[Bioperl-l] bioperl is not playing nice with DProf on aix

[Mike Cariaso]

Now looking at Bio/Root/IO.pm:328 bells and whistles
go off.

    # we need to dup() the original filehandle because
    # doing fdopen() calls on an already open handle
causes
    # the handle to go stale. is this going to work
for non-unix
    # filehandles? -allen


Raising the question. Is this a non unix system where
it doesn't work. Oh how I loathe you aix.

If its any easier I'm instant messenger as
cariaso at yahoo or cariaso001 at aim at the moment.





--- "Aaron J. Mackey" <amackey at pcbi.upenn.edu> wrote:

> 
> Not very informative, unfortunately.  What happens
> when you "use 
> Bio::Root" or "use Bio::Root::IO" instead of
> Bio::SeqIO? Do you also 
> get coredumps with these?
> 
> I'm sorry to be debugging remotely (no AIX access
> anymore), perhaps we 
> should take this off the list; we'll post back when
> (if?) we get to the 
> bottom of this.
> 
> -Aaron
> 
> On Aug 3, 2004, at 6:15 PM, Mike Cariaso wrote:
> 
> > sorry I missed the bt on first read.
> >
> > (gdb) bt
> > #0  0x110220a30 in ?? () from (unknown load
> module)
> > Cannot access memory at address 0x1102208f0
> >
> >
> >
> >
> >
> >
> >
> > --- "Aaron J. Mackey" <amackey at pcbi.upenn.edu>
> wrote:
> >
> >>
> >> If you fire up gdb like so:
> >>
> >> % gdb /usr/local/bin/perl core
> >> % bt
> >>
> >> What do you get?
> >>
> >> -Aaron
> >>
> >> On Aug 3, 2004, at 5:24 PM, Mike Cariaso wrote:
> >>
> >>> Don't you hate it when someone asks a question
> and
> >>> then includes pages of code? What you really
> need
> >> is a
> >>> small, tight example which can easily reproduce
> >> the
> >>> problem. Ok, I've trimmed this down as much as I
> >>> could.
> >>>
> >>> Here is the problem:
> >>>
> >>>> cat f2.pl
> >>> use Bio::SeqIO;
> >>> print "hello world\n";
> >>>
> >>>> /usr/local/bin/perl -d:DProf f2.pl
> >>> Illegal instruction (core dumped)
> >>>
> >>>
> >>>
> >>> To put that in some context...
> >>>
> >>>
> >>>> cat f1.pl
> >>> print "hello world\n";
> >>>
> >>>> /usr/local/bin/perl -d:DProf f1.pl
> >>> hello world
> >>>
> >>>> cat f2.pl
> >>> use Bio::SeqIO;
> >>> print "hello world\n";
> >>>
> >>>> /usr/local/bin/perl -d:DProf f2.pl
> >>> Illegal instruction (core dumped)
> >>>
> >>>> cat f3.pl
> >>> use Data::Dumper;
> >>> use POSIX;
> >>> print "hello world\n";
> >>>
> >>>> /usr/local/bin/perl -d:DProf f3.pl
> >>> hello world
> >>>
> >>>> /usr/local/bin/perl f2.pl
> >>> hello world
> >>>
> >>> This is perl, v5.6.1 built for aix-64all
> >>>
> >>> So...
> >>>  DProf alone works.
> >>>  DProf + 'use' works.
> >>>  bioperl alone works.
> >>> But...
> >>>  DProf + bioperl doesn't work
> >>>
> >>> The error may be with DProf. But I don't think
> >> there
> >>> is much of a DProf community to speak of.
> >>>
> >>> Can anyone else replicate, this?
> >>> Or better yet shed light on a solution?
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> =====
> >>> Mike Cariaso
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Bioperl-l at portal.open-bio.org
> >>>
> >>
> >
>
http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >>>
> >>>
> >> --
> >> Aaron J. Mackey, Ph.D.
> >> Dept. of Biology, Goddard 212
> >> University of Pennsylvania       email:
> >> amackey at pcbi.upenn.edu
> >> 415 S. University Avenue         office:
> >> 215-898-1205
> >> Philadelphia, PA  19104-6017     fax:
> >> 215-746-6697
> >>
> >>
> >
> >
> > =====
> > Mike Cariaso
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> >
>
http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> --
> Aaron J. Mackey, Ph.D.
> Dept. of Biology, Goddard 212
> University of Pennsylvania       email: 
> amackey at pcbi.upenn.edu
> 415 S. University Avenue         office:
> 215-898-1205
> Philadelphia, PA  19104-6017     fax:   
> 215-746-6697
> 
> 


=====
Mike Cariaso