[Bioperl-l] Bio::SeqIO::staden::read make test error

Joel Martin j_martin at lbl.gov
Thu Apr 23 05:32:08 EDT 2009

   Maybe they put the headers back in the separate distribution, they seem
to be there now.

ls -l io_lib-1.11.6/io_lib/abi.h 
4 -rw-r--r-- 1 me mypeeps 793 Dec 10 06:54 io_lib-1.11.6/io_lib/abi.h

And I can get the ABI-tests to pass with the bioperl-ext on linux, though
it takes some odd contortions of the Makefile to get it to compile here.

#    Expected: <UNDEF> (Can't write valid ctf files until we have a trace object)
All tests successful.
Files=1, Tests=94,  1 wallclock secs ( 0.95 cusr +  0.06 csys =  1.01 CPU)

  I might find time to take a shot at getting it to compile cleanerly for
linux and solaris, unless you think that's pointless as the BioLib conversion
might happen before summer?


On Wed, Apr 15, 2009 at 07:26:15AM -0500, Chris Fields wrote:
> Joel,
> They haven't stopped supporting it.  IIRC the separate io_lib distribution 
> no longer has the ABI headers, but the io_lib with the full staden package 
> does (a little confusing, yes).  I have 1.11.6 and ABI-related tests for 
> bioperl and bioperl-ext don't pass, but compiling with an earlier version 
> does work.  It may be as simple as including the header files from an old 
> version, but I haven't tried that.
> chris
> On Apr 15, 2009, at 1:50 AM, Joel Martin wrote:
>> Hello,
>>   Do you know where it says io_lib will stop supporting ABI?  We use
>> the latest ( 1.11.6 ) for this so I know it does read them and I just
>> checked with one fresh off a sequencer. But I couldn't find an active
>> forum for staden.
>> Thanks,
>> Joel
>> On Tue, Apr 14, 2009 at 10:20:00AM -0500, Chris Fields wrote:
>>> For ABI files you'll need an older version of io_lib that supports ABI or
>>> the io_lib that comes with the full staden package.  Recent versions of
>>> io_lib don't have ABI support built-in anymore.
>>> chris
>>> On Apr 14, 2009, at 9:54 AM, Roy Chaudhuri wrote:
>>>> Hi Mike.
>>>> I did get that problem solved in the end, thanks to lots of help from
>>>> Aaron Mackey. Looking at the bioperl-l archives it seems like we stopped
>>>> cc-ing the mailing list at some point. The last archived message in the
>>>> thread (http://bioperl.org/pipermail/bioperl-l/2005-May/018925.html) had
>>>> the correct solution - the code change was incorporated into the
>>>> bioperl-ext CVS, and is in the latest version that you can get from SVN
>>>> (see http://www.bioperl.org/wiki/Ext_package). If that doesn't solve the
>>>> problem you must be experiencing a different issue.
>>>> You should also bear in mind the message Chris Fields sent to the list a
>>>> few days ago, and have a look at using BioLib instead:
>>>>> Just to note, we're not actively supporting much of the bioperl-ext
>>>>> code, in favor of the BioLib initiative:
>>>>> http://biolib.open-bio.org/wiki/Main_Page
>>>>> If you do use bioperl-ext I suggest only using the latest code from  
>>>>> svn
>>>>> (and that in combination with bioperl-live).
>>>>> chris
>>>> Hope this helps.
>>>> Roy.
>>>> Michael Stubbington wrote:
>>>>> Dear Dr. Chaudhuri,
>>>>> I am currently trying to write a bioperl script that parses .abi 
>>>>> sequence
>>>>> files. I am having exactly the same problem as you did when
>>>>> you posted this enquiry to the bioperl mailing list
>>>>> http://bioperl.org/pipermail/bioperl-l/2005-May/018898.html. I was
>>>>> wondering if you ever solved the problem and, if so, can you remember
>>>>> what you did? I’d be very grateful for any help you can provide. I
>>>>> can’t find this problem mentioned anywhere else online.
>>>>> Thank you for your time.
>>>>> Mike
>>>> --
>>>> Dr. Roy Chaudhuri
>>>> Department of Veterinary Medicine
>>>> University of Cambridge, U.K.
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