question for GBrowse

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question for GBrowse

曲俊杰
Dear GBrowse author:

Sorry to trouble you. I met a problem when install GBrowse.
I point your web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox and type in "ctgA" in the search box.But the result page is not as the turiual.
The log is attached.

hope you can help me. Thank you very much in advace.

Junjie Qu

------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
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Re: question for GBrowse

Scott Cain
Hello,

I'm away from my laptop and can't open your log files on my ipad; can you please read the error log and send items that look like they might be related to your problem?  You want to look in the error_log file, near the end. 

Scott


Sent from my iPad

On Jun 30, 2014, at 3:20 AM, 曲俊杰 <[hidden email]> wrote:

Dear GBrowse author:

Sorry to trouble you. I met a problem when install GBrowse.
I point your web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox and type in "ctgA" in the search box.But the result page is not as the turiual.
The log is attached.

hope you can help me. Thank you very much in advace.

Junjie Qu
<httpd.zip>
------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: question for GBrowse

曲俊杰
Dear Scott:

Many thanks for your reply.
The detail log is blow, hope it is useful.

Thank you very much again.
Junjie Qu

===========================================
[Mon Jun 30 14:48:38 2014] [notice] Digest: generating secret for digest authentication ...
[Mon Jun 30 14:48:38 2014] [notice] Digest: done
[Mon Jun 30 14:48:38 2014] [warn] mod_wsgi: Compiled for Python/2.6.2.
[Mon Jun 30 14:48:38 2014] [warn] mod_wsgi: Runtime using Python/2.6.5.
[Mon Jun 30 14:48:38 2014] [notice] Apache/2.2.15 (Unix) DAV/2 PHP/5.3.2 mod_ssl/2.2.15 OpenSSL/1.0.0-fips mod_wsgi/3.2 Python/2.6.5 mod_perl/2.0.4 Perl/v5.10.1 configured -- resuming normal operations
[Mon Jun 30 14:49:05 2014] [error] [client 127.0.0.1] couldn't create lock file '/var/lib/gbrowse2/sessions/cgisess.db.lck': Permission denied at /usr/local/share/perl5/CGI/Session/Driver/db_file.pm line 98., referer: http://localhost/gbrowse2/tutorial/tutorial.html
[Mon Jun 30 14:49:06 2014] [error] [client 127.0.0.1] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2845., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:06 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:06 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:06 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:06 2014] [error] [client 127.0.0.1] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2901., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:06 2014] [error] [client 127.0.0.1] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2058., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:06 2014] [error] [client 127.0.0.1] Premature end of script headers: gbrowse, referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:40 2014] [error] [client 127.0.0.1] couldn't create lock file '/var/lib/gbrowse2/sessions/cgisess.db.lck': Permission denied at /usr/local/share/perl5/CGI/Session/Driver/db_file.pm line 98., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:41 2014] [error] [client 127.0.0.1] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2845., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:41 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:41 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:41 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:41 2014] [error] [client 127.0.0.1] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2901., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:41 2014] [error] [client 127.0.0.1] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2058., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:41 2014] [error] [client 127.0.0.1] Premature end of script headers: gbrowse, referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:46 2014] [error] [client 127.0.0.1] Use of uninitialized value in subtraction (-) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2970., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:46 2014] [error] [client 127.0.0.1] Use of uninitialized value in subtraction (-) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2970., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:46 2014] [error] [client 127.0.0.1] Use of uninitialized value in addition (+) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2971., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:46 2014] [error] [client 127.0.0.1] Use of uninitialized value in numeric eq (==) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2978., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:46 2014] [error] [client 127.0.0.1] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2845., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:46 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:46 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:46 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:46 2014] [error] [client 127.0.0.1] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2901., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:46 2014] [error] [client 127.0.0.1] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2058., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:46 2014] [error] [client 127.0.0.1] Premature end of script headers: gbrowse, referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:48 2014] [error] [client 127.0.0.1] Use of uninitialized value in subtraction (-) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2970., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:48 2014] [error] [client 127.0.0.1] Use of uninitialized value in subtraction (-) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2970., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:48 2014] [error] [client 127.0.0.1] Use of uninitialized value in addition (+) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2971., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:48 2014] [error] [client 127.0.0.1] Use of uninitialized value in numeric eq (==) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2978., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:48 2014] [error] [client 127.0.0.1] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2845., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:48 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:48 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:48 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:48 2014] [error] [client 127.0.0.1] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2901., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:48 2014] [error] [client 127.0.0.1] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2058., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:48 2014] [error] [client 127.0.0.1] Premature end of script headers: gbrowse, referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:49 2014] [error] [client 127.0.0.1] Use of uninitialized