That's a shame. Did you completely remove all the old TPP files in between 
installs?

The only difference I can see between our installs at the moment, is that I 
removed the space in my variable assignment, between '=' and '/usr'...
What I will do is list all the things I did that were worth writing down 
(i.e. differed from the install guide...), and hope it helps:

Install pre-req that wasn't listed:
*# apt-get install libgd2-xpm-dev*
*
*
*After install, when configuring Apache*
*

# chown -R www-data:www-data /usr/local/tpp/

# chmod -R 711 /usr/local/tpp/
# chmod -R a+X /usr/local/tpp/**
*

Does this help at all?

On Sunday, April 21, 2013 6:44:14 PM UTC+1, Liam Bell wrote:
>
> Nope - no dice...
>
> Changed the PERL_LIB_CORE= /usr/lib/perl/15.4.2/CORE in the 
> makefile.conf.incl file before re-running the compiling/building.
>
> Ran through the rest fo the steps from 
> http://tools.proteomecenter.org/wiki/index.php?title=TPP_4.5.2:_Installing_on_Ubuntu_10.04.3
>  as 
> I have done successfully before.
>
> The server is working still (localhost => It works!) but I can't load up 
> http://localhost/tpp/cgi-bin/tpp_gui.pl - still getting "The requested 
> URL /tpp/cgi-bin/tpp_gui.pl was not found on this server."
>
> Any other ideas?
>
>
> On 21 April 2013 19:10, Ross <rbg...@york.ac.uk <javascript:>> wrote:
>
>> Hi Liam,
>> I set mine to /usr/lib/perl/5.14/CORE, but using 5.14.2 shouldn't make a 
>> difference, since the 5.14 folder is a symlink to 5.14.2.
>>
>> Yes, I would do that. Let's hope this is the fix.
>>
>> On Sunday, April 21, 2013 6:02:16 PM UTC+1, Liam Bell wrote:
>>
>>> Hi Ross,
>>>
>>> Here you go:
>>> PERL_LIB_CORE= /usr/lib/perl/5.10/CORE/
>>>
>>> The CORE folder does exist at /usr/lib/perl/5.14.2/CORE.
>>>
>>> Should I recompile and change that variable before I do?
>>>
>>>
>>> On 21 April 2013 18:05, Ross <rbg...@york.ac.uk> wrote:
>>>
>>>> Hm. In your Makefile.config.incl, what is your PERL_LIB_CORE variable ? 
>>>> Does the version of Perl in that variable match the version installed on 
>>>> your computer? (command line: $ perl --version)
>>>>
>>>> To test if the variable is viable, I navigated down the path of the 
>>>> variable in the terminal to see if the CORE folder actually existed. If I 
>>>> remember correctly I had to change the variable.
>>>>
>>>>  Let me know if that yields something, and I'll get on my TPP computer 
>>>> to find out what I did.
>>>>
>>>> On Sunday, April 21, 2013 4:56:08 PM UTC+1, Liam Bell wrote:
>>>>
>>>>> It was set to root but I changed it to your settings and restarted 
>>>>> apache but still not working...
>>>>>
>>>>> It's rather vexing!
>>>>>
>>>>>
>>>>>  On 21 April 2013 17:24, Ross <rbg...@york.ac.uk> wrote:
>>>>>
>>>>>> Hi Liam,
>>>>>>
>>>>>> I'm sorry this hasn't helped. I've cross checked the TPP entries of 
>>>>>> our two httpd.conf files (the one you posted above) and they are 
>>>>>> identical. 
>>>>>>
>>>>>> Alternatively it could be your permissions. For the entire 
>>>>>> /usr/local/tpp folder I have ownership set to apache (www-data) and 
>>>>>> permissions as drwxr-xr-x.
>>>>>>
>>>>>> Does this help?
>>>>>>
>>>>>> R
>>>>>>
>>>>>> On Sunday, April 21, 2013 3:55:55 PM UTC+1, Liam Bell wrote:
>>>>>>
>>>>>>> Hi Ross,
>>>>>>>
>>>>>>> Thanks for the tip but it hasn't helped, would you be able to post 
>>>>>>> the contents of your httpd.conf file for me so I can make sure it is 
>>>>>>> the 
>>>>>>> same as what I currently have?
