Hi Vincent, Thanks for your reply. I once can run much more iterations in another similar code file using getSeq  and even all iterations and have no errors until my program was finished. But sometimes I got errors at different iterations. As I said, this error is sporadic and non-reproducible". I will update R in my machine. Hopefully the problem will be solved. Best wishes, Shuying --- On Sun, 5/23/10, Vincent Carey <stvjc@channing.harvard.edu> wrote: From: Vincent Carey <stvjc@channing.harvard.edu> Subject: Re: [BioC] Error: formal argument "envir" matched by multiple actual arguments To: "Shuying" <stat.course@yahoo.com> Cc: bioconductor@stat.math.ethz.ch, shuying.sun@case.edu Date: Sunday, May 23, 2010, 9:43 PM 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]]