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

[Paul Boutros]

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
>