Open frederikvand opened 3 years ago
Dear PopGenome admin,
I am unable to read or process any (small) vcf format with the PopGenome package (on windows and Centos HPC). The vcf only contains about 1000 SNP's.
The traceback from the HPC is as following:
loc <- "/ddn1/vol1/site_scratch/leuven/330/vsc33060/VCF/vcf_compressed/load" GENOME.class <- readData(loc, format = "VCF", SNP.DATA = T, include.unknown=T) : : 100 % caught segfault address (nil), cause 'unknown'
caught segfault address (nil), cause 'unknown'
Traceback: 1: myReadVCF(filepath) 2: PopGenread(liste[xx], format) 3: doTryCatch(return(expr), name, parentenv, handler) 4: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5: tryCatchList(expr, classes, parentenv, handlers) 6: 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 sm <- strsplit(conditionMessage(e), "\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 <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 7: try(PopGenread(liste[xx], format), silent = TRUE) 8: readData(loc, format = "VCF", SNP.DATA = T, include.unknown = T)
Thank you for your insights, With kind regards, Frederik Van Daele
Dear PopGenome admin,
I am unable to read or process any (small) vcf format with the PopGenome package (on windows and Centos HPC). The vcf only contains about 1000 SNP's.
The traceback from the HPC is as following:
Traceback: 1: myReadVCF(filepath) 2: PopGenread(liste[xx], format) 3: doTryCatch(return(expr), name, parentenv, handler) 4: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5: tryCatchList(expr, classes, parentenv, handlers) 6: 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 sm <- strsplit(conditionMessage(e), "\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 <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 7: try(PopGenread(liste[xx], format), silent = TRUE) 8: readData(loc, format = "VCF", SNP.DATA = T, include.unknown = T)
Thank you for your insights, With kind regards, Frederik Van Daele