Re: [Gmod-gbrowse] init_code package breaks with latest SVN checkout

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Re: [Gmod-gbrowse] init_code package breaks with latest SVN checkout

Wes Barris
Lincoln Stein wrote:
> Can you confirm that this is related to GBrowse and not to
> Bio::Graphics? I am asking because I made changes to the latter which
> could cause this behavior.

I am pretty sure it is related to Gbrowse.  Here are the combinations
that I tried and the order in which I tried them:

gbrowse2.04 (revision 230xx) + Bio-Graphics-2.04: works
gbrowse2.05 (revision 23189) + Bio-Graphics-2.04: gbrowse failed tests, won't build
gbrowse2.05 (revision 23189) + Bio-Graphics-2.07: init_code breaks
gbrowse2.04 (revision 230xx) + Bio-Graphics-2.07: works

> I will attempt to reproduce and fix. This is a pity, because 2.05 is a
> lot better than previous versions.
>
> Lincoln
>
> On Wed, May 12, 2010 at 11:58 PM, Wes Barris <[hidden email]> wrote:
>
>     I just tried updating to gbrowse revision 23189 using SVN.  However, I
>     had to back out to my previously downloaded revision 230xx because
>     revision 23189 broke something related to my use of an external package
>     in the init_code section.
>
>     Here are the lines I am using in my .conf file:
>
>     init_code = use lib '/htdocs/gbrowse/gbrowse.conf';
>                 use init_code;
>     .
>     .
>     .
>     [FERT:overview]
>     feature       = SNP:fertility
>     glyph         = diamond
>     key           = Fertility SNPs
>     restrict      = sub { return &init_code::restrictToGroup('snpgroup',
>     @_); }
>
>
>     Here is some sample content from my init_code.pm
>     <http://init_code.pm> file:
>
>     package init_code;
>     use strict;
>     sub restrictToGroup {
>        my ($group, $host, $ip, $user) = @_;
>        my @members = ();
>        .
>        .
>        .
>        return myRestrict($ip, @members);
>        }
>     1;
>
>     With revision 23189 I get these errors in my apache log file:
>
>     [Thu May 13 13:36:09 2010] [error] [client 140.253.153.217]
>     Undefined subroutine &init_code::restrictToGroup called at (eval
>     163) line 4., referer:
>     https://www.biolives.csiro.au/cgi-bin/gbrowse/btauUMD3/
>     [Thu May 13 13:36:09 2010] [error] [client 140.253.153.217]
>     Premature end of script headers: gbrowse, referer:
>     https://www.biolives.csiro.au/cgi-bin/gbrowse/btauUMD3/
>
>     Is there a syntax change I need to make when using init_code stored
>     as a separate file?
>     --
>     Wes Barris
>
>     ------------------------------------------------------------------------------
>
>     _______________________________________________
>     Gmod-gbrowse mailing list
>     [hidden email]
>     <mailto:[hidden email]>
>     https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
>
> --
> 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 <[hidden email]
> <mailto:[hidden email]>>


--
Wes Barris

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