[R-sig-DB] RODBC Error when fetching tables: 'Calloc' could not allocate memory

[Brad P]

Sorry if replying to this is not OK.

I now see that RODBC can not handle cases where length is huge, evidently >
8000, see this:

http://stackoverflow.com/questions/18477994/rodbc-does-not-save-greater-than-8k-varchar-text-from-a-data-frame

I also noticed that one column in the table previously mentioned had a
length of  2147483647

Anyway, my goal was to pull all tables in and saving them as .rds files.
I wrote a quick work around that identifies which tables have these long
lengths and selects all columns but those columns. This is not ideal, but
at least I get most of the data.

##################################
# get list of all table names
tables <- sqlQuery(con, "SELECT * FROM information_schema.tables")
tables <- subset(tables, subset=TABLE_TYPE!="VIEW")
tables <- as.character(tables$TABLE_NAME)

# for loop to pull in tables 1 at a time
for(i in 1:length(tables) ){
  x <- sqlQuery(con, paste("exec sp_columns", tables[i], sep=" ")  )
  if(length(which(x$LENGTH > 8000))>0){
     drop.cols <- as.character( x[which(x$LENGTH > 8000),]$COLUMN_NAME )
     print ( paste(tables[i], "had", paste(drop.cols, collapse=","),
"column(s) dropped", sep=" ") )
     keep.cols <- as.character( x[which(x$LENGTH < 8000),]$COLUMN_NAME )
     dat <- sqlQuery(con, paste( "SELECT", paste(keep.cols, collapse=","),
"FROM", tables[i], sep=" ") )
  }else{
    dat <- try( sqlFetch(con, tables[i]), silent=F)
  }
  print(i)
  print( paste(tables[i]) )
  print( object.size(dat),  units = "auto" )
  saveRDS(dat, paste(tables[i], "rds", sep=".") )
}
##################################

##################################

Cheers!
Patrick


On Wed, Jul 22, 2015 at 8:50 PM, Brad P <bpschn01 using gmail.com> wrote:

> Hello,
>
> I have used R for a while in Linux, but am trying to become familiar with
> using R in Windows as well as using MS SQL and the RODBC package. I have a
> problem described below when trying to fetch SOME tables.
>
> I am using:
>
> OS:
> Windows 7 64-bit
> Intel quad i5 650 using 320GHz
> 12GB RAM
>
> R:
> Rstudio Version 0.99.467
> Revolution R Open 3.2.0
> Using CRAN snapshot taken on 2015-05-01
>
> > sessionInfo()
> R version 3.2.0 (2015-04-16)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 7 x64 (build 7601) Service Pack 1
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> States.1252
> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] SOAR_0.99-11 pryr_0.1.2   RODBC_1.3-12
>
> loaded via a namespace (and not attached):
> [1] magrittr_1.5     tools_3.2.0      Rcpp_0.11.6      stringi_0.5-5
> [5] codetools_0.2-11 stringr_1.0.0
>
> > Sys.getlocale()
> [1] "LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252"
>
> SQL:
> MS SQL server 2012
> Example database: AdventureWorksDW2012
>
>
> # Here is some code and the problem I am having:
>
> library(RODBC)
> con <- odbcDriverConnect('driver={SQL Server}; server=SQLEXPRESS;
> Database=AdventureWorksDW2012; uid=BPS; trusted_connection=true')
>
>
> # The problem is that some tables are fetched OK, while some tables lead
> to the following error:
>
> # increasing memory
> memory.limit(size=10000000000)
> round(memory.limit()/2^30, 2)
> [1] 9.31 # GB
>
>
> dat <- sqlFetch(con, DimEmployee)
> Error in odbcQuery(channel, query, rows_at_time) :
>   'Calloc' could not allocate memory (214748364800 of 1 bytes)
>
> traceback()
> 4: .Call(C_RODBCQuery, attr(channel, "handle_ptr"), as.character(query),
>        as.integer(rows_at_time))
> 3: odbcQuery(channel, query, rows_at_time)
> 2: sqlQuery(channel, paste("SELECT * FROM", dbname), ...)
> 1: sqlFetch(con, DimEmployee)
>
>
> # Here are 2 examples of databases that can be fetched and can not:
>
> # DimAccount does work, here is some info regarding its size:
> sqlQuery(con, "exec sp_spaceused DimCustomer")
>          name  rows reserved     data index_size unused
> 1 DimCustomer 18484 13608 KB 12552 KB     920 KB 136 KB
>
> # DimEmployee (example given above) does not work, here is some info
> regarding its size:
> sqlQuery(con, "exec sp_spaceused DimEmployee")
>          name rows reserved     data index_size unused
> 1 DimEmployee  296 18992 KB 18856 KB      48 KB  88 KB
>
>
> # 4 of 31 tables in this SQL database give this exact error when
> attempting to fetch them as shown above, the rest are fetched without error.
>
> # Also, please know that when I run this in regular 64-bit R (not
> Revolution R) it does the same thing, and when I do it in 32-bit R, it
> literally crashes
>
> Please let me know if you have any suggestions.
> -Patrick
>

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