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

[Brian Osborne]

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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