[ome-users] Install problems

[Ilya Goldberg]

Hi Glenn
I would highly recommend the 2.6.0 release candidate 3.  It is  
literally an announcement away from actual release, superseding 2.4.0.

Our OME servers here in Baltimore are all running FC4 now (with OS X  
10.4 developer boxes).  We used to have a variety of FCs around, but  
that got kind of out of hand.  I know that FC releases come pretty  
fast and furious, and we generally try to stay away from the "tip of  
the spear" while still maintaining a semblance of modernity.

As you have seen there is a great number of various independent  
projects and technologies that all need to come together in one place  
to make it all work.  For this reason we recommend using the exact  
version of one of the officially supported operating systems -  
especially for a first install.  Some people assume that Linux is  
Linux, but nothing could be further from the truth.

I have never tried FC5, so I don't know what surprises lie in wait  
for us there.  Apparently there are some.

I would not worry about the test cases for DBD::Pg.  Usually there is  
failure because we do not define a test database when installing  
DBD::Pg, though apparently in your case the failure is more serious.

The 2.6.0 installer isn't so easily fooled by bad DBD::Pg versions  
(so it prompted you to install a good version), but clearly it is not  
fool-proof.  The problem is that only certain combinations of DBD::Pg  
and DBI work together.  Execute this:
perl -e 'use DBD::Pg; print "$DBI::VERSION\n";'
and this:
perl -e 'use DBD::Pg; print "$DBD::Pg::VERSION\n";'

DBI should be 1.48 and DBD::Pg should be 1.43.  This is the current  
"blessed combination" known to work on 32-bit and 64-bit FC4 on Xeon,  
P4 and Opteron, as well as PPC and "Core Duo" OS X 10.4.  Postgres  
can also be a problem, though much less frequently.  We use 8.0.8  
(FC4) and 8.1.4 (OS X).
You can get DBI and DBD::Pg from our mirror here:
http://openmicroscopy.org/packages/perl/DBI-1.48.tar.gz
http://openmicroscopy.org/packages/perl/DBD-Pg-1.43.tar.gz
Let me know if you need help installing this manually (its the  
standard "perl Makefile.PL ; make ; sudo make install").

Believe it or not, this DBD::Pg/DBI tomfoolery has been going on for  
over 5 years.  I'm basically fed up with it, and we will probably  
start including our own DBI/DBD::Pg right in the distribution.   
People include everything under the sun in their Java apps, so why  
not us?  Of course, all this only works with certain versions of  
postgres as well, so maybe we need to include that?  Considering the  
problems that are now popping up with compiler incompatibility with  
Apache, and long-standing issues with mod_perl/apache combinations,  
heck - we should just put together our own Linux distro at that  
point.  It would certainly make a lot of these installation issues go  
away.

Cheer up, you're very close to the end.  The next hurdle is apache/ 
mod_perl, which from the looks of your 2.4.0 installation seems to be  
OK.  RedHat is better at maintaining a sane Apache/mod_perl combo  
than other distros, but lets not count any chickens just yet.
It will be good to collect some initial data on FC5.  Bet you didn't  
know you were a guinea pig!

-Ilya


On Sep 28, 2006, at 9:03 AM, Glenn Pierce wrote:

> Hi I am running Fedora Core 5 and I am having trouble with the  
> install.
>
> First I tried the stable version and I can get to the point where  
> the database is setup but one of the import xml files fails to import.
> The error is
>
> SUCCESS LOADING XML FILE "/home/glenn/development/OME/src/xml/OME/ 
> Core/Experiment.ome"
> SUCCESS LOADING XML FILE "/home/glenn/development/OME/src/xml/OME/ 
> Core/Plate.ome"
> SUCCESS LOADING XML FILE "/home/glenn/development/OME/src/xml/OME/ 
> Core/Screen.ome"
> SUCCESS LOADING XML FILE "/home/glenn/development/OME/src/xml/OME/ 
> Core/Experimenter.ome"
> SUCCESS LOADING XML FILE "/home/glenn/development/OME/src/xml/OME/ 
> Core/Group.ome"
> SUCCESS LOADING XML FILE "/home/glenn/development/OME/src/xml/OME/ 
> Core/Instrument.ome"
> SUCCESS LOADING XML FILE "/home/glenn/development/OME/src/xml/OME/ 
> Core/Image.ome"
> SUCCESS LOADING XML FILE "/home/glenn/development/OME/src/xml/OME/ 
> Core/OMEIS/Repository.ome"
> SUCCESS LOADING XML FILE "/home/glenn/development/OME/src/xml/OME/ 
> Core/OMEIS/OriginalFile.ome"
> ERROR LOADING XML FILE "/home/glenn/development/OME/src/xml/OME/ 
> Import/ImportModule.ome" -- OUTPUT: "DBD::Pg::st execute failed:  
> ERROR:  syntax error at or near "$1" at character 172
>
>
> I then tried the development version and when tring to install  
> DBD::Pg it fails to run the test cases.
>
> The error is
>
> Would you like to install the module from the OME repository ? [y/ 
> n]: y
>     \_ Pre-install [SUCCESS].
>     \_ Downloading http://openmicroscopy.org/packages/perl/DBD- 
> Pg-1.43.tar.gz [SUCCESS].
>     \_ Unpacking [SUCCESS].
>     \_ Configuring [SUCCESS].
>     \_ Compiling [SUCCESS].
>     \_ Testing [FAILURE].
>
>
> error is the folling repeated many times.
>
> Test returned status 255 (wstat 65280, 0xff00)
>  t/03dbmethod........Can't load '/usr/lib/perl5/vendor_perl/5.8.8/ 
> i386-linux-thread-multi/auto/DBI/DBI.so' for module DBI: /usr/lib/ 
> perl5/vendor_perl/5.8.8/i386-linux-thread-multi/auto/DBI/DBI.so:  
> undefined symbol: Perl_sv_2iv_flags at /usr/lib/perl5/5.8.8/i386- 
> linux-thread-multi/DynaLoader.pm line 230.
>   at /usr/lib/perl5/vendor_perl/5.8.8/i386-linux-thread-multi/ 
> DBI.pm line 259
>  BEGIN failed--compilation aborted at /usr/lib/perl5/vendor_perl/ 
> 5.8.8/i386-linux-thread-multi/DBI.pm line 259.
>  Compilation failed in require at t/03dbmethod.t line 15.
>  BEGIN failed--compilation aborted at t/03dbmethod.t line 15.
>  # Looks like your test died before it could output anything.
>  dubious
>
> Ideally I would like to run the developemt version as we have plans  
> to contribute.
> Has anyone seen this error ?
>
> Thanks
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