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

[Lincoln Stein]

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
>
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-- 
Lincoln Stein
lstein@cshl.org