[R-sig-DB] RODBC Error when fetching tables: 'Calloc' could not allocate memory
Edward Vanden Berghe
evberghe @end|ng |rom gm@||@com
Thu Jul 23 13:25:48 CEST 2015
Hi,
I had some similar issues, working with a PostgreSQL/PostGIS database and
RODBC - RODBC seems to have problems dealing with long fields. I tried with
R on both Ubuntu and Windows (PostGIS was always on Ubuntu), but larger
polygons always got truncated. Problems disappeared when I switched over to
DBI and RPostregeSQL. Don't forget to also set 'stringsAsFactors' to false
if you want to read into R instead of just writing out to the database.
HTH
Edward
-----Original Message-----
From: R-sig-DB [mailto:r-sig-db-bounces using r-project.org] On Behalf Of Brad P
Sent: Thursday, July 23, 2015 07:41 AM
To: r-sig-db using r-project.org
Subject: Re: [R-sig-DB] RODBC Error when fetching tables: 'Calloc' could not
allocate memory
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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