GBrowse2 throwing various errors (Sean O'Keeffe)

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GBrowse2 throwing various errors (Sean O'Keeffe)

Bob Sinclair
 From Mike, our SysAd:

"I did, in fact reinstall and rebuild gbrowse2 at least a dozen times.
  It STILL gives me these same errors when I use my firefox browser. Bob
and others can see the pages properly.  I can also, so long as I use a
different browser.  We're running Gbrowse 2.12 at the moment.  My
suggestion is to try having someone else look at the page."

Mike is using the most current Firefox. Mine is a little older (3.6.8)
still ut Firefox. There are also differences in that Mike is inside our
firewall, while I have to come in via a VPN client. Definitely some
oddness that I don't think we have a handle on.

Bob.

> Message: 1
> Date: Thu, 19 Aug 2010 15:36:34 +0200
> From: Sean O'Keeffe<[hidden email]>
> Subject: Re: [Gmod-gbrowse] GBrowse2 throwing various errors
> To: Bob Sinclair<[hidden email]>
> Cc: [hidden email]
> Message-ID:<[hidden email]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Bob,
> I am experiencing your problems on a test server here now too.
> I am getting them on all configured datasets (not yeast which we don't
> use and which has been removed).
> The page displays but tracks are all missing - nothing loads.
> Error log reports exactly as you did:
>
> [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Reverting
> coordinates to last known good region (user probably hit 'back' button).
> at
> /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/Render.pm
> line 2609., referer:
> http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
> [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Use of
> uninitialized value in concatenation (.) or string at
> /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/Render.pm
> line 2623., referer:
> http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
> [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Use of
> uninitialized value in multiplication (*) at
> /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/RenderPanels.pm
> line 931., referer:
> http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
> [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Illegal
> division by zero at
> /project/gbrowse/httpd_perllib_new/lib/perl5/Bio/Graphics/Panel.pm line
> 237., referer:
> http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
> [Thu Aug 19 15:23:19 2010] [error] [client 141.14.29.50] Premature end
> of script headers: gbrowse, referer:
> http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
>
> Did you ever get a fix for these issues?
> Gbrowse is 2.13 with up to date bio-graphics
>
> Thx,
> Sean.

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Re: GBrowse2 throwing various errors (Sean O'Keeffe)

Lincoln Stein
Hi,

GBrowse loads in two steps. First it loads the framework of the page, and then it loads the tracks and other bits of the content. If the server is running behind the firewall and there is some address translation in use (for example, the server sees one IP address and the external client sees another), then the server might be reporting one IP address on the first step, but the browser client cannot access that IP address on the second step.

The best way to fix this is to make sure that the Apache server's hostname is set to the externally visible IP address or hostname.

Lincoln

On Thu, Aug 19, 2010 at 2:26 PM, Bob Sinclair <[hidden email]> wrote:
 From Mike, our SysAd:

"I did, in fact reinstall and rebuild gbrowse2 at least a dozen times.
 It STILL gives me these same errors when I use my firefox browser. Bob
and others can see the pages properly.  I can also, so long as I use a
different browser.  We're running Gbrowse 2.12 at the moment.  My
suggestion is to try having someone else look at the page."

Mike is using the most current Firefox. Mine is a little older (3.6.8)
still ut Firefox. There are also differences in that Mike is inside our
firewall, while I have to come in via a VPN client. Definitely some
oddness that I don't think we have a handle on.

Bob.

> Message: 1
> Date: Thu, 19 Aug 2010 15:36:34 +0200
> From: Sean O'Keeffe<[hidden email]>
> Subject: Re: [Gmod-gbrowse] GBrowse2 throwing various errors
> To: Bob Sinclair<[hidden email]>
> Cc: [hidden email]
> Message-ID:<[hidden email]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Bob,
> I am experiencing your problems on a test server here now too.
> I am getting them on all configured datasets (not yeast which we don't
> use and which has been removed).
> The page displays but tracks are all missing - nothing loads.
> Error log reports exactly as you did:
>
> [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Reverting
> coordinates to last known good region (user probably hit 'back' button).
> at
> /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/Render.pm
> line 2609., referer:
> http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
> [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Use of
> uninitialized value in concatenation (.) or string at
> /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/Render.pm
> line 2623., referer:
> http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
> [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Use of
> uninitialized value in multiplication (*) at
> /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/RenderPanels.pm
> line 931., referer:
> http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
> [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Illegal
> division by zero at
> /project/gbrowse/httpd_perllib_new/lib/perl5/Bio/Graphics/Panel.pm line
> 237., referer:
> http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
> [Thu Aug 19 15:23:19 2010] [error] [client 141.14.29.50] Premature end
> of script headers: gbrowse, referer:
> http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
>
> Did you ever get a fix for these issues?
> Gbrowse is 2.13 with up to date bio-graphics
>
> Thx,
> Sean.

