information about GBROWSE installation

classic Classic list List threaded Threaded
6 messages Options
Reply | Threaded
Open this post in threaded view
|

information about GBROWSE installation

Dino Ienco
Dear Mailing List,
I'm a beginner with GBROWSE.
I download gbrowse and I installed it on my ubuntu.
Now I start the demo application, but when I click on the example link (for instance the first example on yeast)
I obtain the following message
500 Internal Server Error.


I look at the log of apache2 and I see this error message:

[Mon May 31 16:29:17 2010] [error] [client ::1] File does not exist: /var/www/favicon.ico
GBrowse/ConfigData.pm did not return a true value at /usr/local/lib/perl/5.10.0/Bio/Graphics/Browser2.pm line 18.
BEGIN failed--compilation aborted at /usr/local/lib/perl/5.10.0/Bio/Graphics/Browser2.pm line 18.
Compilation failed in require at /usr/lib/cgi-bin/gb2/gbrowse line 8.
BEGIN failed--compilation aborted at /usr/lib/cgi-bin/gb2/gbrowse line 8.


Anybody can help/explain me about this error and how to deal with this one?

All the best

Dino Ienco, PhD
Department of Computer Science
University of Turin
C.so Svizzera 185
10149 - Turin
Italy

Phone +39 011 67 06 839
Fax +39 011 75 16 03
e-mail ienco[hidden email]

------------------------------------------------------------------------------


_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: information about GBROWSE installation

Dave Clements, GMOD Help Desk-3
Hi dino,

On my Ubuntu the complaining file is at:
  /usr/local/lib/perl/5.10.0/GBrowse/ConfigData.pm

Does that file exist, and is it world readable, on your system?

Dave C.

On Mon, May 31, 2010 at 7:36 AM, Dino Ienco <[hidden email]> wrote:
Dear Mailing List,
I'm a beginner with GBROWSE.
I download gbrowse and I installed it on my ubuntu.
Now I start the demo application, but when I click on the example link (for instance the first example on yeast)
I obtain the following message
500 Internal Server Error.


I look at the log of apache2 and I see this error message:

[Mon May 31 16:29:17 2010] [error] [client ::1] File does not exist: /var/www/favicon.ico
GBrowse/ConfigData.pm did not return a true value at /usr/local/lib/perl/5.10.0/Bio/Graphics/Browser2.pm line 18.
BEGIN failed--compilation aborted at /usr/local/lib/perl/5.10.0/Bio/Graphics/Browser2.pm line 18.
Compilation failed in require at /usr/lib/cgi-bin/gb2/gbrowse line 8.
BEGIN failed--compilation aborted at /usr/lib/cgi-bin/gb2/gbrowse line 8.


Anybody can help/explain me about this error and how to deal with this one?

All the best

Dino Ienco, PhD
Department of Computer Science
University of Turin
C.so Svizzera 185
10149 - Turin
Italy

Phone +39 011 67 06 839
Fax +39 011 75 16 03
e-mail ienco[hidden email]

------------------------------------------------------------------------------


_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
===> PLEASE KEEP RESPONSES ON THE LIST <===
http://gmod.org/wiki/GMOD_News
http://gmod.org/wiki/Calendar
http://gmod.org/wiki/Help_Desk_Feedback


------------------------------------------------------------------------------


_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: information about GBROWSE installation

Dino Ienco
Dear Dave,
I check the problem and the file is in the correct folder. (The one that you suggest me).
What should I try to solve this problem?

All the best

Dino


On Jun 2, 2010, at 12:38 AM, Dave Clements, GMOD Help Desk wrote:

Hi dino,

On my Ubuntu the complaining file is at:
  /usr/local/lib/perl/5.10.0/GBrowse/ConfigData.pm

Does that file exist, and is it world readable, on your system?

Dave C.

On Mon, May 31, 2010 at 7:36 AM, Dino Ienco <[hidden email]> wrote:
Dear Mailing List,
I'm a beginner with GBROWSE.
I download gbrowse and I installed it on my ubuntu.
Now I start the demo application, but when I click on the example link (for instance the first example on yeast)
I obtain the following message
500 Internal Server Error.


