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