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Liam
>>>>>>>
>>>>>>>
>>>>>>> On 21 April 2013 10:43, Ross <rbg...@york.ac.uk> wrote:
>>>>>>>
>>>>>>>> Bear in mind that in some httpd.conf files there is a dedicated 
>>>>>>>> section for this: ### Section 3: Virtual Hosts
>>>>>>>>  
>>>>>>>> On Sunday, 21 April 2013 09:42:29 UTC+1, Ross wrote:
>>>>>>>>>
>>>>>>>>> Hi all,
>>>>>>>>>
>>>>>>>>> I encountered this issue myself on Ubuntu 12.04: I found that 
>>>>>>>>> making the tpp.4.6.2 file in /etc/apache2/sites-available didn't work 
>>>>>>>>> either.
>>>>>>>>>
>>>>>>>>> Instead, I found the following solved the issue:
>>>>>>>>>
>>>>>>>>>    - Paste the contents of the tpp-x.y.z file into 
>>>>>>>>>    /etc/apache2/httpd.conf
>>>>>>>>>    
>>>>>>>>> This definitely worked for me. I'm by no means an expert on 
>>>>>>>>> Apache, however.
>>>>>>>>>
>>>>>>>>> Hope this helps,
>>>>>>>>> Ross
>>>>>>>>>
>>>>>>>>> On Thursday, 21 March 2013 13:19:31 UTC, raju wrote:
>>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>> I hope you can help.
>>>>>>>>>> I've been trying to install TPP on a linux vm, specifically 
>>>>>>>>>> Ubuntu 12.04 LTS in virtual box.
>>>>>>>>>>
>>>>>>>>>> I've been following the TPP installation guide on http://tools.**
>>>>>>>>>> proteomecenter******.org/wiki/index.**php?title=TPP_******4.5.2:_
>>>>>>>>>> **Installing_on_Ubuntu_**10****.04.3<http://tools.proteomecenter.org/wiki/index.php?title=TPP_4.5.2:_Installing_on_Ubuntu_10.04.3>
>>>>>>>>>> .
>>>>>>>>>>
>>>>>>>>>> I've been copying and pasting where possible and it looked like 
>>>>>>>>>> everything was working during the setup i.e. no error messages.
>>>>>>>>>>
>>>>>>>>>> However when i go to my web browser, google chrome, and go to 
>>>>>>>>>> http://localhost/tpp/cgi-**bi******n/tpp_gui.pl<http://localhost/tpp/cgi-bin/tpp_gui.pl>
>>>>>>>>>>
>>>>>>>>>> I get the following error:
>>>>>>>>>>
>>>>>>>>>> ------------------------------********
>>>>>>>>>> ------------------------------********
>>>>>>>>>> ------------------------------********
>>>>>>>>>> ----------------------------
>>>>>>>>>> Not Found
>>>>>>>>>>
>>>>>>>>>> The requested URL /tpp/cgi-bin/tpp_gui.pl was not found on this 
>>>>>>>>>> server.
>>>>>>>>>>
>>>>>>>>>> Apache/2.2.22 (Ubuntu) Server at localhost Port 80
>>>>>>>>>> ------------------------------********
>>>>>>>>>> ------------------------------********
>>>>>>>>>> ------------------------------********
>>>>>>>>>> ----------------------------
>>>>>>>>>>
>>>>>>>>>> Apache is working, as i can see the page.
>>>>>>>>>> I've checked port 80 is free
>>>>>>>>>> I've ensured the firewall has been disabled - just in case.
>>>>>>>>>>
>>>>>>>>>> When I look in to the apache error log: 
>>>>>>>>>> The following errors were recorded:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> ------------------------------********
>>>>>>>>>> ------------------------------********
>>>>>>>>>> ------------------------------********
>>>>>>>>>> ----------------------------
>>>>>>>>>> [Thu Mar 21 13:01:06 2013] [error] [client 127.0.0.1] File does 
>>>>>>>>>> not exist: /var/www/tpp
>>>>>>>>>> [Thu Mar 21 13:01:06 2013] [error] [client 127.0.0.1] File does 
>>>>>>>>>> not exist: /var/www/favicon.ico
>>>>>>>>>> ------------------------------********
>>>>>>>>>> ------------------------------********
>>>>>>>>>> ------------------------------********
>>>>>>>>>> ----------------------------
>>>>>>>>>>
>>>>>>>>>> I've checked that the file 
>>>>>>>>>> /etc/apache2/sites-**availa******ble/tpp-x.y.z 
>>>>>>>>>> is as described in the installation guide
>>>>>>>>>>
>>>>>>>>>> The file exists in the path stated and I copied and pasted the 
>>>>>>>>>> text into the file to avoid typos.