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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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Re: GBrowse2 throwing various errors

okeeffe
In reply to this post by Bob Sinclair
Bob Sinclair wrote:

>  From Mike, our SysAd:
>
> "I did, in fact reinstall and rebuild gbrowse2 at least a dozen times.
>   It STILL gives me these same errors when I use my firefox browser. Bob
> and others can see the pages properly.  I can also, so long as I use a
> different browser.  We're running Gbrowse 2.12 at the moment.  My
> suggestion is to try having someone else look at the page."
>
> Mike is using the most current Firefox. Mine is a little older (3.6.8)
> still ut Firefox. There are also differences in that Mike is inside our
> firewall, while I have to come in via a VPN client. Definitely some
> oddness that I don't think we have a handle on.
>
> Bob.
>
>  
>> Message: 1
>> Date: Thu, 19 Aug 2010 15:36:34 +0200
>> From: Sean O'Keeffe<[hidden email]>
>> Subject: Re: [Gmod-gbrowse] GBrowse2 throwing various errors
>> To: Bob Sinclair<[hidden email]>
>> Cc: [hidden email]
>> Message-ID:<[hidden email]>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> Hi Bob,
>> I am experiencing your problems on a test server here now too.
>> I am getting them on all configured datasets (not yeast which we don't
>> use and which has been removed).
>> The page displays but tracks are all missing - nothing loads.
>> Error log reports exactly as you did:
>>
>> [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Reverting
>> coordinates to last known good region (user probably hit 'back' button).
>> at
>> /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/Render.pm
>> line 2609., referer:
>> http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
>> [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Use of
>> uninitialized value in concatenation (.) or string at
>> /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/Render.pm
>> line 2623., referer:
>> http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
>> [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Use of
>> uninitialized value in multiplication (*) at
>> /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/RenderPanels.pm
>> line 931., referer:
>> http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
>> [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Illegal
>> division by zero at
>> /project/gbrowse/httpd_perllib_new/lib/perl5/Bio/Graphics/Panel.pm line
>> 237., referer:
>> http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
>> [Thu Aug 19 15:23:19 2010] [error] [client 141.14.29.50] Premature end
>> of script headers: gbrowse, referer:
>> http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
>>
>> Did you ever get a fix for these issues?
>> Gbrowse is 2.13 with up to date bio-graphics
>>
>> Thx,
>> Sean.
>>    
>
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>
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>  
Hi Bob & Mike,
Yes it works fine on IE within the institute and also on a konqueror
browser (kde default browser) at home.
Firefox 3.6.3 doesn't work in any situation.

Odd.


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Re: GBrowse2 throwing various errors

Lincoln Stein
Hi,

Could you summarize again the various configurations that do and don't' work? Are the hostnames and IP addresses the same from within the LAN and when using VPN?

