We only have one copy of Browser.pm and it's the one from CVS.
Does it sound like it's a GBrowse or BioPerl problem?
Or possible a 64bit problem?
Russell
From: Lincoln Stein [mailto:[EMAIL PROTECTED]
Sent: Thursday, 31 January 2008 4:27 a.m.
To: Wes Barris
Cc: Smithies, Russell; [email protected]
Subject: Re: [Gmod-gbrowse] CVS stable version broke?
Yes, inline comments are broken due to a bioperl "fix". I will unfix it.
Russ, it sounds like there's an old version of Browser.pm in your perl
library path. Is it possible that you have multiple copies of that
library file installed? I just did a completely fresh CVS install on a
new machine, and everything worked the first time.
Lincoln
On Jan 29, 2008 9:03 PM, Wes Barris <[EMAIL PROTECTED]> wrote:
Smithies, Russell wrote:
> We've just installed (finally!) from the cvs stable version and the
layout of the page appears corrupted and no region or detail panel
appears.
> Also, the overview panel comes and goes.
> Initially, after installing we had errors about x_cook.js and
x_core.js being missing so I copied them from my Windows install (done
with the GBrowse_netinstall script) and that fixed it.
> Now the only message in the error log is this:
> [Wed Jan 30 14:26:07 2008] [error] [client 147.158.129.160]
Can't use string ("segment") as a HASH ref while "strict refs" in use at
/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/
Browser.pm line 874., referer:
http://devgbrowse.agresearch.co.nz/cgi-bin/gbrowse/yeast_chr1/?name=memb
rane%20trafficking
>
> Also, the version number at the bottom of the page says this:
> Generic genome browser version %s
>
> Any ideas?
> Is it BioPerl or GBrowse that's borked this time?
Hi Russell,
I installed from CVS last week (a couple times). The first time I did
I had problems similar to what you are describing: many errors in the
web error log and no display after the Data Source / Overview area.
One of the many error messages referred to an error in my "init_code".
What I found was that gbrowse was no longer able to parse inline perl
comments in the init_code. For example, this would cause errors in
the web server log file:
init_code = sub color {
my ($color) = @_; # this is a comment
return $color;
}
I had to remove all comments from all .conf files (a comment line like
this in any .conf file will affect the display of all .conf files).
I know that this is a long shot, but do you have an init_code section
with inline comments (in any of your .conf files)?
--
Wes Barris <[EMAIL PROTECTED]>
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