[R-SIG-Mac] using RMySQL on OS X 10.6.6 - R 2.12.2

[Simon Urbanek]

Jan,

can you, please, supply the crash report? Also it would be useful to have a minimal reproducible example and exact details of your MySQL setup (version, where you got it from..) so we can try to reproduce it to track the issue.

Thanks,
Simon


On Mar 24, 2011, at 8:52 AM, Verbesselt, Jan wrote:

> Hi,
> 
> 
> I trying to export data from large images (satellite data) in to MySQL data via R using RMySQL (RMySQL_0.7-5.tgz installed via R Console). The code works fine but after some time it gives to following error:
> 
> "
> *** caught bus error ***
> address 0x100000012, cause 'non-existent physical address'
> 
> Traceback:
> 1: match.fun(FUN)
> 2: lapply(z, is.object)
> 3: unlist(lapply(z, is.object))
> 4: order(jseq)
> 5: `[<-.data.frame`(`*tmp*`, , value = list(gid = 78014, yr = 2009,     dy = 49, ndvi = 6448, rel = 0))
> 6: `[<-`(`*tmp*`, , value = list(gid = 78014, yr = 2009, dy = 49,     ndvi = 6448, rel = 0))
> 7: write.table(value[from:to, , drop = FALSE], file = conb, append = TRUE,     quote = FALSE, sep = "\t", na = .MySQL.NA.string, row.names = FALSE,     col.names = FALSE, eol = "\n", ...)
> 8: safe.write(value, file = fn)
> 9: mysqlWriteTable(conn, name, value, ...)
> 10: is(object, Cl)
> 11: is(object, Cl)
> 12: .valueClassTest(standardGeneric("dbWriteTable"), "logical", "dbWriteTable")
> 13: dbWriteTable(con, "datamod13q1", datamod13q1, append = T, row.names = 0)
> aborting ...
> Bus error
> cube008:MODIS janv$ 
> "
> 
> As an example I am adding the R script that I am using: 
> Which runs through each pixel and exports the data to add table:
> 
> # read all pixels within a certain boundary
> gid <- 1
> col <- 7:428
> row <- 2557:2760
> 
> "
> # Create first xy table from one image
> for (i in row) {
>   for (j in col) {  
>     rc <- c(i,j)-1 # line, sample !
>     # read data for specific row and column
>     ndvi <- getRasterTable(rndvi, offset=rc, region.dim=c(1, 1))
>     rel <- getRasterTable(rrel, offset=rc, region.dim=c(1, 1))
> 
>     # prepare to insert into MySQL database
>     (datamod13q1 <- data.frame(gid=gid,yr=yr, dy=dy, ndvi=ndvi$band1/10000,rel=rel$band1))
>     # THIS IS ONE ROW WITH 4 COLUMNS OF NUMERIC DATA
>     dbWriteTable(con, "datamod13q1", datamod13q1, append = T, row.names = 0)
>     gid <- gid + 1
>   }
> }
> "
> 
> Any advice to solve this error and make this script more efficient are welcome.
> 
> Thanks for your help
> J
> 
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