Lincoln

On Fri, Aug 20, 2010 at 9:01 AM, Sean O'Keeffe <[hidden email]> wrote:
Bob Sinclair wrote:
>  From Mike, our SysAd:
>
> "I did, in fact reinstall and rebuild gbrowse2 at least a dozen times.
>   It STILL gives me these same errors when I use my firefox browser. Bob
> and others can see the pages properly.  I can also, so long as I use a
> different browser.  We're running Gbrowse 2.12 at the moment.  My
> suggestion is to try having someone else look at the page."
>
> Mike is using the most current Firefox. Mine is a little older (3.6.8)
> still ut Firefox. There are also differences in that Mike is inside our
> firewall, while I have to come in via a VPN client. Definitely some
> oddness that I don't think we have a handle on.
>
> Bob.
>
>
>> Message: 1
>> Date: Thu, 19 Aug 2010 15:36:34 +0200
>> From: Sean O'Keeffe<[hidden email]>
>> Subject: Re: [Gmod-gbrowse] GBrowse2 throwing various errors
>> To: Bob Sinclair<[hidden email]>
>> Cc: [hidden email]
>> Message-ID:<[hidden email]>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> Hi Bob,
>> I am experiencing your problems on a test server here now too.
>> I am getting them on all configured datasets (not yeast which we don't
>> use and which has been removed).
>> The page displays but tracks are all missing - nothing loads.
>> Error log reports exactly as you did:
>>
>> [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Reverting
>> coordinates to last known good region (user probably hit 'back' button).
>> at
>> /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/Render.pm
>> line 2609., referer:
>> http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
>> [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Use of
>> uninitialized value in concatenation (.) or string at
>> /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/Render.pm
>> line 2623., referer:
>> http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
>> [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Use of
>> uninitialized value in multiplication (*) at
>> /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/RenderPanels.pm
>> line 931., referer:
>> http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
>> [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Illegal
>> division by zero at
>> /project/gbrowse/httpd_perllib_new/lib/perl5/Bio/Graphics/Panel.pm line
>> 237., referer:
>> http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
>> [Thu Aug 19 15:23:19 2010] [error] [client 141.14.29.50] Premature end
>> of script headers: gbrowse, referer:
>> http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
>>
>> Did you ever get a fix for these issues?
>> Gbrowse is 2.13 with up to date bio-graphics
>>
>> Thx,
>> Sean.
>>
>
> ------------------------------------------------------------------------------
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>
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>
Hi Bob & Mike,
Yes it works fine on IE within the institute and also on a konqueror
browser (kde default browser) at home.
Firefox 3.6.3 doesn't work in any situation.

Odd.


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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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Re: GBrowse2 throwing various errors

okeeffe
Lincoln Stein wrote:

> Hi,
>
> Could you summarize again the various configurations that do and
> don't' work? Are the hostnames and IP addresses the same from within
> the LAN and when using VPN?
>
> Lincoln
>
> On Fri, Aug 20, 2010 at 9:01 AM, Sean O'Keeffe <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Bob Sinclair wrote:
>     >  From Mike, our SysAd:
>     >
>     > "I did, in fact reinstall and rebuild gbrowse2 at least a dozen
>     times.
>     >   It STILL gives me these same errors when I use my firefox
>     browser. Bob
>     > and others can see the pages properly.  I can also, so long as I
>     use a
>     > different browser.  We're running Gbrowse 2.12 at the moment.  My
>     > suggestion is to try having someone else look at the page."
>     >
>     > Mike is using the most current Firefox. Mine is a little older
>     (3.6.8)
>     > still ut Firefox. There are also differences in that Mike is
>     inside our
>     > firewall, while I have to come in via a VPN client. Definitely some
>     > oddness that I don't think we have a handle on.
>     >
>     > Bob.
>     >
>     >
>     >> Message: 1
>     >> Date: Thu, 19 Aug 2010 15:36:34 +0200
>     >> From: Sean O'Keeffe<[hidden email]
>     <mailto:[hidden email]>>
>     >> Subject: Re: [Gmod-gbrowse] GBrowse2 throwing various errors
>     >> To: Bob Sinclair<[hidden email]
>     <mailto:[hidden email]>>
>     >> Cc: [hidden email]
>     <mailto:[hidden email]>
>     >> Message-ID:<[hidden email]
>     <mailto:[hidden email]>>
>     >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>     >>
>     >> Hi Bob,
>     >> I am experiencing your problems on a test server here now too.
>     >> I am getting them on all configured datasets (not yeast which
>     we don't
>     >> use and which has been removed).
>     >> The page displays but tracks are all missing - nothing loads.
>     >> Error log reports exactly as you did:
>     >>
>     >> [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Reverting
>     >> coordinates to last known good region (user probably hit 'back'
>     button).
>     >> at
>     >>
>     /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/Render.pm
>     >> line 2609., referer:
>     >>
>     http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
>     >> [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Use of
>     >> uninitialized value in concatenation (.) or string at
>     >>
>     /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/Render.pm
>     >> line 2623., referer:
>     >>
>     http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
>     >> [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Use of
>     >> uninitialized value in multiplication (*) at
>     >>
>     /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/RenderPanels.pm
>     >> line 931., referer:
>     >>
>     http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
>     >> [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Illegal
>     >> division by zero at
>     >>
>     /project/gbrowse/httpd_perllib_new/lib/perl5/Bio/Graphics/Panel.pm
>     line
>     >> 237., referer:
>     >>
>     http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
>     >> [Thu Aug 19 15:23:19 2010] [error] [client 141.14.29.50]
>     Premature end
>     >> of script headers: gbrowse, referer:
>     >>
>     http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
>     >>
>     >> Did you ever get a fix for these issues?
>     >> Gbrowse is 2.13 with up to date bio-graphics
>     >>
>     >> Thx,
>     >> Sean.
>     >>
>     >
>     >
>     ------------------------------------------------------------------------------
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>     >
>     > Make an app they can't live without
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>     > [hidden email]
>     <mailto:[hidden email]>
>     > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>     >
>     Hi Bob & Mike,
>     Yes it works fine on IE within the institute and also on a konqueror
>     browser (kde default browser) at home.
>     Firefox 3.6.3 doesn't work in any situation.
>
>     Odd.
>
>
>     ------------------------------------------------------------------------------
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>     Make an app they can't live without
>     Enter the BlackBerry Developer Challenge
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>     [hidden email]
>     <mailto:[hidden email]>
>     https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <[hidden email]
> <mailto:[hidden email]>>
Hi Lincoln,
I have an internal institute wide server running GB1 & GB2 without problems.
I also have an external server for GB2 (was GB1 up to yesterday) - and
anyone can access it at:

