[ome-users] Help with OME installation on Fedora Core 6, (mod_perl not configured error...)
Jerome Avondo
jeromeavondo at msn.com
Wed Jan 23 09:41:22 GMT 2008
hi,
Thanks for the reply.
I tried rerunnig the installation script, but it still produces the same error. Im a bit stuck as out of ideas for what it could be...
Ive copied the contents of my /var/tmp/ OME/install/ApacheConfigTask.log logfile at the end of this message. Had a look at it but to be honest couldnt spot anything....
j.
--------------------------------------
ApacheConfigTask.log
--------------------------------------
Apache setup
Apache binary: /usr/sbin/httpd
apachectl binary: /usr/sbin/apachectl
httpd root: /etc/httpd
httpd conf: /etc/httpd/conf/httpd.conf
httpd version: 2
Apache configuration:
Configure Apache?: yes
Developer configuration: no
Server restart?: yes
Install OME servers:
Images (omeis): yes
Data (omeds): yes
Web: yes
Apache directories:
httpd binary: /usr/sbin/httpd
apachectl binary: /usr/sbin/apachectl
DocumentRoot: /var/www/html
cgi-bin: /var/www/cgi-bin
Web-UI HTML Templates:
Developer configuration: no
Configuring Apache
httpd.conf is /etc/httpd/conf/httpd.conf
Installing OMEIS
Copying src/C/omeis/omeis to /var/www/cgi-bin/omeis
chmod 0755 /var/www/cgi-bin/omeis
chown /var/www/cgi-bin/omeis to uid: 48 gid: 501
Set APACHE_OMEIS_INCLUDE to Include /OME/conf/httpd2.omeis.conf
Forking a process to upgrade OMEIS
Installing OMEDS
Set APACHE_OMEDS_INCLUDE to Include /OME/conf/httpd2.omeds.conf
Installing WEB
Copying src/perl2/serve.pl to /OME/perl2/serve.pl
chmod 0755 /OME/perl2/serve.pl
chown /OME/perl2/serve.pl to uid: 48 gid: 501
Copying src/html/index.html to /var/www/html/index.html
chmod 0644 /var/www/html/index.html
chmod 0644 /var/www/html/favicon.ico
Set APACHE_WEB_INCLUDE to Include /OME/conf/httpd2.web.conf
Installing DAE web by copying NonblockingSlaveWorkerCGI
Copying src/perl2/OME/Analysis/Engine/NonblockingSlaveWorkerCGI.pl to /OME/perl2/NonblockingSlaveWorkerCGI.pl
chmod 0755 /OME/perl2/NonblockingSlaveWorkerCGI.pl
chown /OME/perl2/NonblockingSlaveWorkerCGI.pl to uid: 48 gid: 501
Installing OME-startup.pl
Copying src/perl2/OME-startup.pl to /OME/conf/OME-startup.pl
chown /OME/conf/OME-startup.pl to uid: 48 gid: 501
Fixing variables in conf/httpd.ome.*.conf
Replacing %OME_DIST_BASE with /home/ut/Desktop/OME-2.6.1
Replacing %OME_INSTALL_BASE with /OME
Reading /OME/conf/httpd.ome.conf
Writing /OME/conf/httpd.ome.conf
Reading /OME/conf/httpd.omeds-dev.conf
Writing /OME/conf/httpd.omeds-dev.conf
Reading /OME/conf/httpd.omeds.conf
Writing /OME/conf/httpd.omeds.conf
Reading /OME/conf/httpd.omeis-dev.conf
Writing /OME/conf/httpd.omeis-dev.conf
Reading /OME/conf/httpd.omeis.conf
Writing /OME/conf/httpd.omeis.conf
Reading /OME/conf/httpd.web-dev.conf
Writing /OME/conf/httpd.web-dev.conf
Reading /OME/conf/httpd.web.conf
Writing /OME/conf/httpd.web.conf
Reading /OME/conf/httpd1.99.omeds-dev.conf
Writing /OME/conf/httpd1.99.omeds-dev.conf
Reading /OME/conf/httpd1.99.omeds.conf
Writing /OME/conf/httpd1.99.omeds.conf
