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

[Aaron J. Mackey]

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