http://promotion.molgen.mpg.de/cgi-bin/gbrowse 
<http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens>

It is this external server that is causing the truoble at the moment.
Admittedly the external server is set up as a virtual server but the
main ServerName is still promotion.molgen.mpg.de.
I can send on conf's if needed.

Sean.


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Re: GBrowse2 throwing various errors

Lincoln Stein
Do others on the list have Firefox 3.6.3 to confirm that this is a general problem? Here is a site to test it on: http://modencode.oicr.on.ca/fgb2/gbrowse/fly

Sean, Bob, if you can install firebug on your Firefox, this will detect any javascript errors (which this sounds like).

Lincoln

On Fri, Aug 20, 2010 at 9:24 AM, Sean O'Keeffe <[hidden email]> wrote:
Lincoln Stein wrote:
Hi,

Could you summarize again the various configurations that do and don't' work? Are the hostnames and IP addresses the same from within the LAN and when using VPN?

Lincoln

On Fri, Aug 20, 2010 at 9:01 AM, Sean O'Keeffe <[hidden email] <mailto:[hidden email]>> wrote:

   Bob Sinclair wrote:
   >  From Mike, our SysAd:
   >
   > "I did, in fact reinstall and rebuild gbrowse2 at least a dozen
   times.
   >   It STILL gives me these same errors when I use my firefox
   browser. Bob
   > and others can see the pages properly.  I can also, so long as I
   use a
   > different browser.  We're running Gbrowse 2.12 at the moment.  My
   > suggestion is to try having someone else look at the page."
   >
   > Mike is using the most current Firefox. Mine is a little older
   (3.6.8)
   > still ut Firefox. There are also differences in that Mike is
   inside our
   > firewall, while I have to come in via a VPN client. Definitely some
   > oddness that I don't think we have a handle on.
   >
   > Bob.
   >
   >
   >> Message: 1
   >> Date: Thu, 19 Aug 2010 15:36:34 +0200
   >> From: Sean O'Keeffe<[hidden email]
   <mailto:[hidden email]>>

   >> Subject: Re: [Gmod-gbrowse] GBrowse2 throwing various errors
   >> To: Bob Sinclair<[hidden email]
   <mailto:[hidden email]>>

