[ome-users] matlab version

Anh Vu anh.q.vu at gmail.com
Thu Aug 4 19:11:58 BST 2005 

ls -lt before installation
total 80
drwxrwxr-x  2 avu avu  4096 Aug  4 23:18 CVS
-rwxrwxr-x  1 avu avu  7089 Jul 15 08:23 MatlabInfo.pl
-rwxrwxr-x  1 avu avu  2578 Jul  8 14:12 test.pl
-rw-rw-r--  1 avu avu  3255 Jul  7 12:26 Makefile.PL
-rw-rw-r--  1 avu avu 14492 Jan 21  2005 Matlab.pm
-rw-rw-r--  1 avu avu 31827 Jan  9  2005 Matlab.xs
-rw-rw-r--  1 avu avu   189 May 25  2004 typemap
-rw-rw-r--  1 avu avu   146 Jul 21  2003 Changes
-rw-rw-r--  1 avu avu    57 Jul 21  2003 MANIFEST

ls -lt after installation
total 216
drwxrwxr-x  5 root root  4096 Aug  4 09:02 blib
-rw-r--r--  1 avu  avu    146 Jul 21  2003 Changes
drwxrwxr-x  2 avu  avu   4096 Jul 22 23:16 CVS
-rw-r--r--  1 root root 25791 Aug  4 09:02 Makefile
-rw-r--r--  1 root root 25791 Jul 22 23:26 Makefile.old
-rw-r--r--  1 avu  avu   7281 Dec 23  2004 Makefile.PL
-rw-r--r--  1 avu  avu     57 Jul 21  2003 MANIFEST
-rw-rw-r--  1 root root 65977 Aug  4 09:02 Matlab.c
-rwxrwxr-x  1 avu  avu   7089 Jul 15 08:23 MatlabInfo.pl
-rw-r--r--  1 avu  avu  14492 Jan 21  2005 Matlab.pm
-rw-r--r--  1 avu  avu  31827 Jan  9  2005 Matlab.xs
-rw-rw-r--  1 root root     0 Aug  4 09:02 pm_to_blib
-rwxr-xr-x  1 avu  avu   2551 Sep  1  2004 test.pl
-rw-r--r--  1 avu  avu    189 May 25  2004 typemap


Also, I encountered an error on newest CVS built this is the details.
I think it searches for the files in /usr/local/matlab/etc in /etc.
This is the log for the error.

----------------------------
 Optional Perl Module Setup
----------------------------

(All verbose information logged in /var/tmp/OME/install/PerlModuleTask.log)

Testing MATLAB configuration
Use of uninitialized value in concatenation (.) or string at
/home/avu/OME/src/perl2/OME/Install/PerlModuleTask.pm line 698,
<STDIN> line 1.
Use of uninitialized value in concatenation (.) or string at
/home/avu/OME/src/perl2/OME/Install/PerlModuleTask.pm line 698,
<STDIN> line 1.
 \_ Checking if user  is licensed to run  Use of uninitialized value
in concatenation (.) or string at
/home/avu/OME/src/perl2/OME/Install/PerlModuleTask.pm line 699,
<STDIN> line 1.
Use of uninitialized value in concatenation (.) or string at
/home/avu/OME/src/perl2/OME/Install/PerlModuleTask.pm line 699,
<STDIN> line 1.
Use of uninitialized value in concatenation (.) or string at
/home/avu/OME/src/perl2/OME/Install/PerlModuleTask.pm line 701,
<STDIN> line 1.
Use of uninitialized value in concatenation (.) or string at
/home/avu/OME/src/perl2/OME/Install/PerlModuleTask.pm line 701,
<STDIN> line 1.
bash: line 1: -nodisplay: command not found
[FAILURE].
Use of uninitialized value in concatenation (.) or string at
/home/avu/OME/src/perl2/OME/Install/PerlModuleTask.pm line 715,
<STDIN> line 1.
MATLAB won't start.  is probably not licensed to run MATLAB.
Use of uninitialized value in concatenation (.) or string at
/home/avu/OME/src/perl2/OME/Install/PerlModuleTask.pm line 718,
<STDIN> line 1.
Use of uninitialized value in concatenation (.) or string at
/home/avu/OME/src/perl2/OME/Install/PerlModuleTask.pm line 718,
<STDIN> line 1.
Use of uninitialized value in concatenation (.) or string at
/home/avu/OME/src/perl2/OME/Install/PerlModuleTask.pm line 718,
<STDIN> line 1.


Errors executing task: Couldn't open /etc/MLM.opt for reading at (eval
33) line 1

        main::run_tasks() called at OME/install.pl line 249
# Looks like your test died before it could output anything.


On 8/3/05, T. J. Macura <tm289 at cam.ac.uk> wrote:
> Anh,
> 
> This means that the OME/Matlab connector can be installed. In the
> worse-case you might be able to install it by hand (i.e. avoiding the
> OME Installer).
> 
> The only way I can reproduce what you are seeing is if I `touch
> Makefile.PL` after `perl Makefile.PL` but before `make`;
> 
> Please try ls -lT in the src/perl2/OME/Matlab directory before and
> after your install (send me the output).
> 
> I would like to see if the date of Makefile.PL date is modified. I
> can't imagine why it would be.
> 
> Tom
> 
> On Aug 3, 2005, at 3:20 PM, Anh Vu wrote:
> 
> > 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%2FPerl
> >> Mo
> >> 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
> >>>
> >>
> >>
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >
> 
>

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