Thanks Duncan, I'll work on reproducibility and possibly getting a core
dump... If I get those I'll post to R-dev or RMySQL-dev.
Nick
On Wed, Dec 30, 2009 at 9:36 AM, Duncan Murdoch <murd...@stats.uwo.ca>wrote:
> On 30/12/2009 9:20 AM, Nick Torenvliet wrote:
>
>> I got the following after running succesfully through this loop 28 million
>> times... the loop opens text files in a directory and inserts line by line
>> into a database...
>>
>>
>
> This looks like a bug in RMySql or possibly R. What versions are you
> using? Can you make it happen reproducibly with the same script? Can you
> simplify the script so it happens quickly, rather than requiring 28 million
> iterations? Without a simple recipe to reproduce it, I doubt if anyone
> would be able to track down the problem.
>
> Duncan Murdoch
>
>> *** caught segfault ***
>> address 0xc0000010, cause 'memory not mapped'
>>
>> Traceback:
>> 1: .getGeneric(f, where, package)
>> 2: getGeneric("coerce", where = where)
>> 3: as(obj, "integer")
>> 4: mysqlConnectionInfo(dbObj, ...)
>> 5: dbGetInfo(conn, "rsId")
>> 6: dbGetInfo(conn, "rsId")
>> 7: dbListResults(con)
>> 8: dbListResults(con)
>> 9: mysqlQuickSQL(conn, statement, ...)
>> 10: dbGetQuery(con, sql)
>> 11: dbGetQuery(con, sql)
>> 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]] if (14L + nchar(dcall, type = "w") + nchar(sm[1L], type
>> =
>> "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(dbGetQuery(con, sql))
>> 17: eval.with.vis(expr, envir, enclos)
>> 18: eval.with.vis(ei, envir)
>> 19: source("~/SoothSayer/EODData/DBScripts/loadEODQuotes.r")
>>
>> 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:
>>
>>
>> The code is pretty simple...
>>
>>
>> library(RMySQL)
>> drv <- dbDriver("MySQL")
>> con <- dbConnect(drv, host="localhost", dbname="markets", user="root",
>> pass="embryoni3")
>> fileList <- list.files(pattern = "[[:upper:]]{2,}", all.files = FALSE,
>> full.names = FALSE, recursive = FALSE, ignore.case = FALSE)
>> for (x in 1:length(fileList)){
>> string <- strsplit(fileList[x], "_", fixed = TRUE)
>> string <- string[[1]][1]
>> fileLines <- read.csv(fileList[x],header = FALSE,row.names = NULL )
>>
>> for ( j in 1:length(fileLines[,1])){
>> sql <- paste("insert into endOfDayData
>> (date,market,symbol,open,high,low,close,volume) values ('",
>>
>> fileLines[j,2],"','",string,"','",as.character(fileLines[j,1]),"','",fileLines[j,3],"','",fileLines[j,4],"','",fileLines[j
>> ,5],"','",fileLines[j,6],"','",fileLines[j,7],"')",sep="")
>> #print(sql)
>> atmpt <- try(dbGetQuery(con,sql))
>> options(show.error.messages = TRUE)
>> if(inherits(atmpt, "try-error")){
>>
>> }
>>
>> }
>>
>> }
>>
>> dbDisconnect(con)
>>
>> My understanding was that in general R liked to put a placekeeper like NA
>> or
>> NULL in for non-existent elements of defined structures... so I was
>> surprised to see a seg fault... I'm having trouble interpretting the
>> error... any clues would be appreciated.
>>
>> Nick
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>
>
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