value in subtraction (-) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2970., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:49 2014] [error] [client 127.0.0.1] Use of uninitialized value in subtraction (-) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2970., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:49 2014] [error] [client 127.0.0.1] Use of uninitialized value in addition (+) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2971., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:49 2014] [error] [client 127.0.0.1] Use of uninitialized value in numeric eq (==) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2978., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:49 2014] [error] [client 127.0.0.1] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2845., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:50 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:50 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:50 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:50 2014] [error] [client 127.0.0.1] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2901., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:50 2014] [error] [client 127.0.0.1] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2058., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:50 2014] [error] [client 127.0.0.1] Premature end of script headers: gbrowse, referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:51 2014] [error] [client 127.0.0.1] Use of uninitialized value in subtraction (-) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2970., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:51 2014] [error] [client 127.0.0.1] Use of uninitialized value in subtraction (-) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2970., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:51 2014] [error] [client 127.0.0.1] Use of uninitialized value in addition (+) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2971., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:51 2014] [error] [client 127.0.0.1] Use of uninitialized value in numeric eq (==) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2978., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:51 2014] [error] [client 127.0.0.1] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2845., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:51 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:51 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:51 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:51 2014] [error] [client 127.0.0.1] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2901., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:51 2014] [error] [client 127.0.0.1] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2058., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:51 2014] [error] [client 127.0.0.1] Premature end of script headers: gbrowse, referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:52 2014] [error] [client 127.0.0.1] Use of uninitialized value in subtraction (-) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2970., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:52 2014] [error] [client 127.0.0.1] Use of uninitialized value in subtraction (-) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2970., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:52 2014] [error] [client 127.0.0.1] Use of uninitialized value in addition (+) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2971., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:52 2014] [error] [client 127.0.0.1] Use of uninitialized value in numeric eq (==) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2978., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:52 2014] [error] [client 127.0.0.1] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2845., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:52 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:52 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:52 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:52 2014] [error] [client 127.0.0.1] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2901., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:52 2014] [error] [client 127.0.0.1] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2058., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:52 2014] [error] [client 127.0.0.1] Premature end of script headers: gbrowse, referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:57 2014] [error] [client 127.0.0.1] Use of uninitialized value in subtraction (-) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2929., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:57 2014] [error] [client 127.0.0.1] Use of uninitialized value in subtraction (-) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2929., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:57 2014] [error] [client 127.0.0.1] Use of uninitialized value in addition (+) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2930., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:57 2014] [error] [client 127.0.0.1] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2845., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:57 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:57 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:57 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:57 2014] [error] [client 127.0.0.1] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2901., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:57 2014] [error] [client 127.0.0.1] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2058., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:49:57 2014] [error] [client 127.0.0.1] Premature end of script headers: gbrowse, referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:01 2014] [error] [client 127.0.0.1] Use of uninitialized value in subtraction (-) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2929., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:01 2014] [error] [client 127.0.0.1] Use of uninitialized value in subtraction (-) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2929., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:01 2014] [error] [client 127.0.0.1] Use of uninitialized value in addition (+) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2930., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:01 2014] [error] [client 127.0.0.1] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2845., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:01 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:01 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:01 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:01 2014] [error] [client 127.0.0.1] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2901., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:02 2014] [error] [client 127.0.0.1] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2058., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:02 2014] [error] [client 127.0.0.1] Premature