Reading /OME/conf/httpd1.99.omeis-dev.conf
Writing /OME/conf/httpd1.99.omeis-dev.conf
Reading /OME/conf/httpd1.99.omeis.conf
Writing /OME/conf/httpd1.99.omeis.conf
Reading /OME/conf/httpd1.99.web-dev.conf
Writing /OME/conf/httpd1.99.web-dev.conf
Reading /OME/conf/httpd1.99.web.conf
Writing /OME/conf/httpd1.99.web.conf
Reading /OME/conf/httpd2.omeds-dev.conf
Writing /OME/conf/httpd2.omeds-dev.conf
Reading /OME/conf/httpd2.omeds.conf
Writing /OME/conf/httpd2.omeds.conf
Reading /OME/conf/httpd2.omeis-dev.conf
Writing /OME/conf/httpd2.omeis-dev.conf
Reading /OME/conf/httpd2.omeis.conf
Writing /OME/conf/httpd2.omeis.conf
Reading /OME/conf/httpd2.web-dev.conf
Writing /OME/conf/httpd2.web-dev.conf
Reading /OME/conf/httpd2.web.conf
Writing /OME/conf/httpd2.web.conf
Reading /OME/conf/httpd.ome.conf
Writing /OME/conf/httpd.ome.conf
Restarting Apache
Executing /usr/sbin/apachectl restart
Getting an OME::Util::cURL user agent
Generated mod_perl test script:
#!/usr/bin/perl -w
use strict;
use CGI qw/-no_xhtml/;
my $CGI = CGI->new();
print $CGI->header(-type => 'text/plain'),
my ($key,$value);
while ( ($key, $value) = each %ENV)
{
print "$key = $value\n";
}
1;
Writing script to /OME/perl2/mod_perl_test.pl
Getting response from http://localhost/perl2/mod_perl_test.pl
Apache/mod_perl is not properly configured. Did not get a response from http://localhost/perl2/mod_perl_test.pl.
----------
----------------------------------------
> CC: ome-users at lists.openmicroscopy.org.uk
> From: igg at nih.gov
> Subject: Re: [ome-users] Help with OME installation on Fedora Core 6, (mod_perl not configured error...)
> Date: Tue, 22 Jan 2008 13:10:45 -0500
> To: jeromeavondo at msn.com
>
> Hi Jerome
> Fedora Core 6 is a supported platform and we use it for both of our
> production servers (lab and department). OS X is mainly used for
> development.
> It would be informative to look at the logfile in /var/tmp/OME/
> install/ApacheConfigTask.log
>
> Although somehow, you were able to run this manually,
> http://localhost/perl2/mod_perl_test.pl
>
> When the installation script tried to run it, it produced an error
> (i.e. the server responded with something other than a 200 response
> code). The logfile should have more details.
> You might just try running the installer again - possibly there were
> some things that didn't "take" the first time. The fact that you
> were able to run the test script manually indicates that the system
> was configured correctly.
>
> We've had very little trouble installing this on "stock" Fedora Core
> OSes.
> If re-running the installer doesn't work, please send the /var/tmp/
> OME/install/ApacheConfigTask.log logfile.
>
> Also, you should change the server name to something other than
> localhost. This will cause your OME system to work only locally
> (i.e. the images, etc will not appear on any other client).
>
> -Ilya
>
>
>
>
> On Jan 22, 2008, at 5:12 AM, Jerome Avondo wrote:
>
>>
>> hi,
>>
>> Dont know if this helps but tried running the following below
>> manually, once apache is started, and the script "seems" to work.
