hitting reset causes apache error
|
View:
New views
6 Messages
—
Rating Filter:
Alert me
|
 |
hitting reset causes apache error
by Ryan Golhar
::
Rate this Message:
I was trying to upload a GFF file that is causing Gbrowse to timeout:
[warn] Timeout waiting for output from CGI script /var/www/cgi-bin/gbrowse, referer: http://localhost/cgi-bin/gbrowse/arabidopsis/ [error] (70007)The timeout specified has expired: ap_content_length_filter: apr_bucket_read() failed, referer: http://localhost/cgi-bin/gbrowse/arabidopsis/ When I hit the reset button to clear the cache and get my display back, I now see the error repeated multiple times: [error] Use of uninitialized value in scalar chomp at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm line 2769., referer: http://localhost/cgi-bin/gbrowse/arabidopsis/ ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
Re: hitting reset causes apache error
by Ryan Golhar
::
Rate this Message:
In addition, the images for the details tracks are broken links...
Any idea why??? Ryan Golhar wrote: > I was trying to upload a GFF file that is causing Gbrowse to timeout: > > [warn] Timeout waiting for output from CGI script > /var/www/cgi-bin/gbrowse, referer: > http://localhost/cgi-bin/gbrowse/arabidopsis/ > [error] (70007)The timeout specified has expired: > ap_content_length_filter: apr_bucket_read() failed, referer: > http://localhost/cgi-bin/gbrowse/arabidopsis/ > > When I hit the reset button to clear the cache and get my display back, > I now see the error repeated multiple times: > > [error] Use of uninitialized value in scalar chomp at > /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm > line 2769., referer: http://localhost/cgi-bin/gbrowse/arabidopsis/ > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
Re: hitting reset causes apache error
by Lincoln Stein-3
::
Rate this Message:
Uh oh. What version of GBrowse is this?
Lincoln On Wed, Nov 4, 2009 at 2:10 PM, Ryan Golhar <golharam@...> wrote: I was trying to upload a GFF file that is causing Gbrowse to timeout: -- 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 <Renata.Musa@...> ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
Re: hitting reset causes apache error
by Scott Cain-4
::
Rate this Message:
Hi Ryan,
Of hand, I don't know why that happened. How large was the file you were trying to upload? How long was it before the error message appeared in the error_log? I think the default timeout for apache is 5 minutes, but I haven't looked at that in in a long time. Does restarting apache help? Are you using mod_perl? Scott On Nov 4, 2009, at 2:14 PM, Ryan Golhar wrote: > In addition, the images for the details tracks are broken links... > > Any idea why??? > > Ryan Golhar wrote: >> I was trying to upload a GFF file that is causing Gbrowse to timeout: >> >> [warn] Timeout waiting for output from CGI script >> /var/www/cgi-bin/gbrowse, referer: >> http://localhost/cgi-bin/gbrowse/arabidopsis/ >> [error] (70007)The timeout specified has expired: >> ap_content_length_filter: apr_bucket_read() failed, referer: >> http://localhost/cgi-bin/gbrowse/arabidopsis/ >> >> When I hit the reset button to clear the cache and get my display >> back, >> I now see the error repeated multiple times: >> >> [error] Use of uninitialized value in scalar chomp at >> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/ >> Graphics/Browser.pm >> line 2769., referer: http://localhost/cgi-bin/gbrowse/arabidopsis/ >> >> ------------------------------------------------------------------------------ >> Let Crystal Reports handle the reporting - Free Crystal Reports >> 2008 30-Day >> trial. Simplify your report design, integration and deployment - >> and focus on >> what you do best, core application coding. Discover what's new with >> Crystal Reports now. http://p.sf.net/sfu/bobj-july >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 > 30-Day > trial. Simplify your report design, integration and deployment - and > focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > 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 ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
Re: hitting reset causes apache error
by Ryan Golhar
::
Rate this Message:
Hi Scott,