>>>>>>>>>>
>>>>>>>>>> Any help would be greatly appreciated!!!
>>>>>>>>>>
>>>>>>>>>> Many thanks,
>>>>>>>>>> Raj
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>  -- 
>>>>>>>> You received this message because you are subscribed to a topic in 
>>>>>>>> the Google Groups "spctools-discuss" group.
>>>>>>>> To unsubscribe from this topic, visit https://groups.google.com/d/*
>>>>>>>> *to****pic/spctools-discuss/**pzyzzSmoB****xY/unsubscribe?hl=en<https://groups.google.com/d/topic/spctools-discuss/pzyzzSmoBxY/unsubscribe?hl=en>
>>>>>>>> .
>>>>>>>>  To unsubscribe from this group and all its topics, send an email 
>>>>>>>> to spctools-discu...@**googlegroups****.com.
>>>>>>>> To post to this group, send email to spctools...@googlegroups.**com
>>>>>>>> .
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>>>>>>>> Visit this group at http://groups.google.com/**group****
>>>>>>>> /spctools-discuss?hl=en<http://groups.google.com/group/spctools-discuss?hl=en>
>>>>>>>> .
>>>>>>>> For more options, visit https://groups.google.com/**grou****
>>>>>>>> ps/opt_out <https://groups.google.com/groups/opt_out>.
>>>>>>>>  
>>>>>>>>  
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> On Sunday, April 21, 2013 3:55:55 PM UTC+1, Liam Bell wrote:
>>>>>>
>>>>>>>  Hi Ross,
>>>>>>>
>>>>>>> Thanks for the tip but it hasn't helped, would you be able to post 
>>>>>>> the contents of your httpd.conf file for me so I can make sure it is 
>>>>>>> the 
>>>>>>> same as what I currently have?
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Liam
>>>>>>>
>>>>>>>
>>>>>>> On 21 April 2013 10:43, Ross <rbg...@york.ac.uk> wrote:
>>>>>>>
>>>>>>>> Bear in mind that in some httpd.conf files there is a dedicated 
>>>>>>>> section for this: ### Section 3: Virtual Hosts
>>>>>>>>  
>>>>>>>> On Sunday, 21 April 2013 09:42:29 UTC+1, Ross wrote:
>>>>>>>>>
>>>>>>>>> Hi all,
>>>>>>>>>
>>>>>>>>> I encountered this issue myself on Ubuntu 12.04: I found that 
>>>>>>>>> making the tpp.4.6.2 file in /etc/apache2/sites-available didn't work 
>>>>>>>>> either.
>>>>>>>>>
>>>>>>>>> Instead, I found the following solved the issue:
>>>>>>>>>
>>>>>>>>>    - Paste the contents of the tpp-x.y.z file into 
>>>>>>>>>    /etc/apache2/httpd.conf
>>>>>>>>>    
>>>>>>>>> This definitely worked for me. I'm by no means an expert on 
>>>>>>>>> Apache, however.
>>>>>>>>>
>>>>>>>>> Hope this helps,
>>>>>>>>> Ross
>>>>>>>>>
>>>>>>>>> On Thursday, 21 March 2013 13:19:31 UTC, raju wrote:
>>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>> I hope you can help.
>>>>>>>>>> I've been trying to install TPP on a linux vm, specifically 
>>>>>>>>>> Ubuntu 12.04 LTS in virtual box.
>>>>>>>>>>
>>>>>>>>>> I've been following the TPP installation guide on http://tools.**
>>>>>>>>>> proteomecenter******.org/wiki/index.**php?title=TPP_******4.5.2:_
>>>>>>>>>> **Installing_on_Ubuntu_**10****.04.3<http://tools.proteomecenter.org/wiki/index.php?title=TPP_4.5.2:_Installing_on_Ubuntu_10.04.3>
>>>>>>>>>> .
>>>>>>>>>>
>>>>>>>>>> I've been copying and pasting where possible and it looked like 
>>>>>>>>>> everything was working during the setup i.e. no error messages.
