Discussion:
[Gmod-gbrowse] question for GBrowse
曲俊杰
2014-06-30 07:20:37 UTC
Permalink
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
<file:///C:/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
Scott Cain
2014-06-30 14:04:41 UTC
Permalink
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
Post by 曲俊杰
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
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
曲俊杰
2014-07-01 09:52:52 UTC
Permalink
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/
Post by 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
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
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
--
曲俊杰
Loading...