I killed the run after 1500 iterations without triggering your error with
the sessionInfo noted below.  please use a current version of R.

when i is: 1550 time is: Sun May 23 21:42:09 2010
^C
> sessionInfo()
R version 2.11.0 Patched (2010-05-01 r51901)
x86_64-apple-darwin10.3.0

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices datasets  tools     utils     methods
[8] base

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg18_1.3.16 biomaRt_2.4.0
 [3] rtracklayer_1.8.1                  RCurl_1.4-1
 [5] bitops_1.0-4.1                     BSgenome_1.16.0
 [7] ShortRead_1.6.0                    Rsamtools_1.0.0
 [9] lattice_0.18-5                     Biostrings_2.16.0
[11] GenomicRanges_1.0.1                IRanges_1.6.1
[13] weaver_1.14.0                      codetools_0.2-2
[15] digest_0.4.2

loaded via a namespace (and not attached):
[1] Biobase_2.8.0 XML_2.8-1     grid_2.11.0   hwriter_1.2


On Sun, May 23, 2010 at 9:30 PM, Shuying <stat.course@yahoo.com> 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.
>
> 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
>

	[[alternative HTML version deleted]]

