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Jayaraman, Pushkala

Hello,

I was able to pin down the errors to this one error. Although, I do not know how to tackle this error:

 

The result of B::Deparse::coderef2text was empty - maybe you're trying to serialize an XS function?, at /usr/local/lib/perl5/site_perl/5.8.8/Bio/Graphics/FeatureFile.pm line 443, referer: http://rgddev.mcw.edu/cgi-bin/gbrowse/yeast/

[Mon May 24 13:55:29 2010] [error] [client 141.106.161.52] Premature end of script headers: gbrowse, referer: http://rgddev.mcw.edu/cgi-bin/gbrowse/yeast/

 

I checked on cpan and this seems to be a part of coderef2text method under B::Deparse. Is this a module that I need to install for Gbrowse2?

 Please help…

 

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 


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Re: (no subject)

Scott Cain
Hi Pushkala,

B::Deparse is a core part of perl, so you don't need to install it.  I
suspect that there is a problem parsing a callback in your
configuration file.  I suggest stripping the conf file down to a
minimum, get it working, and then add things in one at a time and see
where it dies.

Scott


On Mon, May 24, 2010 at 2:58 PM, Jayaraman, Pushkala <[hidden email]> wrote:

> Hello,
>
> I was able to pin down the errors to this one error. Although, I do not know
> how to tackle this error:
>
>
>
> The result of B::Deparse::coderef2text was empty - maybe you're trying to
> serialize an XS function?, at
> /usr/local/lib/perl5/site_perl/5.8.8/Bio/Graphics/FeatureFile.pm line 443,
> referer: http://rgddev.mcw.edu/cgi-bin/gbrowse/yeast/
>
> [Mon May 24 13:55:29 2010] [error] [client 141.106.161.52] Premature end of
> script headers: gbrowse, referer:
> http://rgddev.mcw.edu/cgi-bin/gbrowse/yeast/
>
>
>
> I checked on cpan and this seems to be a part of coderef2text method under
> B::Deparse. Is this a module that I need to install for Gbrowse2?
>
>  Please help…
>
>
>
>
>
> Pushkala Jayaraman
>
> Programmer/Analyst
>
> Rat Genome Database
>
> Human and Molecular Genetics Center
>
> Medical College of Wisconsin
>
> Email: [hidden email]
>
> Work: 414-955-2229
>
> www.rgd.mcw.edu
>
>
>
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> Gmod-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: [Gmod-gbrowse] (no subject)

Lincoln Stein
I agree with Scott. There is a callback that is causing problems with the recent config file caching system. If you can't make it work, then you could back out the changes to Bio/Graphics/Browser2/DataSource.pm by finding the call to new_from_cache(), and replacing it with new(). The call is on line 2430 of the above-referenced file.

Lincoln

On Mon, May 24, 2010 at 12:54 PM, Scott Cain <[hidden email]> wrote:
Hi Pushkala,

B::Deparse is a core part of perl, so you don't need to install it.  I
suspect that there is a problem parsing a callback in your
configuration file.  I suggest stripping the conf file down to a
minimum, get it working, and then add things in one at a time and see
where it dies.

Scott


On Mon, May 24, 2010 at 2:58 PM, Jayaraman, Pushkala <[hidden email]> wrote:
> Hello,
>
> I was able to pin down the errors to this one error. Although, I do not know
> how to tackle this error:
>
>
>
> The result of B::Deparse::coderef2text was empty - maybe you're trying to
> serialize an XS function?, at
> /usr/local/lib/perl5/site_perl/5.8.8/Bio/Graphics/FeatureFile.pm line 443,
> referer: http://rgddev.mcw.edu/cgi-bin/gbrowse/yeast/
>
> [Mon May 24 13:55:29 2010] [error] [client 141.106.161.52] Premature end of
> script headers: gbrowse, referer:
> http://rgddev.mcw.edu/cgi-bin/gbrowse/yeast/
>
>
>
> I checked on cpan and this seems to be a part of coderef2text method under
> B::Deparse. Is this a module that I need to install for Gbrowse2?
>
>  Please help…
>
>
>
>
>
> Pushkala Jayaraman
>
> Programmer/Analyst
>
> Rat Genome Database
>
> Human and Molecular Genetics Center
>
> Medical College of Wisconsin
>
> Email: [hidden email]
>
> Work: 414-955-2229
>
> www.rgd.mcw.edu
>
>
>
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> Gmod-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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--
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]>

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