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

[Shuying]

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. 

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
>