[BioC] Error: formal argument "envir" matched by multiple actual arguments

[Martin Morgan]

On 05/23/2010 06:44 PM, Shuying Sun wrote:
> Dear Martin,
> 
> Here is the R sessionInfo I have. Please let me know if you need more
> information.
> 
>> sessionInfo()
> R version 2.10.1 (2009-12-14)
> x86_64-redhat-linux-gnu

Please update your R to 2.11.0, update or re-install your packages, and
try again. This is a lot of work, but likely this has been fixed in R
and updating is the only way to get the fix.

It is important to please report back when you have tried this, as the
bug was quite difficult to track down and further confirmation that it
is resolved would be encouraging.

Martin

> 
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
>  [1] BSgenome.Hsapiens.UCSC.hg18_1.3.16 biomaRt_2.2.0
>  [3] rtracklayer_1.6.0                  RCurl_1.3-0
>  [5] bitops_1.0-4.1                     ShortRead_1.4.0
>  [7] lattice_0.17-26                    BSgenome_1.14.2
>  [9] Biostrings_2.14.8                  IRanges_1.4.9
> 
> loaded via a namespace (and not attached):
> [1] Biobase_2.6.1 grid_2.10.1   hwriter_1.1   tools_2.10.1  XML_2.6-0
>>
> 
> Shuying
> 
> On Sun, May 23, 2010 at 9:36 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
>> On 05/23/2010 06:30 PM, Shuying wrote:
>>> Hi all,
>>>
>>> I wrote a function using "getSeq" to get DNA sequences from the human reference genome. But I kept having the following sporadic and non-reproducible errors:
>>>
>>> --------------------------------------
>>> Error in assign(".Method", method, envir = envir) :
>>>   formal argument "envir" matched by multiple actual arguments
>>> -------------------------------------
>>>
>>> I searched on line and found Hervé Pagès and Henrik Bengtsson posted some input last year.
>>>
>>> http://tolstoy.newcastle.edu.au/R/e6/devel/09/06/1936.html
>>>
>>> http://tolstoy.newcastle.edu.au/R/e6/devel/09/06/1943.html
>>>
>>> But it is still not clear how I can avoid and/or fix this problem and get correct results.
>>>
>>> May I get some of your feedback? I have attached my code in this email.
>>
>> What is the output of sessionInfo()? The hope was that a fix for this
>> was made in R version 2.11.0.
>>
>> Martin
>>
>>>
>>> Best wishes,
>>>
>>> Shuying
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
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>>
>>
>> --
>> Martin Morgan
>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
>> PO Box 19024 Seattle, WA 98109
>>
>> Location: Arnold Building M1 B861
>> Phone: (206) 667-2793
>>


-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793