[Bioperl-l] bug #1396: *.PL to *.pod conversion is broken, make bailsout

[Hilmar Lapp]

No change, same error. The problem really is that the text is a 
'here'-document enclosed between <<"THEEND" and ^THEEND. Perl doesn't 
treat that as a script nor scans for documentation contained in there, 
but it does substitute variables with their values. In fact, this is 
the whole purpose of the .PL variant: if you look at the start of the 
text, there is $Local{VERSION}, which gets converted to "1.2" in the 
resulting POD.

The problem is - all the 'variables' which are merely in code snippets 
for documentation purposes get substituted as well. Check what happens 
to all the $something variables in the POD text -- do you still see 
them in the generated POD? I just see emptiness in their place in the 
POD ...

This is running perl 5.6.0 on Mac OSX, but the net effect shouldn't be 
much different on any other version > 5.005 (since that's why the .PL 
is there in the first place).

	-hilmar

On Wednesday, February 26, 2003, at 01:27  PM, Brian Osborne wrote:

> Hilmar,
>
> There were missing =cut delimiters in biodatabases.PL and 
> biodesign.PL, I've
> put them in. Could you update and try again? Because I can't reproduce 
> your
> bug I can't tell you whether 1396 is fixed or not. Adding the =cut's 
> should
> enclose all the relevant text in these 2 files in proper POD, so no 
> escaping
> should be necessary.
>
> Thanks again,
>
> Brian O.
>
> -----Original Message-----
> From: bioperl-l-bounces at bioperl.org 
> [mailto:bioperl-l-bounces at bioperl.org]On
> Behalf Of Hilmar Lapp
> Sent: Wednesday, February 26, 2003 2:39 PM
> To: Bioperl
> Subject: [Bioperl-l] bug #1396: *.PL to *.pod conversion is broken, 
> make
> bailsout
>
> At least biodatabases.PL and biodesign.PL contain @arys and $scalars
> which perl
> will (try to) substitute if unescaped. The @arys even choke the perl
> parser, but the $scalars also need to be escaped because otherwise they
> get substituted by empty values. This is a consequence of the text
> being run as a perl script first.
>
> I fixed those errors that make the parser choke, but someone needs to
> look at
> this and resolve the whole issue.
>
> donau: bioperl-live 11:22 85>make test
> /usr/bin/perl -Iblib/arch -Iblib/lib -I/System/Library/Perl/darwin
> -I/System/Library/Perl biodatabases.PL biodatabases.pod
> In string, @seqobjs now must be written as \@seqobjs at biodatabases.PL
> line 9,
> near "$seqobj)
>
> Similarly, one can query the database with id's or using query objects
> and retrieve arrays of Seq objects. For example
>
>    @seqobjs"
> Execution of biodatabases.PL aborted due to compilation errors.
> make: *** [biodatabases.pod] Error 255
>
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
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>
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------