GBrowse Bug

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GBrowse Bug

Jacqueline Lee

Hi Lincoln,

 

I got this from our current GBrowse setup and it said specifically that I was to e-mail you:

 

[Fri Aug 09 14:00:33 2013] [warn] mod_fcgid: stderr: BUG: working around no ref defined bug; tell Lincoln bug is not fixed at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 2463.

 

Thanks,

 

Jacqueline Lee

Xenbase Bioinformatician/ Software Developer

e-mail: [hidden email]

www.xenbase.org

 


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Re: GBrowse Bug

Scott Cain
Hi Jacqueline,

I should really know this, but what version of GBrowse are you using?  I think that warning message has been gone from the code base for a long time.  Is it possible that you have more than one copy of Render.pm floating around?  If so, that could make for some difficult to troubleshoot bugs.

Scott



On Fri, Aug 9, 2013 at 4:05 PM, Jacqueline Lee <[hidden email]> wrote:

Hi Lincoln,

 

I got this from our current GBrowse setup and it said specifically that I was to e-mail you:

 

[Fri Aug 09 14:00:33 2013] [warn] mod_fcgid: stderr: BUG: working around no ref defined bug; tell Lincoln bug is not fixed at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 2463.

 

Thanks,

 

Jacqueline Lee

Xenbase Bioinformatician/ Software Developer

e-mail: [hidden email]

www.xenbase.org

 




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

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Re: GBrowse Bug

Scott Cain
Hi Jacqueline,

I cc'ed GBrowse back in, so when this gets sorted out the result will be archived.

There is nothing weird in your search results; they look exactly as I would expect for one instance of GBrowse.

Interestingly, the bug that caused that message was supposedly fixed long ago (release 2.07).  This was in the Change log:

* Tracked down the "let Lincoln know bug is not fixed" bug, and found a real solution.
          This was happening when user presses "back" button on browser after an unsuccessful
          search. This still triggers a log message until we know the bug is really and truly
          fixed.

So, is this what you did that caused the message?

Scott




On Tue, Aug 13, 2013 at 11:59 AM, Jacqueline Lee <[hidden email]> wrote:

Hi Scott,

 

We are supposed to be running version 2.55, and this is an entirely new machine, so I should have only installed 2.55.

 

To be sure, however, I searched for double copies of Render.pm, HTML.pm, Browser2.pm and Graphics.pm as well as doubles of Bio/Graphics/Browser2

 

Only one copy of Render.pm, Browser2.pm and HTML.pm are installed in the xenbase gbrowse machine. I have two copies of Graphics.pm installed:

 

/usr/local/share/perl5/Bio/Align/Graphics.pm

/usr/local/share/perl5/Bio/Graphics.pm

 

Not sure if that means anything for you? I also have two directories called Bio/Graphics/Browser2:

 

/usr/local/lib64/perl5/Bio/Graphics/Browser2

/usr/local/lib64/perl5/auto/Bio/Graphics/Browser2

 

Does this indicate the remnants of a second GBrowse copy on my machine?

 

Jacqueline

 

 

From: Scott Cain [mailto:[hidden email]]
Sent: Monday, August 12, 2013 11:43 AM
To: Jacqueline Lee
Cc: [hidden email]; [hidden email]
Subject: Re: GBrowse Bug

 

Hi Jacqueline,

 

I should really know this, but what version of GBrowse are you using?  I think that warning message has been gone from the code base for a long time.  Is it possible that you have more than one copy of Render.pm floating around?  If so, that could make for some difficult to troubleshoot bugs.

 

Scott

 

 

On Fri, Aug 9, 2013 at 4:05 PM, Jacqueline Lee <[hidden email]> wrote:

Hi Lincoln,

 

I got this from our current GBrowse setup and it said specifically that I was to e-mail you:

 

[Fri Aug 09 14:00:33 2013] [warn] mod_fcgid: stderr: BUG: working around no ref defined bug; tell Lincoln bug is not fixed at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 2463.

 

Thanks,

 

Jacqueline Lee

Xenbase Bioinformatician/ Software Developer

e-mail: [hidden email]

www.xenbase.org

 



 

--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




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

------------------------------------------------------------------------------
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Re: GBrowse Bug

Jacqueline Lee

Hi Scott,

 

I honestly don’t remember what I did to cause the message. We were looking at the error_log after I’d added some tracks to the new database (that I thought was working) and ended up with an error similar to the original one. As far as I know, we would have only been clicking reload, but there is a possibility we could have pressed the ‘back’ button.

 

Jacqueline

 

From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, August 13, 2013 10:26 AM
To: Jacqueline Lee; Gbrowse (E-mail)
Subject: Re: GBrowse Bug

 

Hi Jacqueline,

 

I cc'ed GBrowse back in, so when this gets sorted out the result will be archived.

 

There is nothing weird in your search results; they look exactly as I would expect for one instance of GBrowse.

 

Interestingly, the bug that caused that message was supposedly fixed long ago (release 2.07).  This was in the Change log:

 

* Tracked down the "let Lincoln know bug is not fixed" bug, and found a real solution.

          This was happening when user presses "back" button on browser after an unsuccessful

          search. This still triggers a log message until we know the bug is really and truly

          fixed.

 

So, is this what you did that caused the message?

 

Scott

 

 

 

On Tue, Aug 13, 2013 at 11:59 AM, Jacqueline Lee <[hidden email]> wrote:

Hi Scott,

 

We are supposed to be running version 2.55, and this is an entirely new machine, so I should have only installed 2.55.

 

To be sure, however, I searched for double copies of Render.pm, HTML.pm, Browser2.pm and Graphics.pm as well as doubles of Bio/Graphics/Browser2

 

Only one copy of Render.pm, Browser2.pm and HTML.pm are installed in the xenbase gbrowse machine. I have two copies of Graphics.pm installed:

 

/usr/local/share/perl5/Bio/Align/Graphics.pm

/usr/local/share/perl5/Bio/Graphics.pm

 

Not sure if that means anything for you? I also have two directories called Bio/Graphics/Browser2:

 

/usr/local/lib64/perl5/Bio/Graphics/Browser2

/usr/local/lib64/perl5/auto/Bio/Graphics/Browser2

 

Does this indicate the remnants of a second GBrowse copy on my machine?

 

Jacqueline

 

 

From: Scott Cain [mailto:[hidden email]]
Sent: Monday, August 12, 2013 11:43 AM
To: Jacqueline Lee
Cc: [hidden email]; [hidden email]
Subject: Re: GBrowse Bug

 

Hi Jacqueline,

 

I should really know this, but what version of GBrowse are you using?  I think that warning message has been gone from the code base for a long time.  Is it possible that you have more than one copy of Render.pm floating around?  If so, that could make for some difficult to troubleshoot bugs.

 

Scott

 

 

On Fri, Aug 9, 2013 at 4:05 PM, Jacqueline Lee <[hidden email]> wrote:

Hi Lincoln,

 

I got this from our current GBrowse setup and it said specifically that I was to e-mail you:

 

[Fri Aug 09 14:00:33 2013] [warn] mod_fcgid: stderr: BUG: working around no ref defined bug; tell Lincoln bug is not fixed at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 2463.

 

Thanks,

 

Jacqueline Lee

Xenbase Bioinformatician/ Software Developer

e-mail: [hidden email]

www.xenbase.org

 



 

--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



 

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


------------------------------------------------------------------------------
Get 100% visibility into Java/.NET code with AppDynamics Lite!
It's a free troubleshooting tool designed for production.
Get down to code-level detail for bottlenecks, with <2% overhead.
Download for free and get started troubleshooting in minutes.
http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk
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Re: GBrowse Bug

Scott Cain
In reply to this post by Scott Cain
Hi Jacqueline,

Thanks for the follow up; sorry it took so long to sort it out.  I'm going to cc this to the GBrowse mailing list so it can be archived and searchable.

Scott



On Wed, Oct 2, 2013 at 1:30 PM, Jacqueline Lee <[hidden email]> wrote:

I just thought I would post the solution to this bug, so if it happens to anyone else, they will be able to fix it.

 

After looking at the bug the first time, and being unable to solve the issue, I created a completely new VM image and installed mysql 5.6 using the rpms available from the mysql site. (Scott had e-mailed me indicating that mysql may be involved in the bug). It is important to note that several different people checked the permissions and ownership on the new configuration file before I re-installed everything. The permissions were set correctly and the file was owned by my GBrowse user.

 

After the re-installation, I su’d into root to change the permissions on certain directories so that I could test my site and it could run properly. Forgetting I was logged in as root,  I copied the volvox.conf file and renamed it xt4_1.conf. This caused the new file to be owned by root, with 700 permissions.

 

The exact same error that I had before I re-installed GBrowse occurred again. This time, I figured out it was because my configuration file did not have the correct permissions set and was not owned by my GBrowse user. After I fixed this, everything worked.

 

Jacqueline

 

From: Scott Cain [mailto:[hidden email]]

Sent: Tuesday, August 13, 2013 10:26 AM
To: Jacqueline Lee; Gbrowse (E-mail)
Subject: Re: GBrowse Bug

 

Hi Jacqueline,

 

I cc'ed GBrowse back in, so when this gets sorted out the result will be archived.

 

There is nothing weird in your search results; they look exactly as I would expect for one instance of GBrowse.

 

Interestingly, the bug that caused that message was supposedly fixed long ago (release 2.07).  This was in the Change log:

 

* Tracked down the "let Lincoln know bug is not fixed" bug, and found a real solution.

          This was happening when user presses "back" button on browser after an unsuccessful

          search. This still triggers a log message until we know the bug is really and truly

          fixed.

 

So, is this what you did that caused the message?

 

Scott

 

 

 

On Tue, Aug 13, 2013 at 11:59 AM, Jacqueline Lee <[hidden email]> wrote:

Hi Scott,

 

We are supposed to be running version 2.55, and this is an entirely new machine, so I should have only installed 2.55.

 

To be sure, however, I searched for double copies of Render.pm, HTML.pm, Browser2.pm and Graphics.pm as well as doubles of Bio/Graphics/Browser2

 

Only one copy of Render.pm, Browser2.pm and HTML.pm are installed in the xenbase gbrowse machine. I have two copies of Graphics.pm installed:

 

/usr/local/share/perl5/Bio/Align/Graphics.pm

/usr/local/share/perl5/Bio/Graphics.pm

 

Not sure if that means anything for you? I also have two directories called Bio/Graphics/Browser2:

 

/usr/local/lib64/perl5/Bio/Graphics/Browser2

/usr/local/lib64/perl5/auto/Bio/Graphics/Browser2

 

Does this indicate the remnants of a second GBrowse copy on my machine?

 

Jacqueline

 

 

From: Scott Cain [mailto:[hidden email]]
Sent: Monday, August 12, 2013 11:43 AM
To: Jacqueline Lee
Cc: [hidden email]; [hidden email]
Subject: Re: GBrowse Bug

 

Hi Jacqueline,

 

I should really know this, but what version of GBrowse are you using?  I think that warning message has been gone from the code base for a long time.  Is it possible that you have more than one copy of Render.pm floating around?  If so, that could make for some difficult to troubleshoot bugs.

 

Scott

 

 

On Fri, Aug 9, 2013 at 4:05 PM, Jacqueline Lee <[hidden email]> wrote:

Hi Lincoln,

 

I got this from our current GBrowse setup and it said specifically that I was to e-mail you:

 

[Fri Aug 09 14:00:33 2013] [warn] mod_fcgid: stderr: BUG: working around no ref defined bug; tell Lincoln bug is not fixed at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 2463.

 

Thanks,

 

Jacqueline Lee

Xenbase Bioinformatician/ Software Developer

e-mail: [hidden email]

www.xenbase.org

 



 

--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



 

--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




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

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