Bug #38248 for bioperl: bug in Bio::Tools::Run::StandAloneBlast

Wed Aug 06 10:38:45 2008 zxiang [...] med.umich.edu - Ticket created

Subject:	bug in Bio::Tools::Run::StandAloneBlast
Date:	Wed, 06 Aug 2008 10:37:31 -0400
To:	bug-bioperl [...] rt.cpan.org
From:	Allen Zuoshuang Xiang <zxiang [...] med.umich.edu>

Hi, In Bio::Tools::Run::StandAloneBlast, line 811 my $status = system($commandstring); always return something other than 0 even if the command has been successfully executed. The fix is to add $SIG{CHLD} = sub {}; before this line. I'm not sure if this is system specific. But anyway here is my system information: perl -version This is perl, v5.8.8 built for i386-linux-thread-multi uname -a Linux HE1.bioinformatics.med.umich.edu 2.6.18-92.1.6.el5PAE #1 SMP Fri Jun 20 02:51:01 EDT 2008 i686 i686 i386 GNU/Linux StandAloneBlast.pm,v 1.63.4.1 2006/10/02 23:10:36 Thanks a lot, Allen

Thu Apr 16 18:07:45 2009 cjfields [...] uiuc.edu - Correspondence added

On Wed Aug 06 10:38:45 2008, zxiang@med.umich.edu wrote: Show quoted text

> Hi, > > In Bio::Tools::Run::StandAloneBlast, line 811 > my $status = system($commandstring); > always return something other than 0 even if the command has been > successfully executed. The fix is to add > $SIG{CHLD} = sub {}; > before this line. I'm not sure if this is system specific. But anyway > here is my system information: > > perl -version > This is perl, v5.8.8 built for i386-linux-thread-multi > > uname -a > Linux HE1.bioinformatics.med.umich.edu 2.6.18-92.1.6.el5PAE #1 SMP Fri > Jun 20 02:51:01 EDT 2008 i686 i686 i386 GNU/Linux > > StandAloneBlast.pm,v 1.63.4.1 2006/10/02 23:10:36 > > Thanks a lot, > Allen

Allen, This may be resolved in the last BioPerl release (1.6.0). I'm closing this ticket; you are more than welcome to reopen it if the problem persists.

Thu Apr 16 18:07:45 2009 The RT System itself - Status changed from 'new' to 'open'

Thu Apr 16 18:07:48 2009 cjfields [...] uiuc.edu - Status changed from 'open' to 'resolved'