>>>>>>>>>>
>>>>>>>>>> However when i go to my web browser, google chrome, and go to 
>>>>>>>>>> http://localhost/tpp/cgi-**bi******n/tpp_gui.pl<http://localhost/tpp/cgi-bin/tpp_gui.pl>
>>>>>>>>>>
>>>>>>>>>> I get the following error:
>>>>>>>>>>
>>>>>>>>>> ------------------------------********
>>>>>>>>>> ------------------------------********
>>>>>>>>>> ------------------------------********
>>>>>>>>>> ----------------------------
>>>>>>>>>> Not Found
>>>>>>>>>>
>>>>>>>>>> The requested URL /tpp/cgi-bin/tpp_gui.pl was not found on this 
>>>>>>>>>> server.
>>>>>>>>>>
>>>>>>>>>> Apache/2.2.22 (Ubuntu) Server at localhost Port 80
>>>>>>>>>> ------------------------------********
>>>>>>>>>> ------------------------------********
>>>>>>>>>> ------------------------------********
>>>>>>>>>> ----------------------------
>>>>>>>>>>
>>>>>>>>>> Apache is working, as i can see the page.
>>>>>>>>>> I've checked port 80 is free
>>>>>>>>>> I've ensured the firewall has been disabled - just in case.
>>>>>>>>>>
>>>>>>>>>> When I look in to the apache error log: 
>>>>>>>>>> The following errors were recorded:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> ------------------------------********
>>>>>>>>>> ------------------------------********
>>>>>>>>>> ------------------------------********
>>>>>>>>>> ----------------------------
>>>>>>>>>> [Thu Mar 21 13:01:06 2013] [error] [client 127.0.0.1] File does 
>>>>>>>>>> not exist: /var/www/tpp
>>>>>>>>>> [Thu Mar 21 13:01:06 2013] [error] [client 127.0.0.1] File does 
>>>>>>>>>> not exist: /var/www/favicon.ico
>>>>>>>>>> ------------------------------********
>>>>>>>>>> ------------------------------********
>>>>>>>>>> ------------------------------********
>>>>>>>>>> ----------------------------
>>>>>>>>>>
>>>>>>>>>> I've checked that the file 
>>>>>>>>>> /etc/apache2/sites-**availa******ble/tpp-x.y.z 
>>>>>>>>>> is as described in the installation guide
>>>>>>>>>>
>>>>>>>>>> The file exists in the path stated and I copied and pasted the 
>>>>>>>>>> text into the file to avoid typos.
>>>>>>>>>>
>>>>>>>>>> Any help would be greatly appreciated!!!
>>>>>>>>>>
>>>>>>>>>> Many thanks,
>>>>>>>>>> Raj
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>  -- 
>>>>>>>> You received this message because you are subscribed to a topic in 
>>>>>>>> the Google Groups "spctools-discuss" group.
>>>>>>>> To unsubscribe from this topic, visit https://groups.google.com/d/*
>>>>>>>> *to****pic/spctools-discuss/**pzyzzSmoB****xY/unsubscribe?hl=en<https://groups.google.com/d/topic/spctools-discuss/pzyzzSmoBxY/unsubscribe?hl=en>
>>>>>>>> .
>>>>>>>>  To unsubscribe from this group and all its topics, send an email 
>>>>>>>> to spctools-discu...@**googlegroups****.com.
>>>>>>>> To post to this group, send email to spctools...@googlegroups.**com
>>>>>>>> .
>>>>>>>>
>>>>>>>> Visit this group at http://groups.google.com/**group****
>>>>>>>> /spctools-discuss?hl=en<http://groups.google.com/group/spctools-discuss?hl=en>
>>>>>>>> .
>>>>>>>> For more options, visit https://groups.google.com/**grou****
>>>>>>>> ps/opt_out <https://groups.google.com/groups/opt_out>.
>>>>>>>>  
>>>>>>>>  
>>>>>>>>
>>>>>>>
>>>>>>>  -- 
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>>>>>> to**pic/spctools-discuss/**pzyzzSmoB**xY/unsubscribe?hl=en<https://groups.google.com/d/topic/spctools-discuss/pzyzzSmoBxY/unsubscribe?hl=en>
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>>>>>> .
>>>>>>  
>>>>>>  
>>>>>>
>>>>>
>>>>>  -- 
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>>>>  
>>>>
>>>
>>>  -- 
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>
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