[Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network

Charles Plessy charles-listes+bioperl at plessy.org
Thu Jan 29 00:44:33 UTC 2009

Le Wed, Jan 28, 2009 at 11:14:22AM -0600, Chris Fields a écrit :
> 2) BioPerl-run TCoffee tests are failing for me, but it appears to be an 
> issue with the executable (I get a bus error).  Is this reproducible for 
> others?

Dear Chris,

I have the following error on my Debian machine: (BioPerl 1.6, BioPerl-run, T-Coffee 5.72). I will try with the latest T-Coffee release later.

t/TCoffee.....................1/25 tcoffee command = /usr/bin/t_coffee -in=AsXxMmCvFWa,Xblosum,Mlalign_id_pair,Mclustalw_pair -profile=oPW6TxnnHq  -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 -output=clustalw -quiet 
tcoffee command = /usr/bin/t_coffee -in=ArhrUiLQHE2,Xblosum,Mlalign_id_pair,Mclustalw_pair -profile=ARxjlEWpL0  -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 -output=clustalw -quiet 

	* Job NOT Completed:[T-COFFEE, Version_5.72]
	* Please CHECK:                                       
	* 	-1 The format of your Input Files                 
	* 	-2 The parameters                                 
	* 	-3 The use of special characters in sequence names:
	* 		 (@, |, %...)
	* 	-4 The Online Doc (http://www.tcoffee.org)                   
	* 	-5 Send the file error_report.T-COFFEE to:
	* 		cedric.notredame at europe.com
	* If you run T-Coffee over the WEB:
	* 	Windows Cut and Paste is sometimes erratic and
	* 	it can loose carriage returns. If you suspect this,
	* 	try to cut and paste through an intermediate application
	* 	(word pad) and inspect the results

	* 	The File error_report.T-COFFEE may contain your personnal DATA
	* 	Remove ALL confidential DATA from this file BEFORE sending it
# Command Line: /usr/bin/t_coffee -in=ArhrUiLQHE2,Xblosum,Mlalign_id_pair,Mclustalw_pair -profile=ARxjlEWpL0 -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 -output=clustalw -quiet  [PROGRAM:T-COFFEE]



------------- EXCEPTION: Bio::Root::Exception -------------
MSG: TCoffee call crashed: 256 [command /usr/bin/t_coffee -in=ArhrUiLQHE2,Xblosum,Mlalign_id_pair,Mclustalw_pair -profile=ARxjlEWpL0  -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 -output=clustalw -quiet]

STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:357
STACK: Bio::Root::RootI::warn /usr/share/perl5/Bio/Root/RootI.pm:179
STACK: Bio::Tools::Run::Alignment::TCoffee::_run /home/charles/debian/med/debian-med/build-area/bioperl-run-
STACK: Bio::Tools::Run::Alignment::TCoffee::profile_align /home/charles/debian/med/debian-med/build-area/bioperl-run-
STACK: t/TCoffee.t:84
# Looks like you planned 25 tests but only ran 15.
# Looks like your test died just after 15.
t/TCoffee..................... Dubious, test returned 255 (wstat 65280, 0xff00)
 Failed 10/25 subtests 

Charles Plessy
Debian Med packaging team,
Tsurumi, Kanagawa, Japan

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