RODBC Error when fetching tables: 'Calloc' could not allocate memory
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 at r-project.org] On Behalf Of Brad P Sent: Thursday, July 23, 2015 07:41 AM To: r-sig-db at 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 at 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 at 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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