   >> Cc: [hidden email]
   <mailto:[hidden email]>

   >> Message-ID:<[hidden email]
   <mailto:[hidden email]>>

   >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
   >>
   >> Hi Bob,
   >> I am experiencing your problems on a test server here now too.
   >> I am getting them on all configured datasets (not yeast which
   we don't
   >> use and which has been removed).
   >> The page displays but tracks are all missing - nothing loads.
   >> Error log reports exactly as you did:
   >>
   >> [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Reverting
   >> coordinates to last known good region (user probably hit 'back'
   button).
   >> at
   >>
   /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/Render.pm
   >> line 2609., referer:
   >>
   http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
   >> [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Use of
   >> uninitialized value in concatenation (.) or string at
   >>
   /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/Render.pm
   >> line 2623., referer:
   >>
   http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
   >> [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Use of
   >> uninitialized value in multiplication (*) at
   >>
   /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/RenderPanels.pm
   >> line 931., referer:
   >>
   http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
   >> [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Illegal
   >> division by zero at
   >>
   /project/gbrowse/httpd_perllib_new/lib/perl5/Bio/Graphics/Panel.pm
   line
   >> 237., referer:
   >>
   http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
   >> [Thu Aug 19 15:23:19 2010] [error] [client 141.14.29.50]
   Premature end
   >> of script headers: gbrowse, referer:
   >>
   http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
   >>
   >> Did you ever get a fix for these issues?
   >> Gbrowse is 2.13 with up to date bio-graphics
   >>
   >> Thx,
   >> Sean.
   >>
   >
   >
   ------------------------------------------------------------------------------
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   >
   > Make an app they can't live without
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   > [hidden email]
   <mailto:[hidden email]>

   > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
   >
   Hi Bob & Mike,
   Yes it works fine on IE within the institute and also on a konqueror
   browser (kde default browser) at home.
   Firefox 3.6.3 doesn't work in any situation.

   Odd.


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   https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email] <mailto:[hidden email]>>
Hi Lincoln,
I have an internal institute wide server running GB1 & GB2 without problems.
I also have an external server for GB2 (was GB1 up to yesterday) - and anyone can access it at:

http://promotion.molgen.mpg.de/cgi-bin/gbrowse <http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens>

It is this external server that is causing the truoble at the moment.
Admittedly the external server is set up as a virtual server but the main ServerName is still promotion.molgen.mpg.de.
I can send on conf's if needed.

Sean.




--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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Re: GBrowse2 throwing various errors

Fields, Christopher J
Don't have Firefox 3.6.3, there have been several updates since that version.  I'm using Firefox 3.6.6 on OS X 10.6 and Firefox 3.6.8 on Ubuntu 9.10, and both the test site and Sean's site look fine with both versions (tracks and rubber-banding work, etc).  

chris

On Aug 20, 2010, at 10:35 AM, Lincoln Stein wrote:

