[EMBOSS] HELP! fdnapars fails with undefined symbol error - ajSeqdbInit

[Wolfgang Rumpf]

Everything I have tried has failed.   I have uninstalled and reinstalled 
the entire EMBOSS/EMBASSY suite.  I have booted from the previous 
kernel.  Recompilation is a bit beyond me, I fear - what are the chances 
that this will just be fixed when 11.04 rolls out?  Has anyone else had 
this problem?

What's perplexing is that this has happened on both of my Ubuntu 
systems; there's nothing that was caused by me "tinkering" - this 
happened after the update to 10.10.  Why didn't this get caught - am I 
the only person using Phylip in Emboss Explorer?

On 03/10/2011 06:48 PM, Marvin Stodolsky wrote:
> There is a:
> http://packages.ubuntu.com/maverick/libnucleus6
>
> $ sudo apt-get update
> $ sudo apt-get libnucleus6
>
> should do all necessary.
>
> MarvS
>
> On Thu, Mar 10, 2011 at 1:27 PM, Henrikki Almusa
> <henrikki.almusa at helsinki.fi>  wrote:
>> On 2011-03-10 17:26, Wolfgang Rumpf wrote:
>>> So as I understand it my options are:
>>>
>>> 1.  Boot with an older kernel - probably the latest one from 10.4, if it
>>> works with 10.10;
>>> 2.  Recompile EMBOSS myself;
>>> 3.  Download and install the 11.04 (unreleased) Emboss/Embassy installs;
>>> 4.  Wait for 11.04 to come out
>>>
>>> Of all of these the "simplest" (other than just waiting) would probably be
>>> to try to boot with an older kernel - I don't want to bring the rest of the
>>> EMBOSS system down for an extended time period, perhaps very extended if the
>>> compilation/install doesn't go as planned.
>>>
>>> Sound about right?
>> The error message complains about missing library file libnucleus.so.6 which
>> was probably removed in update as there was no dependency on it (within the
>> package lists). So here's a way to fix it:
>>   - go to packages.ubuntu.com and search for a package with file called
>> libnucleus.so.6
>>   - get result which tells you that it is in package libnucleus6
>>   - install that named package with your favourite tool (for example apt-get)
>>
>>
>>> Wolfgang
>>>
>>> Dr. Wolfgang Rumpf
>>> Product Specialist, Rescentris Inc.
>>> --------------------------------------------------------
>>> wolfgang.rumpf at rescentris.com
>>>
>>> Mobile - (614) 638-6797
>>> Skype - wolfgang.rumpf
>>>
>>>
>>>
>>>
>>> On Mar 9, 2011, at 8:37 PM, Charles Plessy wrote:
>>>
>>>> Le Wed, Mar 09, 2011 at 07:48:41PM -0500, Marvin Stodolsky a écrit :
>>>>> RE:  undefined symbol: ajSeqdbInit
>>>>> While not an expert at all, on Emboss code,
>>>>> this type of error is typically due to (Emboss) binaries Not Yet
>>>>> being compiled with the newer linux-header resources.  Pending that
>>>>> compilation by the Emboss maintenance team, if you run the compile
>>>>> from Emboss source code on your own  Ubuntu 10.10 system, all will
>>>>> likely be  OK.
>>>> Dear Wolfgang,
>>>>
>>>> you can also give a try to the emboss and embassy-phylip from 11.04
>>>> Ubuntu
>>>> distribution. If you can install them on 10.10, they should work well,
>>>> and
>>>> they are up to date.
>>>>
>>>> http://packages.ubuntu.com/natty/emboss
>>>> http://packages.ubuntu.com/natty/embassy-phylip
>>>>
>>>> Have a nice day,
>>>>
>>>> --
>>>> Charles Plessy
>>>> Debian Med packaging team
>>>> http://www.debian.org/devel/debian-med
>>>> Tsurumi, Kanagawa, Japan
>>>> _______________________________________________
>>>> EMBOSS mailing list
>>>> EMBOSS at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/emboss
>>>
>>> _______________________________________________
>>> EMBOSS mailing list
>>> EMBOSS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/emboss
>>>
>>
>> --
>> Henrikki Almusa
>>
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>>
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