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 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 >

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 > > > > _______________________________________________ > 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]]