain.c tmon.out mon.out
so_locations pm_to_blib *.o *.a perl.exe perl perl Matlab.bs
Matlab.bso Matlab.def libMatlab.def Matlab.exp Matlab.x core
core.*perl.*.? *perl.core core.[0-9] core.[0-9][0-9]
core.[0-9][0-9][0-9] core.[0-9][0-9][0-9][0-9]
core.[0-9][0-9][0-9][0-9][0-9]
mv Makefile Makefile.old > /dev/null 2>&1
[root at batch2112b Matlab]# ls
Changes  Makefile.old  MANIFEST       Matlab.pm  test.pl
CVS      Makefile.PL   MatlabInfo.pl  Matlab.xs  typemap
[root at batch2112b Matlab]# exit
exit
[avu at batch2112b Matlab]$ perl Makefile.PL
Matlab Vers: glnx86
Matlab Arch: /usr/local/matlab
Matlab Home: 7.0.4.352
Include:  -I/usr/local/matlab/extern/include
Lib:      -L/usr/local/matlab/bin/glnx86 -lmx -leng -lut -lmat
-licudata -licui18n -licuuc -lustdio -lz
Lib Path: /usr/local/matlab/bin/glnx86

Checking if your kit is complete...
Looks good
Modifying LD_RUN_PATH...
Modifying LD_LIBRARY_PATH...
Adding LD_LIBRARY_PATH to Make Test ...
Writing Makefile for OME::Matlab
[avu at batch2112b Matlab]$ make
cp Matlab.pm blib/lib/OME/Matlab.pm
cp MatlabInfo.pl blib/lib/OME/MatlabInfo.pl
/usr/bin/perl /usr/lib/perl5/5.8.3/ExtUtils/xsubpp  -typemap
/usr/lib/perl5/5.8.3/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
-DTHREADS_HAVE_PIDS -DDEBUGGING -fno-strict-aliasing
-I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
-I/usr/include/gdbm -O2 -g -pipe -march=i386 -mcpu=i686  
-DVERSION=\"2.004001\" -DXS_VERSION=\"2.004001\" -fPIC
"-I/usr/lib/perl5/5.8.3/i386-linux-thread-multi/CORE"   Matlab.c
In file included from /usr/local/matlab/extern/include/matrix.h:203,
                 from Matlab.xs:41:
/usr/local/matlab/extern/include/tmwtypes.h:682: warning: useless
keyword or type name in empty declaration
/usr/local/matlab/extern/include/tmwtypes.h:682: warning: empty declaration
Matlab.xs: In function `XS_OME__Matlab__Array_getAll':
Matlab.xs:743: warning: use of cast expressions as lvalues is deprecated
Matlab.xs:746: warning: use of cast expressions as lvalues is deprecated
Matlab.xs:749: warning: use of cast expressions as lvalues is deprecated
Matlab.xs:752: warning: use of cast expressions as lvalues is deprecated
Matlab.xs:755: warning: use of cast expressions as lvalues is deprecated
Matlab.xs:758: warning: use of cast expressions as lvalues is deprecated
Matlab.xs:761: warning: use of cast expressions as lvalues is deprecated
Matlab.xs:764: warning: use of cast expressions as lvalues is deprecated
Matlab.xs:767: warning: use of cast expressions as lvalues is deprecated
Matlab.xs:770: warning: use of cast expressions as lvalues is deprecated
Running Mkbootstrap for OME::Matlab ()
chmod 644 Matlab.bs
rm -f blib/arch/auto/OME/Matlab/Matlab.so
gcc  -shared -L/usr/local/lib Matlab.o  -o
blib/arch/auto/OME/Matlab/Matlab.so   -L/usr/local/matlab/bin/glnx86
-lmx -leng -lut -lmat -licudata -licui18n -licuuc -lustdio -lz
-L/usr/local/lib
chmod 755 blib/arch/auto/OME/Matlab/Matlab.so
cp Matlab.bs blib/arch/auto/OME/Matlab/Matlab.bs
chmod 644 blib/arch/auto/OME/Matlab/Matlab.bs
Manifying blib/man3/OME::Matlab.3pm
[avu at batch2112b Matlab]$ make test
PERL_DL_NONLAZY=1 LD_LIBRARY_PATH=/usr/local/matlab/bin/glnx86
/usr/bin/perl "-Iblib/lib" "-Iblib/arch" test.pl
Trying to compute 4x8 using MATLAB ...
Perl: OME::Matlab::Array=SCALAR(0x98f6b3c)
    Class:  double
    Order:  2
    Dims:   1x1
    Values: (32)
Test Passed. Perl Matlab API is correctly installed.
[avu at batch2112b Matlab]$



