[Bioperl-l] RE: All done with Bio::DB::Query

[Lincoln Stein]

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
>
> On Sun, 1 Dec 2002, Lincoln Stein wrote:
> > Hi Paul,
> >
> > Try updating now.  I'm explicitly checking for windows and disabling the
> > fork-on-pipe feature.  It is very annoying, because the Windows error is
> > untrappable by eval{}
> >
> > Lincoln
> >
> > On Sunday 01 December 2002 01:24 pm, Paul Boutros wrote:
> > > I'm still getting the same error:
> > >
> > > C:\Perl\bioperl-live>perl -w t\DB.t | more
> > > 1..78
> > > ok 1
> > > '-' is not recognized as an internal or external command,
> > > operable program or batch file.
> > > not ok 2
> > > # Failed test 2 in t\DB.t at line 70
> > > ok 3 # no network access
> > > ok 4 # no network access
> > > ok 5 # no network access
> > > ok 6 # no network access
> > > ok 7 # no network access
> > > ok 8 # no network access
> > > ok 9 # no network access
> > > ok 10 # no network access
> > > ok 11 # no network access
> > >
> > > The version is:
> > > # $Id: DB.t,v 1.36 2002/11/29 19:42:24 lstein Exp $
> > > # $Id: WebDBSeqI.pm,v 1.23 2002/11/29 19:42:24 lstein Exp $
> > >
> > > And I can verify it on two machines:
> > > 1. WinXP SP1 - Perl 5.8.0
> > > 2. Win98	 - Perl 5.6.1
> > >
> > > The error message is slightly different for the Win98 machine:
> > >
> > > Bad command or file name
> > > 1..78
> > > ok 1
> > > not ok 2
> > > # Failed test 2 in t\DB.t at line 70
> > > ok 3 # no network access
> > > ok 4 # no network access
> > > ok 5 # no network access
> > > ok 6 # no network access
> > > ok 7 # no network access
> > > ok 8 # no network access
> > >
> > > Did you want me to check version number for any supporting modules?
> > >
> > > Paul
> > >
> > > > -----Original Message-----
> > > > From: Lincoln Stein [mailto:lstein@cshl.org]
> > > > Sent: Friday, November 29, 2002 2:54 PM
> > > > To: Paul Boutros
> > > > Cc: bioperl-l@bioperl.org
> > > > Subject: Re: All done with Bio::DB::Query
> > > >
> > > >
> > > > Thanks for reporting this.  I was afraid this might happen on
> > > > windows. I have just modified the detection code for platforms that
> > > > don't support fork-and-ppipe.  Could you do a fresh update from live
> > > > CVS and try it again?
> > > >
> > > > Thanks,
> > > >
> > > > Lincoln
> > > >
> > > > On Wednesday 27 November 2002 03:46 pm, Paul Boutros wrote:
> > > > > (off list)
> > > > >
> > > > > Hi,
> > > > >
> > > > > I tried to run the DB test from today's CVS tarball and I got:
> > > > >
> > > > > C:\Perl\BIOPER~4\t>perl -w DB.t
> > > > > 1..78
> > > > > ok 1
> > > > > '-' is not recognized as an internal or external command,
> > > > > operable program or batch file.
> > > > > not ok 2
> > > > > # Failed test 2 in DB.t at line 70
> > > > > ok 3 # no network access
> > > > > ok 4 # no network access
> > > > > ok 5 # no network access
> > > > > ok 6 # no network access
> > > > > ok 7 # no network access
> > > > > ok 8 # no network access
> > > > > ok 9 # no network access
> > > > >
> > > > > I haven't done any digging on this yet, but hope it helps.
> > > > >
> > > > > My system:
> > > > > WinXP SP1
> > > > > ActiveState 5.8.0 (build 802)
> > > > > BioPerl CVS tarball 11/27/2002
> > > > >
> > > > > Paul
> > > > >
> > > > > You wrote:
> > > > > > Hi,
> > > > > >
> > > > > > I'm all done with the following modules:
> > > > > >
> > > > > > 	Bio::DB::QueryI
> > > > > > 	Bio::DB::Query::WebDBQuery  # web utilities
> > > > > > 	Bio::DB::Query::GenBank   # the only "real" one
> > > > > >
> > > > > > I have tested on a variety of Unix systems, but I need a Windows
> > > > > > tester. I used fork() in a couple of places in order to make
> > > > > > SeqIO streaming pipelineable (otherwise it has to download the
> > > > > > whole set of records before it can start processing the first
> > > > > > one).  The code should detect that it is not
> > > > > > on a platform that supports fork-and-pipe and automatically fall
> > > > > > back to the  old way of doing things, but I'm not 100% certain it
> > > > > > will work as advertised.
> > > > > >
> > > > > > I've also done a touch up here and there on the Bio::DB::
> > > > > > modules, mostly to deprecate Aaron Mackey's get_Stream_by_batch()
> > > > > > methods, which are superseded by the eutils interface.
> > > > > >
> > > > > > Let us all be glad that NCBI has committed to maintain eutils as
> > > > > > its official interface.
> > > > > >
> > > > > > Lincoln
> > > > > >
> > > > > > --
> > > > > > Lincoln Stein
> > > > > > lstein@cshl.org
> > >
> > > _______________________________________________
> > > 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 Stein
lstein@cshl.org