I am trying to download an "exons worth of reads" from a collection of Bam files using a bamViews object. The index files are stored locally al la Rsamtools documentation and suggested code. Typically less that 50 reads per bam file are obtained. Occasionally the connection times out (I think?) which causes the R session to crash (the documentation hits to problems with unreliable connections) I don't mind the connection timing out, or it even being unreliable, but how to I catch the error without losing the session? Codes works fine most of the time and there is no case where I can reliably reproduce the error, but some info is provided which may help those wiser than I... Even without the crash I wonder IF the connection timed out for failed how would I know this occurred for a given file ; is there a success/fail info I can access anywhere... that is, would I know the difference between no reads in that region or the retrieval just failed? (So far I have *found* no cases where an empty list resulted from a failed connection). Thanks Paul > radial<- try(scanBam(bv,param=params)) [kftp_connect_file] 227 Entering Passive Mode (193,62,197,91,149,230) *** caught bus error *** address (nil), cause 'unknown' Traceback: 1: .Call(func, file, index, "rb", list(space(which), .uunlist(start(which)), .uunlist(end(which))), flag, simpleCigar, ...) 2: .io_bam(.scan_bam, file, index, reverseComplement, tmpl, param = param) 3: scanBam(file = bamPaths(bamViews)[i], index = bamIndicies(bamViews)[i], ...) 4: scanBam(file = bamPaths(bamViews)[i], index = bamIndicies(bamViews)[i], ...) 5: FUN(...) 6: doTryCatch(return(expr), name, parentenv, handler) 7: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 8: tryCatchList(expr, classes, parentenv, handlers) 9: tryCatch({ FUN(...)}, error = function(err) { msg <- paste(capture.output(conditionCall(err)), conditionMessage(err), sep = "\n ") if (is.loaded("mpi_comm_size")) SRError("RemoteError", msg) else SRError("UnspecifiedError", msg)}) 10: FUN(c(5L, 13L, 21L, 29L)[[4L]], ...) 11: lapply(S, FUN, ...) 12: doTryCatch(return(expr), name, parentenv, handler) 13: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14: tryCatchList(expr, classes, parentenv, handlers) 15: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste(prefix, "\n ", sep = "") } else prefix <- "Error : " msg <- paste(prefix, conditionMessage(e), "\n", sep = "") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error"))}) 16: try(lapply(S, FUN, ...), silent = TRUE) 17: sendMaster(try(lapply(S, FUN, ...), silent = TRUE)) 18: FUN(1:8[[5L]], ...) 19: lapply(1:cores, inner.do) 20: mcLapply(X, CFUN, ..., verbose = verbose) 21: fapply(X, FUN, ..., verbose = verbose) 22: .srapply(idx, fun, bamViews, ...) 23: .BamViews_delegate("scanBam", file, fun, ..., param = param) 24: scanBam(bv, param = params) 25: scanBam(bv, param = params) 26: doTryCatch(return(expr), name, parentenv, handler) 27: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 28: tryCatchList(expr, classes, parentenv, handlers) 29: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste(prefix, "\n ", sep = "") } else prefix <- "Error : " msg <- paste(prefix, conditionMessage(e), "\n", sep = "") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error"))}) 30: try(scanBam(bv, param = params)) Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: R version 2.12.0 Under development (unstable) (2010-04-18 r51771) 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] Rsamtools_1.0.5 Biostrings_2.16.5 RCurl_1.4-2 [4] bitops_1.0-4.1 GenomicFeatures_1.0.0 GenomicRanges_1.0.3 [7] IRanges_1.6.6 multicore_0.1-3 loaded via a namespace (and not attached): [1] Biobase_2.8.0 biomaRt_2.4.0 BSgenome_1.16.4 DBI_0.2-5 [5] RSQLite_0.9-1 rtracklayer_1.8.1 XML_3.1-0 > [[alternative HTML version deleted]]