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

[Lincoln Stein]

Hi Paul,

Try the latest CVS version.  This contains the "correct" fix.

Lincoln

On Tuesday 03 December 2002 02:46 pm, Paul Boutros wrote:
> 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
>
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-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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