>>
>> http://localhost/perl2/mod_perl_test.pl
>>
>> I get the following output:
>>
>> ----------------------------------------------------------------
>> SCRIPT_NAME = /perl2/mod_perl_test.pl
>> SERVER_NAME = localhost
>> SERVER_ADMIN = root at localhost
>> HTTP_ACCEPT_ENCODING = gzip,deflate
>> HTTP_CONNECTION = keep-alive
>> REQUEST_METHOD = GET
>> HTTP_ACCEPT = text/xml,application/xml,application/xhtml+xml,text/
>> html;q=0.9,text/plain;q=0.8,image/png,*/*;q=0.5
>> SCRIPT_FILENAME = /OME/perl2/mod_perl_test.pl
>> SERVER_SOFTWARE = Apache/2.2.6 (Fedora)
>> HTTP_ACCEPT_CHARSET = ISO-8859-1,utf-8;q=0.7,*;q=0.7
>> QUERY_STRING =
>> REMOTE_PORT = 59930
>> HTTP_USER_AGENT = Mozilla/5.0 (X11; U; Linux i686; en-US; rv:
>> 1.8.0.7) Gecko/20061011 Fedora/1.5.0.7-7.fc6 Firefox/1.5.0.7
>> SERVER_PORT = 80
>> SERVER_SIGNATURE = Apache/2.2.6 (Fedora) Server at localhost Port 80
>>
>> HTTP_ACCEPT_LANGUAGE = en-us,en;q=0.5
>> REMOTE_ADDR = 127.0.0.1
>> HTTP_KEEP_ALIVE = 300
>> SERVER_PROTOCOL = HTTP/1.1
>> PATH = /usr/bin/:/usr/local/bin/:/sw/bin/
>> MOD_PERL_API_VERSION = 2
>> REQUEST_URI = /perl2/mod_perl_test.pl
>> GATEWAY_INTERFACE = CGI/1.1
>> SERVER_ADDR = 127.0.0.1
>> DOCUMENT_ROOT = /var/www/html
>> HTTP_HOST = localhost
>> MOD_PERL = mod_perl/2.0.2
>> ----------------------------------------------------------------
>>
>> Also when I try and start/restart apache I get the following
>> warning message:
>> " [warn] The ScriptAlias directive in /OME/conf/httpd2.omeis.conf
>> at line 2 will probably never match because it overlaps an earlier
>> ScriptAlias."
>>
>> Also found a previous OME-USERS thread with similar symptoms too
>> but wasnt much help, as it seems the user was running an old
>> install.pl script... http://lists.openmicroscopy.org.uk/pipermail/
>> ome-users/2005-July/000068.html
>>
>> Well Im a bit stuck, if any expert has any suggestions/pointers,
>> would be very greatful...
>> Regards,
>>
>> J.
>> ----------------------------------------
>>> From: jeromeavondo at msn.com
>>> To: ome-users at lists.openmicroscopy.org.uk
>>> Date: Mon, 21 Jan 2008 16:32:19 +0000
>>> Subject: Re: [ome-users] Help with OME installation on Fedora Core
>>> 6, (mod_perl not configured error...)
>>>
>>>
>>> Hello,
>>>
>>> Been trying to get the OME server up and running on a fresh Fedora
>>> core 6 installation.
>>> However I am having an error with the install.pl script at the
>>> APACHE SETUP stage.
>>>
>>> You can find the complete install log at the end of this message.
>>>
>>> Basically it seems that its complaining about mod_perl not being
>>> configured correctly.
>>> The exact error message I get is: "Errors executing task: Apache/
>>> mod_perl is not properly configured."
>>>
>>> when I run "yum list mod_perl" mod_perl is shown as installed and
>>> the version number is 2.0.2-6.2.fc6
>>>
>>> Anybody have any suggestion about how to go about sorting this
>>> problem? Do I have to do anything more to setup mod_perl correctly?
>>>
>>> many thanks,
>>>
>>> j.
