[BioC] Error in AnnotationDbi 1.7.8

[Patrick Aboyoun]

Simon,
The issue you are experiencing is to do a change in base R in the 
R-devel code line. The signature of base::eapply changed and so 
AnnotationDbi in BioC 2.5 changed accordingly. If you update your 
R-devel installation, this issue will be resolved.


Patrick


Tony Chiang wrote:
> Hi Simon,
>
> I guess so as to avoid confusion, maybe this should go to the Bioc-Devel
> list? I think that AnnotationDbi works for the current release version of
> Bioc. But I am sure that Marc will appreciate the update anyhow.
>
> Cheers,
> --tony
>
> On Thu, Aug 6, 2009 at 7:42 AM, Simon Anders <anders at ebi.ac.uk> wrote:
>
>   
>> Hi
>>
>> I've just tried to update my Bioc 2.5 installation (on Ubuntu Intrepid
>> x86_64) to the current packages, and AnnotationDbi 1.7.8 fails to install:
>>
>> ---8<---
>> * installing *source* package ‘AnnotationDbi’ ...
>> [...]
>> Creating a new generic function for "mget" in "AnnotationDbi"
>> Creating a new generic function for "eapply" in "AnnotationDbi"
>> Error in rematchDefinition(definition, fdef, mnames, fnames, signature) :
>>  arguments after '...' in the generic (all.names) must appear in the
>> method, in the same place at the end of the argument list
>> Error : unable to load R code in package 'AnnotationDbi'
>> ---8<---
>>
>> Note that the build cluster currently reports the same error message on
>> gewurz and liverpool (the Windows machines), so I suppose you are aware of
>> the problem. However, I wanted to add that I observe the same error on my
>> Linux box too, even though wilson2 seems to see no problem.
>>
>> The error occurred with v1.7.8; v1.7.7 is fine.
>>
>> Cheers
>>  Simon
>>
>>     
>>> sessionInfo()
>>>       
>> R version 2.10.0 Under development (unstable) (2009-06-26 r48838)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>>  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>>  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>>  [5] LC_MONETARY=C              LC_MESSAGES=en_GB.UTF-8
>>  [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
>>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> loaded via a namespace (and not attached):
>> [1] tools_2.10.0
>>
>>
>>
>> +---
>> | Dr. Simon Anders, Dipl.-Phys.
>> | European Molecular Biology Laboratory (EMBL), Heidelberg
>> | preferred (permanent) e-mail: sanders at fs.tum.de
>>
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>>     
>
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