[ome-users] ome install failure on mac OS 10.4.7

Ilya Goldberg igg at nih.gov
Wed Sep 6 18:38:33 BST 2006 

Hi Steve
Wow, that's a doozie.
OMEIS cannot be reached because the wrong user owns the files.  The  
user that's running the apache process must own (recursively) all the  
files in /OME/OMEIS.  The permissions are restrictive enough that the  
owner really must be right.

A couple of things make me think that this isn't your average run of  
the mill OS X installation.
The apache user has been 'www' on OS X seemingly forever.  Did you  
compile Apache yourself?
We haven't had problems with creating users/groups on OS X in a very  
long time (years?).

If you're very lucky, you might be able to modify your Apache  
configuration file and change:
# User nobody
User www
(comment out the User nobody line, and insert the User www line).
The configuration file is /etc/httpd/httpd.conf.  If you installed  
apache yourself, then all bets are off - you have to figure out where  
the apache conf file went.  You may still have /etc/httpd/httpd.conf,  
but it may not be the "active" one, so changes there may have no  
effect.  About the only way to tell is to put a syntax error in the  
conf file on purpose, restart apache and make sure it fails.  This is  
just a glimpse of the world of hurt that normally ensues when  
replacing core components of the stock OS.  If it were me, I would  
take the 30 minutes and reinstall the OS because the chances of  
diagnosing and fixing this in less time are pretty nil.

The user/group thing is a complete mystery.  Haven't ever seen that  
before, and we've used every version of OS X pretty extensively.  Is  
your computer "bound" to an external authentication service (like  
ldap/active directory)?
-Ilya



On Sep 6, 2006, at 2:59 AM, Stephen Ogg wrote:

>
> Dear OME team-
> I have tried installing ome on my powerbook G4 (sorry no intel  
> chip) and have failed. I include the OME-install.log for any help  
> you could give me.
> It seems to fail because the omeis script tries to change  
> directories to /OME/OMEIS and fails with some permission problems.  
> I include the terminal ouput from a number of commands to outline  
> what I think has gone wrong (see below).  Additionally, the first  
> time I tried the installation, I got some errors in the log about  
> users (specifically "ome" and "steve") not able to be added to the  
> "ome" group. It told me to fix this in the /etc/group file before  
> continuing. Knowing just enough to be dangerous, I added those two  
> users to the ome group in the / domain using the netinfo manager  
> and didn't change the files as suggested in the install log.   
> During my next attempt at installation, the error of manually  
> adding users to the ome group was gone, but the install failed at  
> the same point.   I think the problem is the following:
>
> =======================portion of output from ps - 
> aux========================
> root       388   0.0  0.3    30020   1668  ??  Ss    2:17PM    
> 0:00.19 /usr/sbin/httpd
> ome       3468   0.0  0.6    39708   3124  ??  SNs   2:18PM    
> 0:00.53 /System/Library/Frameworks/CoreServices.framework/Versions/ 
> A/Frameworks/Metadata.framework/Versions/A/Support/mdimportserver
> www       5912   0.0  0.5    40372   2644  ??  SNs   2:20PM    
> 0:00.24 /System/Library/Frameworks/CoreServices.framework/Versions/ 
> A/Frameworks/Metadata.framework/Versions/A/Support/mdimportserver
> nobody    5916   0.0  0.5    28852   2544  ??  S     2:20PM    
> 0:00.10 /usr/sbin/httpd
> nobody    5917   0.0  0.2    28700    904  ??  S     2:20PM    
> 0:00.01 /usr/sbin/httpd
> nobody    5918   0.0  0.2    28700    912  ??  S     2:20PM    
> 0:00.01 /usr/sbin/httpd
> nobody    5919   0.0  0.2    28700    972  ??  S     2:20PM    
> 0:00.01 /usr/sbin/httpd
> nobody    5920   0.0  0.1    28700    492  ??  S     2:20PM    
> 0:00.00 /usr/sbin/httpd
> nobody    5924   0.0  0.1    28700    596  ??  S     2:21PM    
> 0:00.00 /usr/sbin/httpd
> ====================================================================== 
> ==================
>
> "nobody" is the user on my machine who is running the webserver and  
> yet only user "www" can enter the /OME/OMEIS directory--
>
> ============================= output form ls -ls
>
> steve:/OME steve$ ls -ls
> total 0
> 0 drwxr-sr-x    5 ome  ome  170 Sep  6 11:22 Inline
> 0 drwxrwxr-x   11 ome  ome  374 Sep  6 11:20 JavaScript
> 0 drwx--S---    4 www  ome  136 Sep  6 11:20 OMEIS
> 0 drwxr-xr-x   21 ome  ome  714 Sep  6 14:19 bin
> 0 drwxr-sr-x    2 ome  ome   68 Sep  6 11:20 cgi
> 0 drwxrwxr-x   22 ome  ome  748 Sep  6 11:22 conf
> 0 drwxr-sr-x    2 ome  ome   68 Sep  6 11:20 crontab
> 0 drwxrwxr-x    6 ome  ome  204 Sep  6 11:20 html
> 0 drwxrwxr-x   14 ome  ome  476 Sep  6 11:20 images
> 0 drwxr-sr-x    2 ome  ome   68 Sep  6 11:20 lib
> 0 drwxr-sr-x    2 ome  ome   68 Sep  6 11:20 matlab
> 0 drwxr-sr-x    3 ome  ome  102 Sep  6 14:20 perl2
> 0 drwxr-sr-x    4 ome  ome  136 Sep  6 11:20 xml
> steve:/OME steve$
> =============================================
>
> That's I think why the following happens
> ================================contents of /var/tmp/OME/install/ 
> ApacheConfigTask.log==================
> steve:/var/tmp/OME/install steve$ more ApacheConfigTask.log
> Apache setup
> Apache binary: /usr/sbin/httpd
> apachectl binary: /usr/sbin/apachectl
> httpd conf: /etc/httpd/httpd.conf
> httpd version: 1
> 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: /Library/WebServer/Documents/OME
>                   cgi-bin: /Library/WebServer/CGI-Executables
> Web-UI HTML Templates:
>   Developer configuration: no
> Configuring Apache
> httpd.conf is /etc/httpd/httpd.conf
> Installing OMEIS
> Copying src/C/omeis/omeis to /Library/WebServer/CGI-Executables/omeis
> chmod 0755 /Library/WebServer/CGI-Executables/omeis
> chown /Library/WebServer/CGI-Executables/omeis to uid: 70 gid: 502
> Set APACHE_OMEIS_INCLUDE to Include /OME/conf/httpd.omeis.conf
> Forking a process to upgrade OMEIS
> Installing OMEDS
> Set APACHE_OMEDS_INCLUDE to Include /OME/conf/httpd.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: 70 gid: 502
> Copying src/html/index.html to /Library/WebServer/Documents/OME/ 
> index.html
> chmod 0755 /Library/WebServer/Documents/OME/index.html
> Set APACHE_WEB_INCLUDE to Include /OME/conf/httpd.web.conf
> Installing OME-startup.pl
> Copying src/perl2/OME-startup.pl to /OME/conf/OME-startup.pl
> chown /OME/conf/OME-startup.pl to uid: 70 gid: 502
> Fixing variables in conf/httpd.ome.*.conf
> Replacing %OME_DIST_BASE with /private/var/tmp/OME/install/OME
> 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
> Checking response from http://localhost/perl2/mod_perl_test.pl
> Parsing response from http://localhost/perl2/mod_perl_test.pl
> mod_perl is configured correctly
> Testing omeis installation
> Getting an OME::Util::cURL user agent
> Getting response from http://localhost/cgi-bin/omeis
> Parsing response from http://localhost/cgi-bin/omeis
> OMEIS could not be reached.
> Incorrect response from OMEIS at http://localhost/cgi-bin/omeis:
> Error calling Initialization: Could not change working directory  
> to /OME/OMEIS: Permission denied
> System Error: Permission denied
> ====================================================================== 
> ============
>
>
> All of this is just conjecture though, As I'm a lowly biologist, I  
> could be way off base.
>
> Any help would be appreciated.
>
> Thanks in advance
>
> Steve
> stephen at cmm.a-star.edu.sg
>
>
>
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
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