[Bioperl-l] fatalsToBrowser and BioPerl a odd behavior.

[Marco Aurelio Valtas Cunha]

Hi Bioperls and specially bug trackers,

Here's the story,

After an Upgrade og my CGI.pm to 2.89, I got something like:

--snip.
<h1>Software error:</h1>
<pre>Your vendor has not defined Fcntl macro O_EXLOCK, used at
/usr/lib/perl5/site_perl/5.6.0/File/Temp.pm line 208.
</pre>
<p>
For help, please send mail to this site's webmaster, giving this error message
and the time and date of the error.
--snip.

After a extensive research ( this time google didnt't helped ), I found two
things. One, I could be trouble, cause Temp.pm uses Fcntl.pm and Fcntl is
involved with glibc and this is not my area at all, or Two, something wrong with
CGI::Carp. Well after some testing I could isolate this situation:

=>Compile-time error script:

#!/usr/bin/perl
use CGI::Carp qw(fatalsToBrowser);
use Bio::SeqIO;

=> Compile-time OK script:

#!/usr/bin/perl
use Bio::SeqIO;
use CGI::Carp qw(fatalsToBrowser);

Turns out that maybe BioPerl is the problem.

So, what is happening? Maybe BioPerl likes to be the first to be called? :)


PS: I think that any  Bio perl module will cause the error.I've tested with
SeqIO, SearchIO and Graphics, same problem always.

PS2: fatalsToBrowser need to be called, just CGI::Carp will compile OK.


Some information of my system that could be involved:

bioperl: CVS copy of 12 Nov 2002 ( 30 minutes before this email. )
CGI    : the v2.89 package.
perl   : 5.6.0
glib   : 1.2.10 ( from glibc-config --version )
uname  : Linux  2.4.5-9cl i686 unknown


[]'s Marco.


-- 
     _ _ _ _ _ Marco A Valtas Cunha     http://scarecrow.fmrp.usp.br/~mavcunha/
    /  '`    / Lab de Bioinformatica    http://bit.fmrp.usp.br
   /  '  `  /  Hemocentro de Rib Preto  http://ctc.fmrp.usp.br
  /_ _`..'_/   Fax: 55 16 3963-9309     Tel: 55 16 3963-9300 R:9603