I look at the log of apache2 and I see this error message:

[Mon May 31 16:29:17 2010] [error] [client ::1] File does not exist: /var/www/favicon.ico
GBrowse/ConfigData.pm did not return a true value at /usr/local/lib/perl/5.10.0/Bio/Graphics/Browser2.pm line 18.
BEGIN failed--compilation aborted at /usr/local/lib/perl/5.10.0/Bio/Graphics/Browser2.pm line 18.
Compilation failed in require at /usr/lib/cgi-bin/gb2/gbrowse line 8.
BEGIN failed--compilation aborted at /usr/lib/cgi-bin/gb2/gbrowse line 8.


Anybody can help/explain me about this error and how to deal with this one?

All the best

Dino Ienco, PhD
Department of Computer Science
University of Turin
C.so Svizzera 185
10149 - Turin
Italy

Phone +39 011 67 06 839
Fax +39 011 75 16 03
e-mail ienco[hidden email]

------------------------------------------------------------------------------


_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
===> PLEASE KEEP RESPONSES ON THE LIST <===
http://gmod.org/wiki/GMOD_News
http://gmod.org/wiki/Calendar
http://gmod.org/wiki/Help_Desk_Feedback


Dino Ienco, PhD
Department of Computer Science
University of Turin
C.so Svizzera 185
10149 - Turin
Italy

Phone +39 011 67 06 839
Fax +39 011 75 16 03
e-mail [hidden email]
web http://www.di.unito.it/~ienco




------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: information about GBROWSE installation

Dino Ienco
<base href="x-msg://86/">I check better, and I verify that the file exists but the file is empty

How can I deal with this problem?

Where could I find the .pm file?

All the best
Dino


On Jun 7, 2010, at 5:25 PM, Jayaraman, Pushkala wrote:

Hello Dino,
Favicon.ico error is not a problem..
Try going to the ConfigData.pm. There has to be a line that lets you activate debugging.
Something like CONSTANT DEBUG => 0
Make it CONSTANT_DEBUG =>1
See what debug statements it gives..
 
Pushkala Jayaraman
Programmer/Analyst
Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
Work: 414-955-2229
 
From: Dino Ienco [mailto:[hidden email]] 
Sent: Monday, June 07, 2010 4:46 AM
To: Dave Clements, GMOD Help Desk
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] information about GBROWSE installation
 
Dear Dave,
            I check the problem and the file is in the correct folder. (The one that you suggest me).
What should I try to solve this problem?
 
All the best
 
Dino
 
 
On Jun 2, 2010, at 12:38 AM, Dave Clements, GMOD Help Desk wrote:


Hi dino,
 
On my Ubuntu the complaining file is at:
  /usr/local/lib/perl/5.10.0/GBrowse/ConfigData.pm
 
Does that file exist, and is it world readable, on your system?
 
Dave C.
 
On Mon, May 31, 2010 at 7:36 AM, Dino Ienco <[hidden email]> wrote:
Dear Mailing List,
            I'm a beginner with GBROWSE.
I download gbrowse and I installed it on my ubuntu.
Now I start the demo application, but when I click on the example link (for instance the first example on yeast)
I obtain the following message
            500 Internal Server Error.
 
 
I look at the log of apache2 and I see this error message:
 
[Mon May 31 16:29:17 2010] [error] [client ::1] File does not exist: /var/www/favicon.ico
GBrowse/ConfigData.pm did not return a true value at /usr/local/lib/perl/5.10.0/Bio/Graphics/Browser2.pm line 18.
BEGIN failed--compilation aborted at /usr/local/lib/perl/5.10.0/Bio/Graphics/Browser2.pm line 18.
Compilation failed in require at /usr/lib/cgi-bin/gb2/gbrowse line 8.
BEGIN failed--compilation aborted at /usr/lib/cgi-bin/gb2/gbrowse line 8.
 
 
Anybody can help/explain me about this error and how to deal with this one?
 
All the best
 
Dino Ienco, PhD
Department of Computer Science
University of Turin
C.so Svizzera 185
10149 - Turin
Italy

Phone +39 011 67 06 839
Fax +39 011 75 16 03
e-mail ienco[hidden email]


------------------------------------------------------------------------------


_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




-- 
===> PLEASE KEEP RESPONSES ON THE LIST <===
http://gmod.org/wiki/GMOD_News
http://gmod.org/wiki/Calendar
http://gmod.org/wiki/Help_Desk_Feedback

 
Dino Ienco, PhD
Department of Computer Science
University of Turin
C.so Svizzera 185
10149 - Turin
Italy

Phone +39 011 67 06 839
Fax +39 011 75 16 03
e-mail [hidden email]
web http://www.di.unito.it/~ienco



 

Dino Ienco, PhD
Department of Computer Science
University of Turin
C.so Svizzera 185
10149 - Turin
Italy

Phone +39 011 67 06 839
Fax +39 011 75 16 03
e-mail [hidden email]
web http://www.di.unito.it/~ienco




------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: information about GBROWSE installation

Jayaraman, Pushkala
In reply to this post by Dino Ienco
<base href="x-msg://77/">

Hello Dino,

If your Config.pm file is empty…I suggest that you reinstall Gbrowse. I would also suggest to check with the developers in the GMOD forum as well..

