On Sun, May 23, 2010 at 9:44 PM, Shuying Sun <sxs1066@case.edu> 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)
>

Hi, Shuying.  The first thing to do is to upgrade to the current version of
R and Bioconductor.

Sean



> 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@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@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
> >
>
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