Hi all,

I'm having problems getting php installed. I'm trying to install some software called 'base' which is a database and general software environment for handling microarray data from biological experiments (I'm really a scientist in my day job). To run this I need to install apache, mysql and php which I have done according to the instructions on the websites for those programs.

I have been through a series of configuration steps described here http://base.thep.lu.se/index.phtml
as written.

Then I get as far as the command bin/startBase.php which returns the following:
PHP Parse error: parse error, unexpected '@' in /home/marraydb/base-1.2.17/config.inc.php.in on line 171

Parse error: parse error, unexpected '@' in /home/marraydb/base-1.2.17/config.inc.php.in on line 171
I have checked the code line specified and it's this:
$config["useJobRunner"] = @JobRunner@;

I have looked and the file JobRunner is installed under this path:
/usr/local/base/bin/jobRunner

Is it possible for me to edit the line in the startBase php script to correct this or can anyone suggest what I should do?

Rich

I would assume that those "@" around Jobrunner should read like this as single quotes, not @'s:

$config["useJobRunner"] = 'JobRunner';

Apologies it's taken me so long to come back on this I've been a bit busy. Changing @JobRunner@ to 'JobRunner' has got rid of one error message to be replaced by another. Now if I run the command:

/home/marraydb/base-1.2.17/bin/startBase.php
I get the following:

PHP Warning: main(common.inc.php): failed to open stream: No such file or directory in /home/marraydb/base-1.2.17/config.inc.php.in on line 180

Warning: main(common.inc.php): failed to open stream: No such file or directory in /home/marraydb/base-1.2.17/config.inc.php.in on line 180
PHP Fatal error: main(): Failed opening required 'common.inc.php' (include_path='@prefix@/include/classes:@prefix@/home/marraydb/base-1.2.17/include/common:@prefix@/include/local:@prefix@/include/web') in /home/marraydb/base-1.2.17/config.inc.php.in on line 180

Fatal error: main(): Failed opening required 'common.inc.php' (include_path='@prefix@/include/classes:@prefix@/home/marraydb/base-1.2.17/include/common:@prefix@/include/local:@prefix@/include/web') in /home/marraydb/base-1.2.17/config.inc.php.in on line 180

I don't understand this, here is the relevent section of config.inc.php.in

// Here you can choose to enable the JobRunner, which will let all
// plugins run as a different user (for better security). JobRunner
// must be installed as described in the documentation, with a user
// who is in the same group as the main user for BASE. The umask
// (above) should be set to 0077 to prevent the plugins from accessing
// the data directory. However, the data directory and the jobDir must
// be group executable. BASE itself will make sure that if this
// feature is used, the job user can access job files while the
// jobs are running but not otherwise.
$config["useJobRunner"] = 'JobRunner';

// Files should only be included from these four directories.
ini_set("include_path",
"$config[rootDir]/include/classes:".
"$config[rootDir]/home/marraydb/base-1.2.17/include/common:".
"$config[rootDir]/include/local:".
"$config[rootDir]/include/web");

require_once("common.inc.php");

?>

According to the line counter in Kwrite line 180 is the blank line just above '?>' the >? figure is the the end of the file, is this an end of file problem? Can anyone tell me what is going on?