On 8/3/05, T. J. Macura <tm289 at cam.ac.uk> wrote:
> Dear Anh,
> 
> The complications with the MATLAB/perl connector have been resolved
> just now.  Basically, on our smoke-test system the user that is
> licensed to run MATLAB changed but the OME installer didn't catch this.
> The OME installer now always checks that a specified user is licensed
> to run MATLAB.
> 
> Here is what I did:
> http://cvs.openmicroscopy.org.uk/horde/chora/diff.php?
> r1=1.48&r2=1.49&ty=h&num=10&f=OME%2Fsrc%2Fperl2%2FOME%2FInstall%2FPerlMo
> duleTask.pm
> 
> Although this OME-MATLAB connector runs on at least four different
> architectures in our lab, including Fedora Core 1, 2, 3 I have never
> seen what you are describing so I am very interested in finding the
> source of your problem.
> 
> Please try this and email me the output
> 
> Please login as anh (i.e. the Matlab user)
> goto src/perl2/OME/Matlab
> make clean
> perl Makefile.PL
> make
> make test
> 
> Tom
> On Aug 3, 2005, at 2:24 PM, Anh Vu wrote:
> 
> > I checked and I have the correct date and I just downloaded the latest
> > CVS version to install again but I still have no luck at the part
> > where it begins testing the matlab perl module. IIya was saying in an
> > earlier email that there was some complications with the matlab/perl
> > connector so could it be that it is something still unresolved?
> >
> > Thanks!
> > -Anh
> >
> > On 8/2/05, T. J. Macura <tm289 at cam.ac.uk> wrote:
> >> Dear Anh,
> >>
> >> Sorry for the delay. In the last week I was very close to Bisons,
> >> Bears, Moose, and Mountains but far from internet access.
> >>
> >> According to some sites I found googling, you might have date skew
> >> Please verify that your date is correct (i.e. not set to the past),
> >>
> >> http://www.google.com/search?client=safari&rls=en&q=Makefile+out-of-
> >> date+with+respect+to+Makefile.PL
> >>
> >> Please let me know how it goes,
> >>
> >> Tom
> >>
> >> On Jul 28, 2005, at 10:30 AM, Ilya Goldberg wrote:
> >>
> >>> Hi Anh
> >>> We're having some issues with the matlab/perl connector right now (it
> >>> started blowing up our automated nightly builds a couple of days ago
> >>> as well).
> >>> I'm sorry to inflict you with this, but please understand that this
> >>> is
> >>> pre-release (i.e. experimental) code, so you can't expect it to be as
> >>> robust.
> >>> We'll see if we can get to the bottom of this in the next day or so,
> >>> and keep you posted.
> >>>
> >>> -Ilya
> >>>
> >>>
> >>> On Jul 27, 2005, at 4:31 PM, Anh Vu wrote:
> >>>
> >>>> I did a fresh CVS checkout. I first delete the OME folder in my home
> >>>> dir then used the following commands.
> >>>>
> >>>> $ cvs -d ':pserver:anoncvs at cvs.openmicroscopy.org.uk:/ome' login
> >>>> (Enter "anoncvs" for the password)
> >>>> $ cvs -z3 -d ':pserver:anoncvs at cvs.openmicroscopy.org.uk:/ome'
> >>>> checkout OME
> >>>>
> >>>> then i ran the install after su and this is the result I get from
> >>>> the
> >>>> log file.
> >>>>
> >>>>
> >>>
> >>>
> >>> [SNIP]
> >>>
> >>> _______________________________________________
> >>> ome-users mailing list
> >>> ome-users at lists.openmicroscopy.org.uk
> >>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >>>
> >>
> >>
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >
> 
>

More information about the ome-users mailing list