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