Warning and error message in Apache error log

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

Warning and error message in Apache error log

kkarimi
Hi all,
 
 We are seeing quite a few GBrowse warning and error messages in the Xenbase project's Apache logs, and wonder whether this is an issue with our installation, or a problem with GBrowse. I've included sample lines from our error log. There are thousands more of them:
 
[Wed Dec 05 12:39:24 2012] [warn] mod_fcgid: stderr: Can't call method "plugins" on an undefined value at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 1183.
[Wed Dec 05 12:39:24 2012] [notice] child pid 28308 exit signal Illegal instruction (4)
[Wed Dec 05 12:39:32 2012] [notice] mod_fcgid: process /var/www/cgi-bin/gb2/gbrowse(30375) exit(normal exit), terminated by calling exit(), return code: 255
[Wed Dec 05 12:39:32 2012] [warn] mod_fcgid: cleanup zombie process 30375
[Wed Dec 05 12:40:34 2012] [warn] mod_fcgid: stderr: Can't call method "plugins" on an undefined value at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 1183.
[Wed Dec 05 12:40:35 2012] [notice] child pid 24856 exit signal Illegal instruction (4)
[Wed Dec 05 12:40:38 2012] [notice] mod_fcgid: process /var/www/cgi-bin/gb2/gbrowse(30447) exit(normal exit), terminated by calling exit(), return code: 255
[Wed Dec 05 12:40:38 2012] [warn] mod_fcgid: cleanup zombie process 30447
[Wed Dec 05 12:40:52 2012] [error] [client 143.248.22.90] Use of uninitialized value in concatenation (.) or string at /var/www/cgi-bin/gb2/gbrowse_details line 122., referer: http://www.xenbase.org/fgb2/gbrowse/Xenopus_tropicalis_7_1/?source=Xenopus_tropicalis_7_1&name=scaffold_5:118075219-118127020
[Wed Dec 05 12:40:52 2012] [error] [client 143.248.22.90] Use of uninitialized value in concatenation (.) or string at /var/www/cgi-bin/gb2/gbrowse_details line 123., referer: http://www.xenbase.org/fgb2/gbrowse/Xenopus_tropicalis_7_1/?source=Xenopus_tropicalis_7_1&name=scaffold_5:118075219-118127020
[Wed Dec 05 12:40:52 2012] [error] [client 143.248.22.90] Use of uninitialized value in string eq at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm line 267., referer: http://www.xenbase.org/fgb2/gbrowse/Xenopus_tropicalis_7_1/?source=Xenopus_tropicalis_7_1&name=scaffold_5:118075219-118127020
[Wed Dec 05 12:41:48 2012] [warn] mod_fcgid: stderr: Can't call method "plugins" on an undefined value at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 1183.
[Wed Dec 05 12:41:48 2012] [notice] child pid 30343 exit signal Segmentation fault (11)
 
 Please let me know if additional information is required for diagnosing the problem, and thanks for any help.
 
-Kamran
 

------------------------------------------------------------------------------
LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
Remotely access PCs and mobile devices and provide instant support
Improve your efficiency, and focus on delivering more value-add services
Discover what IT Professionals Know. Rescue delivers
http://p.sf.net/sfu/logmein_12329d2d
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Fwd: Warning and error message in Apache error log

girlwithglasses
Can anyone provide Kamran with insight as to what is causing the errors seen in the Apache error log, below?

---------- Forwarded message ----------
From: Kamran Karimi <[hidden email]>
Date: Thu, Dec 13, 2012 at 9:08 AM
Subject: RE: [Gmod-gbrowse] Warning and error message in Apache error log
To: Amelia Ireland <[hidden email]>


Hi Amelia,
 
 No I didn't, and I would appreciate any help.
 
-Kamran
 
Kamran Karimi, Ph.D., P.Eng.
Xenbase manager
ICT 753
University of Calgary
Phone: <a href="tel:403-210-8136" value="+14032108136" target="_blank">403-210-8136
 
 

From: Amelia Ireland [[hidden email]]
Sent: December-12-12 5:18 PM
To: Kamran Karimi
Subject: Re: [Gmod-gbrowse] Warning and error message in Apache error log

Hello,

Did you get a response to your question, and if not, do you still need help with it?



