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

[Martin Morgan]

On 05/24/2010 08:50 PM, Shuying wrote:
> Hi Martin,
> 
> After updating R and bioconductor, I re-ran my code on two
> chromosomes. It seems fine now because it has been running for more
> than 100,000 iterations and did not see any previous problem. So I
> think this problem has been fixed in the new version R and
> bioconductor packages.
> 
> Many thanks for your kind reply.

Great! Thanks for reporting back. Martin

> 
> Thank Sean and Vincent for your reply too.
> 
> Best wishes,
> 
> Shuying
> 
> --- On Sun, 5/23/10, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> 
>> From: Martin Morgan <mtmorgan at fhcrc.org> Subject: Re: [BioC] Error:
>> formal argument "envir" matched by multiple actual  arguments To:
>> "Shuying Sun" <sxs1066 at case.edu> Cc: "Shuying"
>> <stat.course at yahoo.com>, bioconductor at stat.math.ethz.ch,
>> shuying.sun at case.edu Date: Sunday, May 23, 2010, 9:56 PM 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
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>> _______________________________________________
>>>>> Bioconductor mailing list Bioconductor at stat.math.ethz.ch 
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the
>>>>> archives:
>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>
>>>>
>>>>
>>>>> 
--
>>>> 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
>> 
> 
> 
> 


-- 
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