[ensembl-dev] Transcript Adaptor

[Patrick Meidl]

On Tue, Nov 16 2010, Hardip Patel <H.Patel at victorchang.edu.au> wrote:

> Exception weaken is only available with the XS version of Scalar::Util at /usr/lib/perl5/5.8.8/Ensembl/ensembl/modules/Bio/EnsEMBL/Translation.pm line 55

reading the stack traces sometimes helps ;-)

$ perldoc Scalar::Util

--8<----------------------------------------------------------
DIAGNOSTICS

[...]
       "NAME" is only available with the XS version of Scalar::Util
           "Scalar::Util" contains both perl and C implementations of
            many of its functions so that those without access to a C
            compiler may still use it. However some of the functions are
            only available when a C compiler was available to compile
            the XS version of the extension.

            At present that list is: weaken, isweak, dualvar, isvstring,
            set_prototype

--8<----------------------------------------------------------

that suggests that you do not have the XS version of Scalar::Util
installed.

there are several possible explanations why this is the case.  maybe you
installed a pre-packaged version of the module from your OS distribution
which didn't include the XS functions; or you installed from CPAN and
had no C compiler installed on your system, so `make` couldn't compile
these functions.

HTH

    patrick

-- 
Patrick Meidl, Mag.
Bioinformatician

Ce-M-M-
Research Centre for Molecular Medicine
of the Austrian Academy of Science

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