[Bioperl-l] Bioperl CPAN installation issues

[Francisco J. Ossandón]

This has happened to me since long ago in previous installations, but I had
forgot about it until today...

Looking around in Google led me to this page:
http://mail.pm.org/pipermail/pdx-pm-list/2010-April/005803.html

It says:
###
MakeMaker (MM) has to use heuristics to find the line where $VERSION is 
defined for each .pm file and eval that line.  In the case of 
Bio::Ontology::SimpleGOEngine::GraphAdaptor it does not define a $VERSION
for 
itself, which is fine, but it does mention it later on.

   sub new {
     my( $class ) = @_;
     $class = ref $class || $class;

     my $self=
       ( defined $Graph::VERSION && $Graph::VERSION >= 0.5 ) ?
         bless ( {}, $class ) :
	  bless ( {}, 'Bio::Ontology::SimpleGOEngine::GraphAdaptor02' );
     $self->{_graph}=new Graph::Directed;
     $self->{_vertex_attributes}={};
     $self->{_edge_attributes}={};
     return $self;
   }

MM->parse_version picked up on that, tried to eval it, and it blew up. 
###

So apparently, the "( defined $Graph::VERSION && $Graph::VERSION >= 0.5 ) ?"
line is read when the CPAN Client is trying to find a $VERSION that it can
use for upgrade reference, and it gets confused at this point.

Since "Bio::Ontology::SimpleGOEngine::GraphAdaptor" depends on
"Bio::Root::Root", maybe adding a "use Bio::Root::Version;" to the Root.pm
module will let the $VERSION global variable to reach the GraphAdaptor
module and all the other modules who depends on it??? I noticed that
"RootI.pm" have a Bio::Root::Version dependency but Root.pm don’t have it
(at least explicitly). I still need more experience using global variables,
but it could be that the reason that Bioperl modules shows "undef" after
installation is because CPAN don’t reach $VERSION properly for the all
modules of the bundle.

Cheers,
 
Francisco J. Ossandon

-----Mensaje original-----
De: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] En nombre de Fields,
Christopher J
Enviado el: martes, 13 de marzo de 2012 13:40
Para: Francisco J. Ossandón
CC: <bioperl-l at bioperl.org>
Asunto: Re: [Bioperl-l] Bioperl CPAN installation issues

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
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


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