>>>
>>> --------------------------------------
>>> COMPLETE INSTALL LOG:
>>> --------------------------------------
>>>
>>> [root at JIC4367 OME-2.6.1]# perl install.pl
>>> ------------------
>>> Pre-Installation
>>> ------------------
>>>
>>> Term::ReadKey - Version 2.30
>>> Storable - Version 2.15
>>>
>>> ----------------------------
>>> C Library Dependency Setup
>>> ----------------------------
>>>
>>> (All verbose information logged in /var/tmp/ome-lib-check/
>>> LibraryTask.log)
>>>
>>> Checking libraries
>>> \_ libssl 0.9.8 [OK].
>>> \_ libpng 1.2.10 [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].
>>>
>>> -------------------
>>> Core System Setup
>>> -------------------
>>>
>>> Dropping umask to "0002".
>>>
>>> This part of the OME install will collect the initial information
>>> required.
>>> Basic directory structure and system users will be created and the
>>> install
>>> environment setup. If you are unsure of a particular question, please
>>> choose the default as that will be more than adequate for most
>>> people.
>>>
>>> Base OME directory: /OME
>>> Base OMEIS directory: /OME/OMESIS
>>> Base temporary directory: /var/tmp/OME
>>> OME groupname: ome
>>> OME Unix username: ome
>>> Apache Unix username: apache
>>> Postgres admin username: postgres
>>> OME Unix admin username: ut
>>>
>>> Are these values correct ? [y/n]: y
>>>
>>> Building the core system
>>> \_ Checking directory "/OME".
>>> \_ Checking child "/OME/xml".
>>> \_ Checking child "/OME/bin".
>>> \_ Checking child "/OME/perl2".
>>> \_ Checking child "/OME/cgi".
>>> \_ Checking child "/OME/crontab".
>>> \_ Checking child "/OME/matlab".
>>> \_ Checking child "/OME/Inline".
>>> \_ Checking child "/OME/lib".
>>> \_ Checking child "/OME/java".
>>> \_ Checking directory "/OME/OMESIS".
>>> \_ Checking child "/OME/OMESIS/Files".
>>> \_ Checking child "/OME/OMESIS/Pixels".
>>> \_ Checking directory "/var/tmp/OME".
>>> \_ Checking child "/var/tmp/OME/lock".
>>> \_ Checking child "/var/tmp/OME/sessions".
>>> \_ Checking child "/var/tmp/OME/install".
>>>
>>> Copying stylesheets
>>> \_ src/xml/xslt/OME-CA2OME.xslt
>>> \_ src/xml/xslt/OME2OME-CA.xslt
>>>
>>> Copying IMAGE directories
>>> \_ images
>>> Copying CONFIG directories
>>> \_ conf
>>> Copying HTML directories
>>> \_ JavaScript
>>> \_ html
>>>
>>> -------------------
>>> Core Binary Setup
>>> -------------------
>>>
>>> (All verbose information logged in /var/tmp/OME/install/
>>> BinaryBuilds.log)
>>>
>>> OME can optionally be configured to work with BioFormats which is an
>>> external Java library that can read 50+ common microscopy file
>>> formats.
>>> BioFormats requires Sun Java, but if you don't need BioFormats you
>>> can
>>> continue the install without Sun Java.
>>>
>>> Installing BioFormats
>>> \_ Checking for Sun Java [FOUND].
>>> \_ Checking for /OME/java/loci_tools.jar [FOUND].
>>> Installing OMEIS
>>> \_ Configuring [SUCCESS].
>>> \_ Compiling [SUCCESS].
>>> \_ Installing [SUCCESS].
>>> Installing omeis-http
>>> \_ Configuring [SUCCESS].
>>> \_ Compiling [SUCCESS].
>>> Installing core binaries
>>> \_ Compiling [SUCCESS].
>>> \_ Installing [SUCCESS].
>>>
>>> ------------------------------
>>> Perl Module Dependency Setup
>>> ------------------------------
>>>
>>> (All verbose information logged in /var/tmp/OME/install/
>>> PerlModuleTask.log)
>>>
>>> Checking modules
>>> \_ 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].
>>> \_ Date::Parse 2.27 [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 3.55 [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 1.62 [OK].
>>> \_ XML::Parser 2.34 [OK].
