Hello, I am using getSeq function from Bsgenome to extract a set of sequence. When I try the example in the RD file : library(BSgenome.Celegans.UCSC.ce2) myseqs <- data.frame( chr=c("chrI", "chrX", "chrM", "chrM", "chrX", "chrI", "chrM", "chrI"), start=c(NA, -40, 8510, 301, 30001, 9220500, -2804, -30), end=c(50, NA, 8522, 324, 30011, 9220555, -2801, -11), strand=c("+", "-", "+", "+", "-", "-", "+", "-") ) getSeq(Celegans, myseqs$chr, start=myseqs$start, end=myseqs$end) a following message appear : Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : object '.normargSEW' not found I am wondering if anyone knows this problems. Thanks Arnaud. > sessionInfo() R version 2.9.0 (2009-04-17) i386-apple-darwin9.6.0 locale: en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BSgenome.Celegans.UCSC.ce2_1.3.13 BSgenome.Hsapiens.UCSC.hg18_1.3.11 [3] BSgenome_1.12.2 Biostrings_2.12.1 [5] GADEM_1.0.0 IRanges_1.2.0 loaded via a namespace (and not attached): [1] Biobase_2.4.0 tools_2.9.0

Hi Arnaud, Droit Arnaud wrote: > Hello, > > I am using getSeq function from Bsgenome to extract a set of sequence. > When I try the example in the RD file : > > library(BSgenome.Celegans.UCSC.ce2) > myseqs <- data.frame( > chr=c("chrI", "chrX", "chrM", "chrM", "chrX", "chrI", "chrM", "chrI"), > start=c(NA, -40, 8510, 301, 30001, 9220500, -2804, -30), > end=c(50, NA, 8522, 324, 30011, 9220555, -2801, -11), > strand=c("+", "-", "+", "+", "-", "-", "+", "-") > ) > getSeq(Celegans, myseqs$chr, > start=myseqs$start, end=myseqs$end) > > a following message appear : > > Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : > object '.normargSEW' not found > > I am wondering if anyone knows this problems. Please update your installation as explained here: http://bioconductor.org/docs/install/ and try again. Let us know if the problem persists. Thanks, H. > > Thanks > > Arnaud. > >> sessionInfo() > R version 2.9.0 (2009-04-17) > i386-apple-darwin9.6.0 > > locale: > en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BSgenome.Celegans.UCSC.ce2_1.3.13 BSgenome.Hsapiens.UCSC.hg18_1.3.11 > [3] BSgenome_1.12.2 Biostrings_2.12.1 > [5] GADEM_1.0.0 IRanges_1.2.0 > > loaded via a namespace (and not attached): > [1] Biobase_2.4.0 tools_2.9.0 > > _______________________________________________ > 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319