When I checked my Configdata.pm file this is what I found:

C<GBrowse::ConfigData> was automatically created using C<Module::Build>

 

Bio/Graphics/Browser2.pm line 18 shows this line:

use GBrowse::ConfigData;

 

According to me, you may need to install Gbrowse again..

Thanks,

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Dino Ienco [mailto:[hidden email]]
Sent: Tuesday, June 08, 2010 9:16 AM
To: Jayaraman, Pushkala
Subject: Re: [Gmod-gbrowse] information about GBROWSE installation

 

I check better, and I verify that the file exists but the file is empty

 

How can I deal with this problem?

 

Where could I find the .pm file?

 

All the best

Dino

 

 

 

 

On Jun 7, 2010, at 5:25 PM, Jayaraman, Pushkala wrote:



Hello Dino,

Favicon.ico error is not a problem..

Try going to the ConfigData.pm. There has to be a line that lets you activate debugging.

Something like CONSTANT DEBUG => 0

Make it CONSTANT_DEBUG =>1

See what debug statements it gives..

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

 

From: Dino Ienco [mailto:[hidden email]] 
Sent: Monday, June 07, 2010 4:46 AM
To: Dave Clements, GMOD Help Desk
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] information about GBROWSE installation

 

Dear Dave,

            I check the problem and the file is in the correct folder. (The one that you suggest me).

What should I try to solve this problem?

 

All the best

 

Dino

 

 

On Jun 2, 2010, at 12:38 AM, Dave Clements, GMOD Help Desk wrote:




Hi dino,

 

On my Ubuntu the complaining file is at:

  /usr/local/lib/perl/5.10.0/GBrowse/ConfigData.pm

 

Does that file exist, and is it world readable, on your system?

 

Dave C.

 

On Mon, May 31, 2010 at 7:36 AM, Dino Ienco <[hidden email]> wrote:

Dear Mailing List,

            I'm a beginner with GBROWSE.

I download gbrowse and I installed it on my ubuntu.

Now I start the demo application, but when I click on the example link (for instance the first example on yeast)

I obtain the following message

            500 Internal Server Error.

 

 

I look at the log of apache2 and I see this error message:

 

[Mon May 31 16:29:17 2010] [error] [client ::1] File does not exist: /var/www/favicon.ico

GBrowse/ConfigData.pm did not return a true value at /usr/local/lib/perl/5.10.0/Bio/Graphics/Browser2.pm line 18.

BEGIN failed--compilation aborted at /usr/local/lib/perl/5.10.0/Bio/Graphics/Browser2.pm line 18.

Compilation failed in require at /usr/lib/cgi-bin/gb2/gbrowse line 8.

BEGIN failed--compilation aborted at /usr/lib/cgi-bin/gb2/gbrowse line 8.

 

 

Anybody can help/explain me about this error and how to deal with this one?

 

All the best

 

Dino Ienco, PhD

Department of Computer Science
University of Turin

C.so Svizzera 185

10149 - Turin
Italy


Phone +39 011 67 06 839

Fax +39 011 75 16 03

e-mail ienco[hidden email]


------------------------------------------------------------------------------


_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




-- 
===> PLEASE KEEP RESPONSES ON THE LIST <===
http://gmod.org/wiki/GMOD_News
http://gmod.org/wiki/Calendar
http://gmod.org/wiki/Help_Desk_Feedback

 

Dino Ienco, PhD
Department of Computer Science
University of Turin
C.so Svizzera 185
10149 - Turin
Italy

Phone +39 011 67 06 839
Fax +39 011 75 16 03
e-mail [hidden email]
web http://www.di.unito.it/~ienco




 

 

Dino Ienco, PhD
Department of Computer Science
University of Turin
C.so Svizzera 185
10149 - Turin
Italy

Phone +39 011 67 06 839
Fax +39 011 75 16 03
e-mail [hidden email]
web http://www.di.unito.it/~ienco



 


------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: information about GBROWSE installation

Scott Cain
In reply to this post by Dino Ienco
Hi Dino,

So ConfigData.pm is present but empty?  That means there was a problem
with installing it.  Perhaps you didn't have sufficient permissions to
install files in that location.  Did you use `sudo` when installing
it?  I would suggest just trying to install it again and see if there
are any error messages during the installation.

