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

[Paul Boutros]

I'm happy to say it passes all tests on WinXP and Win2K now.
Paul

On Tue, 3 Dec 2002, Lincoln Stein wrote:

> 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
> > > > > =====================================================================
> > > > >===
> > > >
> > > > _______________________________________________
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> > > > Bioperl-l@bioperl.org
> > > > http://bioperl.org/mailman/listinfo/bioperl-l
> > >
> > > --
> > > Lincoln Stein
> > > lstein@cshl.org
> >
> > _______________________________________________
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> > 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
> ========================================================================
>