[ome-users] ome-users Digest, Vol 24, Issue 6

Mon Mar 19 15:17:05 GMT 2007

Aaron,

This warning message is "normal" . I talked to Ilya about this some time ago when I was installing OME on Fedora. So far this message didn't have any noticable effect for me.

Great job by the way for installing OME. Hope everything else will work, too....

Best,

Bernd

-----Original Message-----
From: ome-users-bounces at lists.openmicroscopy.org.uk [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Ponti, Aaron
Sent: Monday, March 19, 2007 10:33 AM
To: ome-users at lists.openmicroscopy.org.uk
Subject: Re: [ome-users] ome-users Digest, Vol 24, Issue 6

Hi

With Ilya's help I managed to solve my problem of missing Perl headers: Mandriva Linux does not install devel packages by default, and therefore I was missing the perl-devel package containing the headers. Installing perl-devel, the installation indeed works.

This does _NOT_ mean that installation went smooth: I had at least 10 more problems, but in the end I managed to get ome installed. This to tell people out there with Mandriva: if you are willing to fight a bit you should manage to get ome up and running. Just remember to install perl-DBD-Pg version 1.43 (e.g. from http://rpmseek.com/rpm/perl-DBD-Pg-1.43-2mdk.i586.html?hl=com&cs=perl-dbd-Pg:PN:0:0:0:0:2807253) instead of version 1.49 that comes with Mandriva 2007. You will find all other required packages in Mandriva's standard repositories.

The only thing that is not clear to me is following warning from the apache web server at startup:

Starting httpd: [Mon Mar 19 15:20:47 2007] [warn] The ScriptAlias directive in /OME/conf/httpd2.omeis.conf at line 2 will probably never match because it overlaps an earlier ScriptAlias.

Still, OME seems to work (so far).

Aaron

-----Original Message-----
From: ome-users-bounces at lists.openmicroscopy.org.uk [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of ome-users-request at lists.openmicroscopy.org.uk
Sent: Sunday, March 18, 2007 1:00 PM
To: ome-users at lists.openmicroscopy.org.uk
Subject: ome-users Digest, Vol 24, Issue 6

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Today's Topics:

   1. Re: Installation of OME server 2.6.0 stable fails on	Mandriva
      2007 (Ilya Goldberg)

----------------------------------------------------------------------

Message: 1
Date: Sat, 17 Mar 2007 10:47:54 -0400
From: Ilya Goldberg <igg at nih.gov>
Subject: Re: [ome-users] Installation of OME server 2.6.0 stable fails
	on	Mandriva 2007
To: "Ponti, Aaron" <aaron.ponti at fmi.ch>
Cc: ome-users at lists.openmicroscopy.org.uk
Message-ID: <1B3B8D64-EF22-487D-8324-352FBECCAC52 at nih.gov>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed

It appears that Mandriva 2007 doesn't have a complete installation of
Perl:
>  make[1]: *** No rule to make target `/usr/lib/perl5/5.8.8/i386- 
> linux/CORE/EXTERN.h', needed by `Pix.o'.  Stop.

You might try:
find /usr/lib/perl5/5.8.8 -name "EXTERN.h"

If the header EXTERN.h is in a different path than "/usr/lib/ perl5/5.8.8/i386-linux/CORE/EXTERN.h", then perl isn't configured properly to know where its header files are.  If you don't find EXTERN.h at all, it might simply mean that the perl you've installed was distributed without header files.  In any case, a misconfigured perl on a unix OS doesn't bode very well.

If you are interested in getting OME to run, I would recommend a supported platform (FedoraCore or Debian).  If you're interested in getting it running on Mandriva 2007 specifically, it looks like there might be some trouble.  The fact that there are missing header files isn't encouraging.

This could potentially be an artifact of user permissions, or the location where you're trying to install.  Are you trying to install it from /tmp? Maybe trying it from a normal user's home directory would work better.

