From efg at stowers-institute.org  Tue Jan 30 18:23:03 2007
From: efg at stowers-institute.org (Earl F. Glynn)
Date: Tue, 30 Jan 2007 11:23:03 -0600
Subject: [Rd] calloc bug in RODBC 1.1-7 and later?
Message-ID: <epnutn$tvp$1@sea.gmane.org>

I'm trying to load Affy Annotation data from an Access database into R using 
RODBC.  This has worked fine for quite some time.  The bug seems to be 
correlated to RODBC versions 1.1-7 and later.

Works fine:  R 2.2.0 with RODBC 1.1-4; R 2.3.0 or R 2.4.1 with RODBC 1.1-6
Fails:  R 2.3.1 with RDOBC 1.1-7; R 2.4.1 with RODC 1.1-7 or 1.1-8

Details
=====
This works fine:



Version 2.2.0  (2005-10-06 r35749)

Package:              RODBC

Version:              1.1-4

Date:                 2005-08-04



R Version 2.3.0 (2006-04-24) or R version 2.4.1 (2006-12-18)

Package:              RODBC

Version:              1.1-6

Date:                 2006-04-04



> library("RODBC")

> channel <- 
> odbcConnectAccess("S:/Bioinformatics/Software/Affy/Data/MOE430A/MOE430A.mdb")

> moe430a <- sqlFetch(channel,"Annotation", as.is=TRUE)

> odbcClose(channel)



> dim(moe430a)

[1] 22690    43



= = = = = = = = = =



calloc bug in RODBC 1.1-7 and later?



R Version 2.3.1 (2006-06-01)



Package:              RODBC

Version:              1.1-7

Date:                 2006-05-24



> library("RODBC")

> channel <- 
> odbcConnectAccess("S:/Bioinformatics/Software/Affy/Data/MOE430A/MOE430A.mdb")

> moe430a <- sqlFetch(channel,"Annotation", as.is=TRUE)

Error in odbcQuery(channel, query, rows_at_time) :

        Calloc could not allocate (67108864 of 1) memory

In addition: Warning message:

Reached total allocation of 1024Mb: see help(memory.size)





R version 2.4.1 (2006-12-18)



Package:              RODBC

Version:              1.1-8

Date:                 2007-01-02



> library("RODBC")

> channel <- 
> odbcConnectAccess("S:/Bioinformatics/Software/Affy/Data/MOE430A/MOE430A.mdb")

> moe430a <- sqlFetch(channel,"Annotation", as.is=TRUE)

Error in odbcQuery(channel, query, rows_at_time) :

        Calloc could not allocate (67108864 of 1) memory





The Access table is the MOE430A Affy Chip data from a CSV format from 
NetAffx

http://www.affymetrix.com/Auth/analysis/downloads/na21/ivt/MOE430A.na21.annot.csv.zip

loaded into Access:

http://research.stowers-institute.org/efg/ScientificSoftware/Applications/Affy/Annotations/index.htm


Is there a change I missed in RODBC 1.1-7?  What else should I do to 
troubleshoot this other than reverting to the older version of RODBC?

Thanks for any help with this.

Earl F. Glynn
Scientific Programmer
Stowers Institute for Medical Research



[Rd] calloc bug in RODBC 1.1-7 and later?
Earl F. Glynn