On Wed, Dec 5, 2012 at 11:59 AM, Kamran Karimi <[hidden email]> wrote:
Hi all,
 
 We are seeing quite a few GBrowse warning and error messages in the Xenbase project's Apache logs, and wonder whether this is an issue with our installation, or a problem with GBrowse. I've included sample lines from our error log. There are thousands more of them:
 
[Wed Dec 05 12:39:24 2012] [warn] mod_fcgid: stderr: Can't call method "plugins" on an undefined value at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 1183.
[Wed Dec 05 12:39:24 2012] [notice] child pid 28308 exit signal Illegal instruction (4)
[Wed Dec 05 12:39:32 2012] [notice] mod_fcgid: process /var/www/cgi-bin/gb2/gbrowse(30375) exit(normal exit), terminated by calling exit(), return code: 255
[Wed Dec 05 12:39:32 2012] [warn] mod_fcgid: cleanup zombie process 30375
[Wed Dec 05 12:40:34 2012] [warn] mod_fcgid: stderr: Can't call method "plugins" on an undefined value at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 1183.
[Wed Dec 05 12:40:35 2012] [notice] child pid 24856 exit signal Illegal instruction (4)
[Wed Dec 05 12:40:38 2012] [notice] mod_fcgid: process /var/www/cgi-bin/gb2/gbrowse(30447) exit(normal exit), terminated by calling exit(), return code: 255
[Wed Dec 05 12:40:38 2012] [warn] mod_fcgid: cleanup zombie process 30447
[Wed Dec 05 12:40:52 2012] [error] [client 143.248.22.90] Use of uninitialized value in concatenation (.) or string at /var/www/cgi-bin/gb2/gbrowse_details line 122., referer: http://www.xenbase.org/fgb2/gbrowse/Xenopus_tropicalis_7_1/?source=Xenopus_tropicalis_7_1&name=scaffold_5:118075219-118127020
[Wed Dec 05 12:40:52 2012] [error] [client 143.248.22.90] Use of uninitialized value in concatenation (.) or string at /var/www/cgi-bin/gb2/gbrowse_details line 123., referer: http://www.xenbase.org/fgb2/gbrowse/Xenopus_tropicalis_7_1/?source=Xenopus_tropicalis_7_1&name=scaffold_5:118075219-118127020
[Wed Dec 05 12:40:52 2012] [error] [client 143.248.22.90] Use of uninitialized value in string eq at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm line 267., referer: http://www.xenbase.org/fgb2/gbrowse/Xenopus_tropicalis_7_1/?source=Xenopus_tropicalis_7_1&name=scaffold_5:118075219-118127020
[Wed Dec 05 12:41:48 2012] [warn] mod_fcgid: stderr: Can't call method "plugins" on an undefined value at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 1183.
[Wed Dec 05 12:41:48 2012] [notice] child pid 30343 exit signal Segmentation fault (11)
 
 Please let me know if additional information is required for diagnosing the problem, and thanks for any help.
 
-Kamran
 

------------------------------------------------------------------------------
LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
Remotely access PCs and mobile devices and provide instant support
Improve your efficiency, and focus on delivering more value-add services
Discover what IT Professionals Know. Rescue delivers
http://p.sf.net/sfu/logmein_12329d2d
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
Amelia Ireland
GMOD Community Support || http://gmod.org



--
Amelia Ireland
GMOD Community Support || http://gmod.org

------------------------------------------------------------------------------
LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
Remotely access PCs and mobile devices and provide instant support
Improve your efficiency, and focus on delivering more value-add services
Discover what IT Professionals Know. Rescue delivers
http://p.sf.net/sfu/logmein_12329d2d
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: Warning and error message in Apache error log

Scott Cain
In reply to this post by kkarimi
Hi Kamran,

Let's start with this: are there any noticable problems with GBrowse
at XenBase?  That is, do you have any other symptoms than messages in
the error_log?