Good luck,
Ilya

On Mar 15, 2007, at 11:21 AM, Ponti, Aaron wrote:

> Hello everybody
>
> I have been trying to install the OME server 2.6.0 on Mandriva 2007 
> without success.
>
> All dependencies appear to be fulfilled (I had to downgrade perl- 
> DBD-Pg from 1.49 to 1.43 - although through rpm and not directly from 
> the OME installer since it crashes when it tries). Here the
> output:
>
> ----------------------------------------------------------------------
> ----------
> ----------------------------------------------------------------------
> ----------------------------------------------------------------------
> --------------------
>
> # perl install.pl -a
>   \_ libssl 0.9.8 [OK].
>   \_ libpng 1.2.12 [OK].
>   \_ libjpeg 62 [OK].
>   \_ libcurl 7.15.5 [OK].
>   \_ libtiff 3.8.2 [OK].
>   \_ zlib 1.2.3 [OK].
>   \_ libdb_B-Tree 3 [OK].
>   \_ libxml2 2.6.26 [OK].
>   \_ libxslt 1.1.17 [OK].
>   \_ expat 1.95 [OK].
>   \_ bzlib N/A [OK].
>
>   \_ Term::ReadKey 2.30 [OK].
>   \_ Storable 2.15 [OK].
>   \_ Carp::Assert 0.18 [OK].
>   \_ Compress::Zlib 1.42 [OK].
>   \_ DBI 1.52 [OK].
>   \_ Digest::MD5 2.36 [OK].
>   \_ MD5 [OK].
>   \_ MIME::Base64 3.07 [OK].
>   \_ Log::Agent 0.306 [OK].
>   \_ Time::HiRes 1.86 [OK].
>   \_ DBD::Pg 1.43 [OK].
>   \_ Test::Harness 2.56 [OK].
>   \_ Test::Simple 0.62 [OK].
>   \_ HTML::Template 2.7 [OK].
>   \_ IPC::Run 0.79 [OK].
>   \_ Class::Accessor 0.19 [OK].
>   \_ Class::Data::Inheritable 0.02 [OK].
>   \_ File::Temp 0.16 [OK].
>   \_ Exporter::Lite 0.01 [OK].
>   \_ UNIVERSAL::exports 0.03 [OK].
>   \_ URI 1.35 [OK].
>   \_ HTML::Tagset 3.10 [OK].
>   \_ HTML::Parser 3.54 [OK].
>   \_ Parse::RecDescent 1.94 [OK].
>   \_ Inline::C 0.44 [OK].
>   \_ XML::NamespaceSupport 1.09 [OK].
>   \_ XML::Sax 1.01 [OK].
>   \_ XML::LibXML::Common 0.13 [OK].
>   \_ XML::LibXML 1.60 [OK].
>   \_ XML::Parser 2.34 [OK].
>   \_ SOAP::Lite 0.69 [OK].
>   \_ XML::LibXSLT 1.60 [OK].
>   \_ OLE::Storage_Lite 0.14 [OK].
>   \_ Spreadsheet::ParseExcel 0.2603 [OK].
> Check passed
>
> ----------------------------------------------------------------------
> ----------
> ----------------------------------------------------------------------
> ----------------------------------------------------------------------
> --------------------
>
>
> When I try to install, everything goes smooth until I get to the Core 
> Perl Module Setup, then:
>
> ----------------------------------------------------------------------
> ----------
> ----------------------------------------------------------------------
> ----------------------------------------------------------------------
> --------------------
>
> ------------------------
>  Core Perl Module Setup
> ------------------------
>
> (All verbose information logged in /var/tmp/OME/install/
> PerlModuleTask.log)
>
> Installing modules
>   \_ Configuring [SUCCESS].
>   \_ Compiling [FAILURE].
>
>
> Errors executing task: Unable to compile module, see 
> PerlModuleTask.log for details. at (eval 39) line 1
>
>  at install.pl line 81
>         main::run_tasks() called at install.pl line 265 # Looks like 
> your test died before it could output anything.
>
> Line 265 of install.pl is