> Do others on the list have Firefox 3.6.3 to confirm that this is a general problem? Here is a site to test it on: http://modencode.oicr.on.ca/fgb2/gbrowse/fly
>
> Sean, Bob, if you can install firebug on your Firefox, this will detect any javascript errors (which this sounds like).
>
> Lincoln
>
> On Fri, Aug 20, 2010 at 9:24 AM, Sean O'Keeffe <[hidden email]> wrote:
> Lincoln Stein wrote:
> Hi,
>
> Could you summarize again the various configurations that do and don't' work? Are the hostnames and IP addresses the same from within the LAN and when using VPN?
>
> Lincoln
>
> On Fri, Aug 20, 2010 at 9:01 AM, Sean O'Keeffe <[hidden email] <mailto:[hidden email]>> wrote:
>
>    Bob Sinclair wrote:
>    >  From Mike, our SysAd:
>    >
>    > "I did, in fact reinstall and rebuild gbrowse2 at least a dozen
>    times.
>    >   It STILL gives me these same errors when I use my firefox
>    browser. Bob
>    > and others can see the pages properly.  I can also, so long as I
>    use a
>    > different browser.  We're running Gbrowse 2.12 at the moment.  My
>    > suggestion is to try having someone else look at the page."
>    >
>    > Mike is using the most current Firefox. Mine is a little older
>    (3.6.8)
>    > still ut Firefox. There are also differences in that Mike is
>    inside our
>    > firewall, while I have to come in via a VPN client. Definitely some
>    > oddness that I don't think we have a handle on.
>    >
>    > Bob.
>    >
>    >
>    >> Message: 1
>    >> Date: Thu, 19 Aug 2010 15:36:34 +0200
>    >> From: Sean O'Keeffe<[hidden email]
>    <mailto:[hidden email]>>
>
>    >> Subject: Re: [Gmod-gbrowse] GBrowse2 throwing various errors
>    >> To: Bob Sinclair<[hidden email]
>    <mailto:[hidden email]>>
>
>    >> Cc: [hidden email]
>    <mailto:[hidden email]>
>
>    >> Message-ID:<[hidden email]
>    <mailto:[hidden email]>>
>
>    >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>    >>
>    >> Hi Bob,
>    >> I am experiencing your problems on a test server here now too.
>    >> I am getting them on all configured datasets (not yeast which
>    we don't
>    >> use and which has been removed).
>    >> The page displays but tracks are all missing - nothing loads.
>    >> Error log reports exactly as you did:
>    >>
>    >> [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Reverting
>    >> coordinates to last known good region (user probably hit 'back'
>    button).
>    >> at
>    >>
>    /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/Render.pm
>    >> line 2609., referer:
>    >>
>    http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
>    >> [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Use of
>    >> uninitialized value in concatenation (.) or string at
>    >>
>    /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/Render.pm
>    >> line 2623., referer:
>    >>
>    http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
>    >> [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Use of
>    >> uninitialized value in multiplication (*) at
>    >>
>    /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/RenderPanels.pm
>    >> line 931., referer:
>    >>
>    http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
>    >> [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Illegal
>    >> division by zero at
>    >>
>    /project/gbrowse/httpd_perllib_new/lib/perl5/Bio/Graphics/Panel.pm
>    line
>    >> 237., referer:
>    >>
>    http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
>    >> [Thu Aug 19 15:23:19 2010] [error] [client 141.14.29.50]
>    Premature end
>    >> of script headers: gbrowse, referer:
>    >>
>    http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
>    >>
>    >> Did you ever get a fix for these issues?
>    >> Gbrowse is 2.13 with up to date bio-graphics
>    >>
>    >> Thx,
>    >> Sean.
>    >>
>    >
>    >
>    ------------------------------------------------------------------------------
>    > This SF.net email is sponsored by
>    >
>    > Make an app they can't live without
>    > Enter the BlackBerry Developer Challenge
>    > http://p.sf.net/sfu/RIM-dev2dev
>    > _______________________________________________
>    > Gmod-gbrowse mailing list
>    > [hidden email]
>    <mailto:[hidden email]>
>
>    > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>    >
>    Hi Bob & Mike,
>    Yes it works fine on IE within the institute and also on a konqueror
>    browser (kde default browser) at home.
>    Firefox 3.6.3 doesn't work in any situation.
>
>    Odd.
>
>
>    ------------------------------------------------------------------------------
>    This SF.net email is sponsored by
>
>    Make an app they can't live without
>    Enter the BlackBerry Developer Challenge
>    http://p.sf.net/sfu/RIM-dev2dev
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>    Gmod-gbrowse mailing list
>    [hidden email]
>    <mailto:[hidden email]>
>
>    https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <[hidden email] <mailto:[hidden email]>>
> Hi Lincoln,
> I have an internal institute wide server running GB1 & GB2 without problems.
> I also have an external server for GB2 (was GB1 up to yesterday) - and anyone can access it at:
>
> http://promotion.molgen.mpg.de/cgi-bin/gbrowse <http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens>
>
> It is this external server that is causing the truoble at the moment.
> Admittedly the external server is set up as a virtual server but the main ServerName is still promotion.molgen.mpg.de.
> I can send on conf's if needed.
>
> Sean.
>
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <[hidden email]>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by
>
> Make an app they can't live without
> Enter the BlackBerry Developer Challenge
> http://p.sf.net/sfu/RIM-dev2dev _______________________________________________
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> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


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Re: GBrowse2 throwing various errors

Bob Sinclair
I am also not on 3.6.3. Firefox 3.6.8 seemed to be working for me with
our JAX setup and seems fine with the fly link you provided.

When we were getting the errors, Mike had a more recent Firefox (the
most recent at that time). But after the reinstall the error went away
(although I think failure to clear the browser cache after reinstalling
a component can confuse the issue, the reinstall having fixed something
but an old cookie masking that result).

Lincoln's comment earlier about GBrowse drawing in 2 stages left me
thinking about what I was seeing at the same time as Mike was generating
the errors. It seemed that the frames would draw quite quickly, but that
painting in the details (even with the yeast or volvox data) took a very
long time (well over a minute). Mike has subsequently said that this is
likely due to our test machine being old and slow, but I just looked at
the timing again, and I think it's far faster than it was when Mike was
seeing the errors (with the yeast data, the framework draws in 2 or 3
seconds, the details panel fills for the chrI80,000..120,000 example in
about 10 seconds, and the region panel about 3 seconds later.

I don't know if any of that is helpful, but it's an observation, for
what it's worth.

Bob.



On 8/20/2010 11:52 AM, Chris Fields wrote:

> Don't have Firefox 3.6.3, there have been several updates since that version.  I'm using Firefox 3.6.6 on OS X 10.6 and Firefox 3.6.8 on Ubuntu 9.10, and both the test site and Sean's site look fine with both versions (tracks and rubber-banding work, etc).
>
> chris
>
> On Aug 20, 2010, at 10:35 AM, Lincoln Stein wrote:
>
>    
>> Do others on the list have Firefox 3.6.3 to confirm that this is a general problem? Here is a site to test it on: http://modencode.oicr.on.ca/fgb2/gbrowse/fly
>>
>> Sean, Bob, if you can install firebug on your Firefox, this will detect any javascript errors (which this sounds like).
>>
>> Lincoln
>>
>> On Fri, Aug 20, 2010 at 9:24 AM, Sean O'Keeffe<[hidden email]>  wrote:
>> Lincoln Stein wrote:
>> Hi,
>>
>> Could you summarize again the various configurations that do and don't' work? Are the hostnames and IP addresses the same from within the LAN and when using VPN?
>>
>> Lincoln
>>
>> On Fri, Aug 20, 2010 at 9:01 AM, Sean O'Keeffe<[hidden email]<mailto:[hidden email]>>  wrote:
>>
>>     Bob Sinclair wrote:
>>     >    From Mike, our SysAd:
>>     >
>>     >  "I did, in fact reinstall and rebuild gbrowse2 at least a dozen
>>     times.
>>     >    It STILL gives me these same errors when I use my firefox
>>     browser. Bob
>>     >  and others can see the pages properly.  I can also, so long as I
>>     use a
>>     >  different browser.  We're running Gbrowse 2.12 at the moment.  My
>>     >  suggestion is to try having someone else look at the page."
>>     >
>>     >  Mike is using the most current Firefox. Mine is a little older
>>     (3.6.8)
>>     >  still ut Firefox. There are also differences in that Mike is
>>     inside our
>>     >  firewall, while I have to come in via a VPN client. Definitely some
>>     >  oddness that I don't think we have a handle on.
>>     >
>>     >  Bob.
>>     >
>>     >
>>     >>  Message: 1
>>     >>  Date: Thu, 19 Aug 2010 15:36:34 +0200
>>     >>  From: Sean O'Keeffe<[hidden email]
>>     <mailto:[hidden email]>>
>>
>>     >>  Subject: Re: [Gmod-gbrowse] GBrowse2 throwing various errors
>>     >>  To: Bob Sinclair<[hidden email]
>>     <mailto:[hidden email]>>
>>
>>     >>  Cc: [hidden email]
>>     <mailto:[hidden email]>
>>
>>     >>  Message-ID:<[hidden email]
>>     <mailto:[hidden email]>>
>>
>>     >>  Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>     >>
>>     >>  Hi Bob,
>>     >>  I am experiencing your problems on a test server here now too.
>>     >>  I am getting them on all configured datasets (not yeast which
>>     we don't
>>     >>  use and which has been removed).
>>     >>  The page displays but tracks are all missing - nothing loads.
>>     >>  Error log reports exactly as you did:
>>     >>
>>     >>  [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Reverting
>>     >>  coordinates to last known good region (user probably hit 'back'
