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

Chris Fields cjfields at illinois.edu
Wed Jan 28 21:30:59 EST 2009


Okay, it's definitely a bug.  I'll attempt to look into it.

chris

On Jan 28, 2009, at 6:44 PM, Charles Plessy wrote:

> 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
> 1.5.9.1, 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
>
>
> 	* CONFIDENTIALITY:
> 	* 	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]
>
> # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE]
>
> # TERMINATION STATUS: FAILURE [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-1.5.9.1/blib/lib/Bio/ 
> Tools/Run/Alignment/TCoffee.pm:844
> STACK: Bio::Tools::Run::Alignment::TCoffee::profile_align /home/ 
> charles/debian/med/debian-med/build-area/bioperl-run-1.5.9.1/blib/ 
> lib/Bio/Tools/Run/Alignment/TCoffee.pm:781
> 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,
> http://www.debian.org/devel/debian-med
> Tsurumi, Kanagawa, Japan
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> Bioperl-l mailing list
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