>>> \_ SOAP::Lite 0.60 [OK].
>>> \_ XML::LibXSLT 1.58 [OK].
>>> \_ OLE::Storage_Lite 0.14 [OK].
>>> \_ Spreadsheet::ParseExcel 0.2603 [OK].
>>>
>>> ------------------------
>>> Core Perl Module Setup
>>> ------------------------
>>>
>>> (All verbose information logged in /var/tmp/OME/install/
>>> PerlModuleTask.log)
>>>
>>> Installing modules
>>> \_ Configuring [SUCCESS].
>>> \_ Compiling [SUCCESS].
>>> \_ Installing [SUCCESS].
>>> Use of uninitialized value in concatenation (.) or string at /home/
>>> ut/Desktop/OME-2.6.1/src/perl2/OME/Install/ApacheConfigTask.pm
>>> line 75.
>>>
>>> --------------
>>> Apache Setup
>>> --------------
>>>
>>> (All verbose information logged in /var/tmp/OME/install/
>>> ApacheConfigTask.log)
>>>
>>> OME Apache web server configuration is a critical part of your OME
>>> install.
>>> OME's web interface, remote clients and image server all use this
>>> infrastructure to communicate. If you are unsure of a particular
>>> question,
>>> please choose the default as that will be more than adequate for most
>>> people.
>>>
>>>
>>> Apache configuration:
>>> Configure Apache?: yes
>>> Developer configuration: no
>>> Server restart?: yes
>>> Install OME servers:
>>> Images (omeis): yes
>>> Data (omeds): yes
>>> Web: yes
>>> Apache directories:
>>> httpd binary: /usr/sbin/httpd
>>> apachectl binary: /usr/sbin/apachectl
>>> DocumentRoot: /var/www/html
>>> cgi-bin: /var/www/cgi-bin/
>>> Web-UI HTML Templates:
>>> Developer configuration: no
>>>
>>> Are these values correct ? [y/n]: y
>>> [Mon Jan 21 16:14:00 2008] [warn] The ScriptAlias directive in /
>>> OME/conf/httpd2.omeis.conf at line 2 will probably never match
>>> because it overlaps an earlier ScriptAlias.
>>> Testing Apache configuration
>>> \__ mod_perl [FAILURE].
>>>
>>>
>>> Errors executing task: Apache/mod_perl is not properly
>>> configured. Got an error response from http://localhost/perl2/
>>> mod_perl_test.pl:
>>>
>>> ERROR: The requested URL could not be retrieved
>>>
>>> ERROR
>>> The requested URL could not be retrieved
>>>
>>>
>>> While trying to retrieve the URL:
>>> http://localhost/perl2/mod_perl_test.pl
>>>
>>> The following error was encountered:
>>>
>>>
>>>
>>> Connection Failed
>>>
>>>
>>>
>>>
>>> The system returned:
>>> (111) Connection refused
>>>
>>>
>>> The remote host or network may be down. Please try the request
>>> again.
>>> Your cache administrator is webmstr at bbsrc.ac.uk.
>>>
>>>
>>>
>>>
>>> Generated Mon, 21 Jan 2008 16:13:28 GMT by BBSRC-wwwcache-service
>>> (squid/2.5.STABLE9)
>>>
>>>
>>>
>>> See /var/tmp/OME/install/ApacheConfigTask.log for more details. at
>>> (eval 187) line 1
>>>
>>> at install.pl line 82
>>> main::run_tasks() called at install.pl line 266
>>> # Looks like your test died before it could output anything.
>>>
>>>
>>> _________________________________________________________________
>>> Free games, great prizes - get gaming at Gamesbox.
>>> http://www.searchgamesbox.com
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>> _________________________________________________________________
>> Get Hotmail on your mobile, text MSN to 63463!
>> http://mobile.uk.msn.com/pc/mail.aspx
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>
_________________________________________________________________
Get Hotmail on your mobile, text MSN to 63463!
http://mobile.uk.msn.com/pc/mail.aspx
More information about the ome-users
mailing list