Scott



On Tue, Jun 8, 2010 at 10:46 AM, Dino Ienco <[hidden email]> wrote:

> I check better, and I verify that the file exists but the file is empty
> How can I deal with this problem?
> Where could I find the .pm file?
> All the best
> Dino
>
> On Jun 7, 2010, at 5:25 PM, Jayaraman, Pushkala wrote:
>
> Hello Dino,
> Favicon.ico error is not a problem..
> Try going to the ConfigData.pm. There has to be a line that lets you
> activate debugging.
> Something like CONSTANT DEBUG => 0
> Make it CONSTANT_DEBUG =>1
> See what debug statements it gives..
>
> Pushkala Jayaraman
> Programmer/Analyst
> Rat Genome Database
> Human and Molecular Genetics Center
> Medical College of Wisconsin
> Email: [hidden email]
> Work: 414-955-2229
> www.rgd.mcw.edu
>
> From: Dino Ienco [mailto:[hidden email]]
> Sent: Monday, June 07, 2010 4:46 AM
> To: Dave Clements, GMOD Help Desk
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] information about GBROWSE installation
>
> Dear Dave,
>             I check the problem and the file is in the correct folder. (The
> one that you suggest me).
> What should I try to solve this problem?
>
> All the best
>
> Dino
>
>
> On Jun 2, 2010, at 12:38 AM, Dave Clements, GMOD Help Desk wrote:
>
> Hi dino,
>
> On my Ubuntu the complaining file is at:
>   /usr/local/lib/perl/5.10.0/GBrowse/ConfigData.pm
>
> Does that file exist, and is it world readable, on your system?
>
> Dave C.
>
> On Mon, May 31, 2010 at 7:36 AM, Dino Ienco <[hidden email]> wrote:
> Dear Mailing List,
>             I'm a beginner with GBROWSE.
> I download gbrowse and I installed it on my ubuntu.
> Now I start the demo application, but when I click on the example link (for
> instance the first example on yeast)
> I obtain the following message
>             500 Internal Server Error.
>
>
> I look at the log of apache2 and I see this error message:
>
> [Mon May 31 16:29:17 2010] [error] [client ::1] File does not exist:
> /var/www/favicon.ico
> GBrowse/ConfigData.pm did not return a true value at
> /usr/local/lib/perl/5.10.0/Bio/Graphics/Browser2.pm line 18.
> BEGIN failed--compilation aborted at
> /usr/local/lib/perl/5.10.0/Bio/Graphics/Browser2.pm line 18.
> Compilation failed in require at /usr/lib/cgi-bin/gb2/gbrowse line 8.
> BEGIN failed--compilation aborted at /usr/lib/cgi-bin/gb2/gbrowse line 8.
>
>
> Anybody can help/explain me about this error and how to deal with this one?
>
> All the best
>
> Dino Ienco, PhD
> Department of Computer Science
> University of Turin
> C.so Svizzera 185
> 10149 - Turin
> Italy
> Phone +39 011 67 06 839
> Fax +39 011 75 16 03
> e-mail [hidden email]
> web http://www.di.unito.it/~ienco
>
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
> --
> ===> PLEASE KEEP RESPONSES ON THE LIST <===
> http://gmod.org/wiki/GMOD_News
> http://gmod.org/wiki/Calendar
> http://gmod.org/wiki/Help_Desk_Feedback
>
>
> Dino Ienco, PhD
> Department of Computer Science
> University of Turin
> C.so Svizzera 185
> 10149 - Turin
> Italy
>
> Phone +39 011 67 06 839
> Fax +39 011 75 16 03
> e-mail [hidden email]
> web http://www.di.unito.it/~ienco
>
>
>
>
>
> Dino Ienco, PhD
> Department of Computer Science
> University of Turin
> C.so Svizzera 185
> 10149 - Turin
> Italy
>
> Phone +39 011 67 06 839
> Fax +39 011 75 16 03
> e-mail [hidden email]
> web http://www.di.unito.it/~ienco
>
>
>
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse