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 ------------------------------------------------------------------------------ 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 _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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:
------------------------------------------------------------------------ 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 _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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:
------------------------------------------------------------------------ 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 _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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]] 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]] 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] -- -- ------------------------------------------------------------------------------ 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 _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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:
------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Free forum by Nabble | Edit this page |