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

[Lincoln Stein]

I've found and fixed a few more unescaped $variables and @variables.  It 
actually would have been easier to make the POD convertor do the string 
substitution itself using a @@VERSION@@ string sub, or something else hacky.

Lincoln

On Thursday 27 February 2003 08:32 am, Brian Osborne wrote:
> Hilmar,
>
> The simple solution is to revert to plain documents, drop the *PL. files,
> LocalConfig.pm. All this system does currently is put version numbers in 4
> *pod files and the AUTHORS into bioperl.pod. To make it work somebody has
> to enter a new version number into Makefile.PL, which writes to
> bioperl.conf. The make executes the *PL which uses LocalConfig.pm which
> reads
> bioperl.conf. It could be simpler, but this wouldn't fix your 1396 either.
>
> Note that the maintainer of all this has not offered help during this
> discussion. It's not exactly in the spirit of bioperl to remove work
> contributed with the best of intentions but along with the contribution
> comes a responsibility to maintain.
>
> So: remove system? Or find workaround?
>
> 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 5:02 PM
> To: Brian Osborne
> Cc: Bioperl
> Subject: Re: [Bioperl-l] bug #1396: *.PL to *.pod conversion is broken,
> makebailsout
>
> 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
> > -------------------------------------------------------------
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
========================================================================