>>     button).
>>     >>  at
>>     >>
>>     /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/Render.pm
>>     >>  line 2609., referer:
>>     >>
>>     http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
>>     >>  [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Use of
>>     >>  uninitialized value in concatenation (.) or string at
>>     >>
>>     /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/Render.pm
>>     >>  line 2623., referer:
>>     >>
>>     http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
>>     >>  [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Use of
>>     >>  uninitialized value in multiplication (*) at
>>     >>
>>     /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/RenderPanels.pm
>>     >>  line 931., referer:
>>     >>
>>     http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
>>     >>  [Thu Aug 19 15:23:18 2010] [error] [client 141.14.29.50] Illegal
>>     >>  division by zero at
>>     >>
>>     /project/gbrowse/httpd_perllib_new/lib/perl5/Bio/Graphics/Panel.pm
>>     line
>>     >>  237., referer:
>>     >>
>>     http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
>>     >>  [Thu Aug 19 15:23:19 2010] [error] [client 141.14.29.50]
>>     Premature end
>>     >>  of script headers: gbrowse, referer:
>>     >>
>>     http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens
>>     >>
>>     >>  Did you ever get a fix for these issues?
>>     >>  Gbrowse is 2.13 with up to date bio-graphics
>>     >>
>>     >>  Thx,
>>     >>  Sean.
>>     >>
>>     >
>>     >
>>     ------------------------------------------------------------------------------
>>     >  This SF.net email is sponsored by
>>     >
>>     >  Make an app they can't live without
>>     >  Enter the BlackBerry Developer Challenge
>>     >  http://p.sf.net/sfu/RIM-dev2dev
>>     >  _______________________________________________
>>     >  Gmod-gbrowse mailing list
>>     >  [hidden email]
>>     <mailto:[hidden email]>
>>
>>     >  https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>     >
>>     Hi Bob&  Mike,
>>     Yes it works fine on IE within the institute and also on a konqueror
>>     browser (kde default browser) at home.
>>     Firefox 3.6.3 doesn't work in any situation.
>>
>>     Odd.
>>
>>
>>     ------------------------------------------------------------------------------
>>     This SF.net email is sponsored by
>>
>>     Make an app they can't live without
>>     Enter the BlackBerry Developer Challenge
>>     http://p.sf.net/sfu/RIM-dev2dev
>>     _______________________________________________
>>     Gmod-gbrowse mailing list
>>     [hidden email]
>>     <mailto:[hidden email]>
>>
>>     https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>>
>>
>> --
>> Lincoln D. Stein
>> Director, Informatics and Biocomputing Platform
>> Ontario Institute for Cancer Research
>> 101 College St., Suite 800
>> Toronto, ON, Canada M5G0A3
>> 416 673-8514
>> Assistant: Renata Musa<[hidden email]<mailto:[hidden email]>>
>> Hi Lincoln,
>> I have an internal institute wide server running GB1&  GB2 without problems.
>> I also have an external server for GB2 (was GB1 up to yesterday) - and anyone can access it at:
>>
>> http://promotion.molgen.mpg.de/cgi-bin/gbrowse<http://promotion.molgen.mpg.de/cgi-bin/gbrowse/H.Sapiens/?source=H.Sapiens>
>>
>> It is this external server that is causing the truoble at the moment.
>> Admittedly the external server is set up as a virtual server but the main ServerName is still promotion.molgen.mpg.de.
>> I can send on conf's if needed.
>>
>> Sean.
>>
>>
>>
>>
>> --
>> Lincoln D. Stein
>> Director, Informatics and Biocomputing Platform
>> Ontario Institute for Cancer Research
>> 101 College St., Suite 800
>> Toronto, ON, Canada M5G0A3
>> 416 673-8514
>> Assistant: Renata Musa<[hidden email]>
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by
>>
>> Make an app they can't live without
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