[Bioperl-l] Bioperl CPAN installation issues

[Fields, Christopher J]

That is a bit odd, but it has been reported before.  I haven't been able to dedicate any time to tracing it down, so any help is appreciated:

https://redmine.open-bio.org/issues/3041

chris

On Mar 13, 2012, at 11:21 AM, Francisco J. Ossandón wrote:

> 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
> 
> 
> 
> 
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