end of script headers: gbrowse, referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:03 2014] [error] [client 127.0.0.1] Use of uninitialized value in subtraction (-) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2970., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:03 2014] [error] [client 127.0.0.1] Use of uninitialized value in subtraction (-) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2970., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:03 2014] [error] [client 127.0.0.1] Use of uninitialized value in addition (+) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2971., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:03 2014] [error] [client 127.0.0.1] Use of uninitialized value in numeric eq (==) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2978., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:03 2014] [error] [client 127.0.0.1] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2845., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:03 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:03 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:03 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:03 2014] [error] [client 127.0.0.1] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2901., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:03 2014] [error] [client 127.0.0.1] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2058., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:03 2014] [error] [client 127.0.0.1] Premature end of script headers: gbrowse, referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:05 2014] [error] [client 127.0.0.1] Use of uninitialized value in subtraction (-) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2970., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:05 2014] [error] [client 127.0.0.1] Use of uninitialized value in subtraction (-) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2970., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:05 2014] [error] [client 127.0.0.1] Use of uninitialized value in addition (+) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2971., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:05 2014] [error] [client 127.0.0.1] Use of uninitialized value in numeric eq (==) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2978., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:05 2014] [error] [client 127.0.0.1] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2845., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:05 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:05 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:05 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:05 2014] [error] [client 127.0.0.1] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2901., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:05 2014] [error] [client 127.0.0.1] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2058., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:05 2014] [error] [client 127.0.0.1] Premature end of script headers: gbrowse, referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:08 2014] [error] [client 127.0.0.1] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2845., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:08 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:08 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:08 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:08 2014] [error] [client 127.0.0.1] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2901., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:08 2014] [error] [client 127.0.0.1] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2058., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:08 2014] [error] [client 127.0.0.1] Premature end of script headers: gbrowse, referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:28 2014] [error] [client 127.0.0.1] couldn't create lock file '/var/lib/gbrowse2/sessions/cgisess.db.lck': Permission denied at /usr/local/share/perl5/CGI/Session/Driver/db_file.pm line 98., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:29 2014] [error] [client 127.0.0.1] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2845., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:29 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:29 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:29 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:29 2014] [error] [client 127.0.0.1] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2901., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:29 2014] [error] [client 127.0.0.1] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2058., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:50:29 2014] [error] [client 127.0.0.1] Premature end of script headers: gbrowse, referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Mon Jun 30 14:55:29 2014] [error] [client 127.0.0.1] couldn't create lock file '/var/lib/gbrowse2/sessions/cgisess.db.lck': Permission denied at /usr/local/share/perl5/CGI/Session/Driver/db_file.pm line 98., referer: http://localhost/gbrowse2/tutorial/tutorial.html
[Mon Jun 30 14:55:30 2014] [error] [client 127.0.0.1] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2845., referer: http://localhost/cgi-bin/gb2/gbrowse/pop_demo/
[Mon Jun 30 14:55:30 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/pop_demo/
[Mon Jun 30 14:55:30 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/pop_demo/
[Mon Jun 30 14:55:30 2014] [error] [client 127.0.0.1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost/cgi-bin/gb2/gbrowse/pop_demo/
[Mon Jun 30 14:55:30 2014] [error] [client 127.0.0.1] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2901., referer: http://localhost/cgi-bin/gb2/gbrowse/pop_demo/
[Mon Jun 30 14:55:30 2014] [error] [client 127.0.0.1] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2058., referer: http://localhost/cgi-bin/gb2/gbrowse/pop_demo/
[Mon Jun 30 14:55:30 2014] [error] [client 127.0.0.1] Premature end of script headers: gbrowse, referer: http://localhost/cgi-bin/gb2/gbrowse/pop_demo/


2014-06-30 22:04 GMT+08:00 Scott Cain <[hidden email]>:
Hello,

I'm away from my laptop and can't open your log files on my ipad; can you please read the error log and send items that look like they might be related to your problem?  You want to look in the error_log file, near the end. 

Scott


Sent from my iPad

On Jun 30, 2014, at 3:20 AM, 曲俊杰 <[hidden email]> wrote:

Dear GBrowse author:

Sorry to trouble you. I met a problem when install GBrowse.
I point your web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox and type in "ctgA" in the search box.But the result page is not as the turiual.
The log is attached.

hope you can help me. Thank you very much in advace.

Junjie Qu
<httpd.zip>
------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
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Gmod-gbrowse mailing list
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--
曲俊杰

------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse