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

[Paul Boutros]

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