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

Hilmar Lapp hlapp at gnf.org
Wed Feb 26 11:38:50 EST 2003

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

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

More information about the Bioperl-l mailing list