The original file was about 2 GB. I determined I ran out of space on my HD. My first thought was to delete tmp files from /var/www/html/gbrowse/tmp/arabidopsis/uploaded_file. That didn't clear enough room, so I started deleting the original GFF files I was loading into mysql. That's freed up alot of space. The error appears in the error_log immediately after I hit the reset button. I'm using the standard apache installation that comes with Redhat 5. I tried restarting apache, but that didn't help. It looks like it has something to do with the generation of the images for the tracks. I can consistently get the error simply by hitting the reset button. Scott Cain wrote: > Hi Ryan, > > Of hand, I don't know why that happened. How large was the file you > were trying to upload? How long was it before the error message > appeared in the error_log? I think the default timeout for apache is 5 > minutes, but I haven't looked at that in in a long time. Does > restarting apache help? Are you using mod_perl? > > Scott > > > On Nov 4, 2009, at 2:14 PM, Ryan Golhar wrote: > >> In addition, the images for the details tracks are broken links... >> >> Any idea why??? >> >> Ryan Golhar wrote: >>> I was trying to upload a GFF file that is causing Gbrowse to timeout: >>> >>> [warn] Timeout waiting for output from CGI script >>> /var/www/cgi-bin/gbrowse, referer: >>> http://localhost/cgi-bin/gbrowse/arabidopsis/ >>> [error] (70007)The timeout specified has expired: >>> ap_content_length_filter: apr_bucket_read() failed, referer: >>> http://localhost/cgi-bin/gbrowse/arabidopsis/ >>> >>> When I hit the reset button to clear the cache and get my display back, >>> I now see the error repeated multiple times: >>> >>> [error] Use of uninitialized value in scalar chomp at >>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm >>> >>> line 2769., referer: http://localhost/cgi-bin/gbrowse/arabidopsis/ >>> >>> ------------------------------------------------------------------------------ >>> >>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 >>> 30-Day >>> trial. Simplify your report design, integration and deployment - and >>> focus on >>> what you do best, core application coding. Discover what's new with >>> Crystal Reports now. http://p.sf.net/sfu/bobj-july >>> _______________________________________________ >>> Gmod-gbrowse mailing list >>> Gmod-gbrowse@... >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>> >> >> ------------------------------------------------------------------------------ >> >> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 >> 30-Day >> trial. Simplify your report design, integration and deployment - and >> focus on >> what you do best, core application coding. Discover what's new with >> Crystal Reports now. http://p.sf.net/sfu/bobj-july >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> 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 > > > > > ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
Re: hitting reset causes apache error
by Ryan Golhar
::
Rate this Message:
Version 1.70.
I can send your the URL to view in via private email...don't want to broadcast the URL if you want. Lincoln Stein wrote: > Uh oh. What version of GBrowse is this? > > Lincoln > > On Wed, Nov 4, 2009 at 2:10 PM, Ryan Golhar <golharam@...> wrote: > >> I was trying to upload a GFF file that is causing Gbrowse to timeout: >> >> [warn] Timeout waiting for output from CGI script >> /var/www/cgi-bin/gbrowse, referer: >> http://localhost/cgi-bin/gbrowse/arabidopsis/ >> [error] (70007)The timeout specified has expired: >> ap_content_length_filter: apr_bucket_read() failed, referer: >> http://localhost/cgi-bin/gbrowse/arabidopsis/ >> >> When I hit the reset button to clear the cache and get my display back, >> I now see the error repeated multiple times: >> >> [error] Use of uninitialized value in scalar chomp at >> >> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm >> line 2769., referer: http://localhost/cgi-bin/gbrowse/arabidopsis/ >> >> >> ------------------------------------------------------------------------------ >> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day >> trial. Simplify your report design, integration and deployment - and focus >> on >> what you do best, core application coding. Discover what's new with >> Crystal Reports now. http://p.sf.net/sfu/bobj-july >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> > > > ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
| Free embeddable forum powered by Nabble | Forum Help |
