Hi All, For the last few days I've been coming across a show-stopping bug when performing sequence analysis using BSgenome - my code fails either in getSeq, matchPattern or findOverlaps in a completely intermittent way, with the only consistent error message being inside either a get() or assign() call:
"formal argument "envir" matched by multiple actual arguments" Apparently an internal R problem which gave rise to this error was fixed in June last year (see http://tolstoy.newcastle.edu.au/R/e6/devel/09/06/2080.html ), but as you can see from my examples below I'm running into it with R 2.10.1 and the latest svn R 2.11.0. It usually fails after anywhere from 40 to 500 iterations of the test case below Any suggestions/workarounds? Or would this be better posted to the R-devel list? Aaron Test case script ----------------------- library(BSgenome.Hsapiens.UCSC.hg18) i<-0 repeat{ i <- i+1 x <- getSeq(Hsapiens, "chr1", rep(100,10000), rep(500,10000)) } traceback() sessionInfo() cat(i, "\n") R 2.10.1 example output ----------------------------------- > library(BSgenome.Hsapiens.UCSC.hg18) Loading required package: BSgenome Loading required package: IRanges Attaching package: 'IRanges' The following object(s) are masked from package:base : cbind, Map, mapply, order, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, table Loading required package: Biostrings > > i<-0 > repeat{ + i <- i+1 + x <- getSeq(Hsapiens, "chr1", rep(100,10000), rep(500,10000)) + } Error in get("disabled", envir = .validity_options) : formal argument "envir" matched by multiple actual arguments > traceback() 21: get("disabled", envir = .validity_options) 20: disableValidity() 19: validityMethod(object) 18: identical(x, TRUE) 17: anyStrings(validityMethod(object)) 16: validObject(.Object) 15: initialize(value, ...) 14: initialize(value, ...) 13: new(...) 12: new2("GroupedIRanges", shift(ranges, xvec...@offset), group = ranges_group, check = FALSE) 11: IRanges:::unsafe.newXVectorList1(classname, xvector, ranges) 10: unsafe.newXStringSet(subject(x), ans_ranges, use.names = TRUE, names = names(ans_ranges)) 9: XStringViewsToSet(x, use.names, verbose = check.limits) 8: .local(x, ...) 7: as.character(Views(subject, solved_SEW)) 6: FUN("chr1"[[1L]], ...) 5: lapply(REFSEQnames, extractSeqsFromREFSEQ) 4: lapply(REFSEQnames, extractSeqsFromREFSEQ) 3: .local(x, ...) 2: getSeq(Hsapiens, "chr1", rep(100, 10000), rep(500, 10000)) 1: getSeq(Hsapiens, "chr1", rep(100, 10000), rep(500, 10000)) > sessionInfo() R version 2.10.1 (2009-12-14) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8 [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_AU.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 BSgenome_1.14.2 [3] Biostrings_2.14.7 IRanges_1.4.7 loaded via a namespace (and not attached): [1] Biobase_2.6.0 > cat(i, "\n") 401 R 2.11.0 example output ------------------------------------- > library(BSgenome.Hsapiens.UCSC.hg18) Loading required package: BSgenome Loading required package: IRanges Attaching package: 'IRanges' The following object(s) are masked from 'package:base': cbind, Map, mapply, order, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, table Loading required package: Biostrings > > i<-0 > repeat{ + i <- i+1 + x <- getSeq(Hsapiens, "chr1", rep(100,10000), rep(500,10000)) + } Error in assign(".target", met...@target, envir = envir) : formal argument "envir" matched by multiple actual arguments > traceback() 18: assign(".target", met...@target, envir = envir) 17: loadMethod(function (x, table) match(x, table, nomatch = 0L) > 0L, "%in%", <environment>) 16: loadMethod(function (x, table) match(x, table, nomatch = 0L) > 0L, "%in%", <environment>) 15: argnames %in% c("", NA) 14: extraArgsAsList(valid_argnames, ...) 13: unsafe.update(x, start = ans_start, width = ans_width, names = ans_names) 12: restrict(as(x, "IRanges"), start = 1L, end = nchar(subject(x)), keep.all.ranges = TRUE, use.names = use.names) 11: restrict(as(x, "IRanges"), start = 1L, end = nchar(subject(x)), keep.all.ranges = TRUE, use.names = use.names) 10: XStringViewsToSet(x, use.names, verbose = check.limits) 9: .local(x, ...) 8: as.character(Views(subject, solved_SEW)) 7: as.character(Views(subject, solved_SEW)) 6: FUN("chr1"[[1L]], ...) 5: lapply(REFSEQnames, extractSeqsFromREFSEQ) 4: lapply(REFSEQnames, extractSeqsFromREFSEQ) 3: .local(x, ...) 2: getSeq(Hsapiens, "chr1", rep(100, 10000), rep(500, 10000)) 1: getSeq(Hsapiens, "chr1", rep(100, 10000), rep(500, 10000)) > sessionInfo() R version 2.11.0 Under development (unstable) (2010-03-07 r51225) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8 [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_AU.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 BSgenome_1.15.12 [3] Biostrings_2.15.22 IRanges_1.5.54 loaded via a namespace (and not attached): [1] Biobase_2.7.5 > cat(i, "\n") 177 -- Aaron Statham Postgraduate Scholar, Cancer Epigenetics Garvan Institute of Medical Research Tel: (02) 9295 8393 384 Victoria St Darlinghurst 2010 Fax: (02) 9295 8316 NSW Australia email: [email protected] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
