[Bioperl-l] Bioperl CPAN installation issues

[Francisco J. Ossandón]

Hello,

Today I was updating my Perl modules using the CPAN client, through the
“upgrade” command (Im using strawberry perl, not activestate), and something
weird popped up.

 

I have installed Bioperl version 1.006901, which is the same one in CPAN,
but the client don’t recognize the installed Bioperl version and throws an
“undef” version instead, so it reinstall the whole thing again if told so.
Also, while Perl was checking the versions of the installed modules to
compare them to CPAN latest versions, it throws an error with a lot of code
saying that it could not eval “Bio\Ontology\SimpleGOEngine\GraphAdaptor.pm”.

 

Please see the output below and check the “Bio::Align::AlignI” and
“Bio\Ontology\SimpleGOEngine\GraphAdaptor.pm” outputs.

#####

cpan> upgrade

Database was generated on Mon, 12 Mar 2012 18:06:06 GMT

 

Package namespace         installed    latest  in CPAN file

DBD::mysql                    4.018     4.020
CAPTTOFU/DBD-mysql-4.020.tar.gz

IO::Socket::SSL                1.39      1.59
SULLR/IO-Socket-SSL-1.59.tar.gz

Bio::Align::AlignI            undef  1.006901
CJFIELDS/BioPerl-1.6.901.tar.gz

Could not eval '

                package ExtUtils::MakeMaker::_version;

                no strict;

                BEGIN { eval {

                    # Ensure any version() routine which might have leaked

                    # into this package has been deleted.  Interferes with

                    # version->import()

                    undef *version;

                    require version;

                    "version"->import;

                } }

 

                local $Graph::VERSION;

                $Graph::VERSION=undef;

                do {

                        ( defined $Graph::VERSION && $Graph::VERSION >= 0.5
) ?

                };

                $Graph::VERSION;

            ' in
C:\strawberry\perl\site\lib\Bio\Ontology\SimpleGOEngine\GraphAd

aptor.pm: syntax error at (eval 429) line 17, at EOF

Could not eval '

                package ExtUtils::MakeMaker::_version;

                no strict;

                BEGIN { eval {

                    # Ensure any version() routine which might have leaked

                    # into this package has been deleted.  Interferes with

                    # version->import()

                    undef *version;

                    require version;

                    "version"->import;

                } }

 

                local $Graph::VERSION;

                $Graph::VERSION=undef;

                do {

                        ( defined $Graph::VERSION && $Graph::VERSION >= 0.5
) ?

                };

                $Graph::VERSION;

            ' in
C:\strawberry\perl\site\lib\Bio\Ontology\SimpleGOEngine\GraphAd

aptor.pm: syntax error at (eval 430) line 17, at EOF

Error::Simple                 undef         0  SHLOMIF/Error-0.17017.tar.gz

#####

 

Cheers,

 

Francisco J. Ossandon