[Bioperl-l] Not done with Bio::DB::Query [WAS: All done with Bio::DB::Query]

[Paul Boutros]

Hi Lincoln,

I'm a total novice with the PERL debugger, but I took Ewan's suggestion
to play with it, and I seem to have gotten it to pass all
tests.  

The only change I made was:

if (defined $result) {
to
if ($result) {

To be honest I'm not sure why it works, and perhaps I've broken something
else in there?  It just seemed reasonable to me that since you had already
done a
my $result
then
if (defined $result)
would always be true and enter the loop.

Does this help at all?
Paul

On Tue, 3 Dec 2002, Lincoln Stein wrote:

> I've just changed the subject line of this message, since it is haunting me.  
> I'm beginning to fear that we're running into the weird workarounds required 
> to emulate piped I/O under Windows.  I'll try to run bioperl regression tests 
> on my own windows system (haven't done it till now because of inertia -- 
> getting CVS etc)
> 
> Lincoln
> 
> On Monday 02 December 2002 04:27 pm, Paul Boutros wrote:
> > Weird, definitely weird.
> >
> > On the code fragment:
> > a) the open() isn't executed
> > b) execution never reaches the eval{} block
> >
> > But, DB.t still fails with:
> > 1..78
> > ok 1
> > '-' is not recognized as an internal or external command,
> > operable program or batch file.
> >
> > Paul
> >
> > On Mon, 2 Dec 2002, Lincoln Stein wrote:
> > > H'mm.  Why the h*ll is the open being executed in this code fragment
> > > (WebDBSeqI.pm?
> > >
> > >       my $result = $^O !~ /^MSWin/ && eval { open(STREAM,"-|") };
> > >
> > > Could you test this out in a little perl script and tell me whether the
> > > open() is still executed?
> > >
> > > Lincoln
> > >
> > > On Monday 02 December 2002 11:43 am, Paul Boutros wrote:
> > > > Hi Lincoln,
> > > >
> > > > Running it like that gives:
> > > > =======
> > > > Can't find string terminator "'" anywhere before EOF at -e line 1.
> > > > =======
> > > >
> > > > If I put the print statement in double quotes I get:
> > > > =======
> > > > MSWin32
> > > > =======
> > > >
> > > > Paul
> > > >
> > > > On Mon, 2 Dec 2002, Lincoln Stein wrote:
> > > > > Hi Paul,
> > > > >
> > > > > Send me the output of this command:
> > > > >
> > > > > 	perl -e 'print $^O'
> > > > >
> > > > > That's an Oh.
> > > > >
> > > > > Lincoln
> > > > >
> > > > > On Sunday 01 December 2002 06:23 pm, Paul Boutros wrote:
> > > > > > Hi Lincoln,
> > > > > >
> > > > > > Slightly different output, but same basic idea:
> > > > > > ==================
> > > > > > C:\Perl\bioperl-live>perl -w t\db.t
> > > > > > 1..78
> > > > > > ok 1
> > > > > > '-' is not recognized as an internal or external command,
> > > > > > operable program or batch file.
> > > > > > ==================
> > > > > >
> > > > > > It does *not* give anything after this at all, but just stops here
> > > > > > without giving results for the rest of the tests as it did
> > > > > > previously. This was on the XP system (Perl 5.8.0).
> > > > > >
> > > > > > Hope this helps,
> > > > > > Paul
> > > >
> > > > <snip previous messages>
> > > >
> > > > _______________________________________________
> > > > Bioperl-l mailing list
> > > > Bioperl-l@bioperl.org
> > > > http://bioperl.org/mailman/listinfo/bioperl-l
> > >
> > > --
> > > ========================================================================
> > > Lincoln D. Stein                           Cold Spring Harbor Laboratory
> > > lstein@cshl.org			                  Cold Spring Harbor, NY
> > > ========================================================================
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> 
> -- 
> Lincoln Stein
> lstein@cshl.org
>