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=membrane%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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