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

Stephen Ogg stephen at cmm.a-star.edu.sg
Thu Sep 7 08:56:46 BST 2006 

Ilya-
Thanks for the help. Changing the apache user to www in the  
httpd.conf did the trick. I haven't compiled apache or anything  
strange, although I have allowed a colleague to modify the httpd.conf  
file a while ago. I asked him to restore it the original, but  
apparently he replaced it with a non standard Mac version.
Thanks again for your help-
Steve

61 Biopolis Drive (Proteos)
Singapore 138673
+65 65869844 office
+65 65869841lab
stephen at cmm.a-star.edu.sg



On 07 Sep 2006, at 1:38 AM, Ilya Goldberg wrote:

> 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
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>

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