From alison.gardner from adelaide.edu.au  Sun Feb  1 18:20:54 2009
From: alison.gardner from adelaide.edu.au (alig)
Date: Sun Feb  1 21:43:01 2009
Subject: [Staden] gap4 running problem load_alignment_matrix error
In-Reply-To: <20090131150152.GH21694@TopQuark.net>
References: <21740409.post@talk.nabble.com>
	<20090131150152.GH21694@TopQuark.net>
Message-ID: <21781823.post@talk.nabble.com>


Thank you, that fixed it & now I can run Gap4 so I'm very happy.

This was the error I got after running 'export STADEN_DEBUG=1'

load libcopy_reads.so => couldn't load file "libcopy_reads.so":
/usr/lib/libstdc++.so.5: version `CXXABI_1.2' not found (required by
/usr/local/staden-linux-x86_64-1-7-1b/linux-x86_64-bin/../lib/linux-x86_64-binaries/libmutlib.so)

I had linked it to a newer version.  So I unlinked & reinstalled libstdc++5
& that seemed to fix my problem.

Thanks again   alig



Paul Donohue-4 wrote:
> 
> I don't see anything in particular in your strace output after a quick
> look.
> 
> Try running 'export STADEN_DEBUG=1' before running staden, and see what
> that says.
> You can ignore the 'libiwidgets.so' error, but any other errors need to be
> fixed.
> 
> Note that you can use the 'Search the contents of packages' form at
> http://packages.ubuntu.com/ to figure out the appropriate package to
> install for any missing libraries.
> 
> Hope that helps.
> -Paul
> 
> On Thu, Jan 29, 2009 at 06:27:19PM -0800, alig wrote:
>> 
>> Hi,
>> 
>> I am trying to install Staden Gap4 on a 64 bit machine with Ubuntu
>> installed.
>> 
>> It appears that trev & pregap will start.  But when I type gap4&  I get
>> this
>> message -
>> 
>> invalid command name "load_alignment_matrix"
>>     while executing
>> "load_alignment_matrix       [keylget gap_defs ALIGNMENT.MATRIX_FILE]"
>>     (file
>> "/usr/local/staden-linux-x86_64-1-7-1b/linux-x86_64-bin/../lib/gap/gap.tcl"
>> line 683)
>> 
>> I have followed a number of suggestions from this site & others &
>> installed
>> some missing libraries, but still get this message.
>> Have done strace -o output.txt gap4 and not sure of any more errors in
>> that
>> file.
>> I will try to attach the file
>> http://www.nabble.com/file/p21740409/output.txt output.txt 
>> 
>> Can anyone help please
>> -- 
>> View this message in context:
>> http://www.nabble.com/gap4-running-problem-load_alignment_matrix-error-tp21740409p21740409.html
>> Sent from the Bio.net - Staden mailing list archive at Nabble.com.
>> 
>> _______________________________________________
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>> 
> 
> _______________________________________________
> Staden mailing list
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> 
> 

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