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

[Shuying Sun]

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

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
>