> 	
> 	run_tasks ();
>
> This is the content of the PerlModuleTask.lig file:
>
> ----------------------------------------------------------------------
> ----------
> ----------------------------------------------------------------------
> ----------------------------------------------------------------------
> --------------------
>
> USING PERL CONFIGURE SCRIPT -- 'perl Makefile.PL '
> SUCCESS -- OUTPUT: "You can remove all previous versions of OME with 
> the following command:
>  perl Makefile.PL uninstall
>  --------------------------
>  Performing `make clean` in directory /tmp/OME/src/perl2/OME/Matlab
>  make: *** No rule to make target `clean'.  Stop.
>  Checking if your kit is complete...
>  Warning: the following files are missing in your kit:
>  	OME/ImportEngine/.#AbstractFormat.pm.1.44
>  	OME/ImportEngine/.#TIFFreader.pm.1.42
>  	OME/ImportEngine/FilenamePatternNotes.txt
>  	OME/Remote/XMLRPC.pm
>  	OME/Util/Annotate/Annotate.pm
>  	OME/Util/ChainStats.pm
>  Please inform the author.
>  WARNING:  libtiff must be installed !
>  Checking if your kit is complete...
>  Looks good
>  Writing Makefile for OME::Image::Pix
>  Checking if your kit is complete...
>  Looks good
>  Writing Makefile for Repacker
>  Writing Makefile for OME
> "
>
> COMPILING MODULE -- 'make'
> FAILURE -- OUTPUT: "cp OME/Web/DefaultHeaderBuilder.pm /tmp/OME/src/ 
> perl2/blib/lib/OME/Web/DefaultHeaderBuilder.pm
>  cp OME/Install/CoreSystemTask.pm /tmp/OME/src/perl2/blib/lib/OME/ 
> Install/CoreSystemTask.pm  cp 
> OME/Web/DBObjRender/__OME_AnalysisChain_Link.pm /tmp/OME/src/ 
> perl2/blib/lib/OME/Web/DBObjRender/__OME_AnalysisChain_Link.pm
>  cp OME/LookupTable/Entry.pm /tmp/OME/src/perl2/blib/lib/OME/ 
> LookupTable/Entry.pm
>
> ...
>
>  cp OME/Analysis/Engine/install_worker_node.pl /tmp/OME/src/perl2/ 
> blib/lib/OME/Analysis/Engine/install_worker_node.pl
>  cp OME/Image/Server/File.pm /tmp/OME/src/perl2/blib/lib/OME/Image/
> Server/File.pm
>  cp OME/ImportEngine/DVreader.pm /tmp/OME/src/perl2/blib/lib/OME/ 
> ImportEngine/DVreader.pm  cp OME/Image/Pix/Makefile.PL 
> /tmp/OME/src/perl2/blib/lib/OME/Image/
> Pix/Makefile.PL
>  cp OME/Web/DBObjDetail/__Category.pm /tmp/OME/src/perl2/blib/lib/ 
> OME/Web/DBObjDetail/__Category.pm
>  make[1]: Entering directory `/tmp/OME/src/perl2/OME/Image/Pix'
>  cp Pix.pm /tmp/OME/src/perl2/blib/lib/OME/Image/Pix.pm
>  /usr/bin/perl5.8.8 /usr/lib/perl5/5.8.8/ExtUtils/xsubpp  -typemap / 
> usr/lib/perl5/5.8.8/ExtUtils/typemap -typemap typemap  Pix.xs > 
> Pix.xsc && mv Pix.xsc Pix.c
>  make[1]: *** No rule to make target `/usr/lib/perl5/5.8.8/i386- 
> linux/CORE/EXTERN.h', needed by `Pix.o'.  Stop.
>  make[1]: Leaving directory `/tmp/OME/src/perl2/OME/Image/Pix'
>  make: *** [subdirs] Error 2
> "
>
> ----------------------------------------------------------------------
> ----------
> ----------------------------------------------------------------------
> ----------------------------------------------------------------------
> --------------------
>
> Any idea? Let me know if you need more information.
>
> Aaron
>
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>

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