My first guess is that there is a data/adaptor problem--that is, the
data adaptor isn't passing some data in that GBrowse expects/needs.
There could also be a configuration file problem.  Both could be
difficult to debug remotely :-)

Scott


On Wed, Dec 5, 2012 at 2:59 PM, Kamran Karimi <[hidden email]> wrote:

> Hi all,
>
>  We are seeing quite a few GBrowse warning and error messages in the Xenbase
> project's Apache logs, and wonder whether this is an issue with our
> installation, or a problem with GBrowse. I've included sample lines from our
> error log. There are thousands more of them:
>
> [Wed Dec 05 12:39:24 2012] [warn] mod_fcgid: stderr: Can't call method
> "plugins" on an undefined value at
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
> line 1183.
> [Wed Dec 05 12:39:24 2012] [notice] child pid 28308 exit signal Illegal
> instruction (4)
> [Wed Dec 05 12:39:32 2012] [notice] mod_fcgid: process
> /var/www/cgi-bin/gb2/gbrowse(30375) exit(normal exit), terminated by calling
> exit(), return code: 255
> [Wed Dec 05 12:39:32 2012] [warn] mod_fcgid: cleanup zombie process 30375
> [Wed Dec 05 12:40:34 2012] [warn] mod_fcgid: stderr: Can't call method
> "plugins" on an undefined value at
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
> line 1183.
> [Wed Dec 05 12:40:35 2012] [notice] child pid 24856 exit signal Illegal
> instruction (4)
> [Wed Dec 05 12:40:38 2012] [notice] mod_fcgid: process
> /var/www/cgi-bin/gb2/gbrowse(30447) exit(normal exit), terminated by calling
> exit(), return code: 255
> [Wed Dec 05 12:40:38 2012] [warn] mod_fcgid: cleanup zombie process 30447
> [Wed Dec 05 12:40:52 2012] [error] [client 143.248.22.90] Use of
> uninitialized value in concatenation (.) or string at
> /var/www/cgi-bin/gb2/gbrowse_details line 122., referer:
> http://www.xenbase.org/fgb2/gbrowse/Xenopus_tropicalis_7_1/?source=Xenopus_tropicalis_7_1&name=scaffold_5:118075219-118127020
> [Wed Dec 05 12:40:52 2012] [error] [client 143.248.22.90] Use of
> uninitialized value in concatenation (.) or string at
> /var/www/cgi-bin/gb2/gbrowse_details line 123., referer:
> http://www.xenbase.org/fgb2/gbrowse/Xenopus_tropicalis_7_1/?source=Xenopus_tropicalis_7_1&name=scaffold_5:118075219-118127020
> [Wed Dec 05 12:40:52 2012] [error] [client 143.248.22.90] Use of
> uninitialized value in string eq at
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm
> line 267., referer:
> http://www.xenbase.org/fgb2/gbrowse/Xenopus_tropicalis_7_1/?source=Xenopus_tropicalis_7_1&name=scaffold_5:118075219-118127020
> [Wed Dec 05 12:41:48 2012] [warn] mod_fcgid: stderr: Can't call method
> "plugins" on an undefined value at
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
> line 1183.
> [Wed Dec 05 12:41:48 2012] [notice] child pid 30343 exit signal Segmentation
> fault (11)
>
>  Please let me know if additional information is required for diagnosing the
> problem, and thanks for any help.
>
> -Kamran
>
>
> ------------------------------------------------------------------------------
> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
> Remotely access PCs and mobile devices and provide instant support
> Improve your efficiency, and focus on delivering more value-add services
> Discover what IT Professionals Know. Rescue delivers
> http://p.sf.net/sfu/logmein_12329d2d
> _______________________________________________
> 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

------------------------------------------------------------------------------
LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
Remotely access PCs and mobile devices and provide instant support
Improve your efficiency, and focus on delivering more value-add services
Discover what IT Professionals Know. Rescue delivers
http://p.sf.net/sfu/logmein_12329d2d
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse