Dear Sean and others,

I am exploring the functionality of 'GEOmetadb'. I am specifically interested in downloading all CEL files performed on a certain platform.
To this end I am using the example mentioned in the vignette of GEOmetadb, which should retrieve the number of GEO entries and CEL files performed on the Affymetrix array HGU133A (page 8 vignette).
However, when executing that code R crashes and needs to exit...
To me the error messages are not informative to me, but may be you can deduce what is going wrong. Any feedback is appreciated.

Regards,
Guido


R version 2.13.0 (2011-04-13)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)

>
> library(GEOmetadb)
Loading required package: GEOquery
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Setting options('download.file.method.GEOquery'='curl')
Loading required package: RSQLite
Loading required package: DBI
> getSQLiteFile()
trying URL 'http://gbnci.abcc.ncifcrf.gov/geo/GEOmetadb.sqlite.gz'
Content type 'text/plain; charset=ISO-8859-1' length 109446149 bytes (104.4 Mb)
opened URL
================================================
downloaded 104.4 Mb

Unzipping...
Metadata associate with downloaded file:
                name               value
1     schema version                 1.0
2 creation timestamp 2011-06-18 09:50:00
[1] "/home.local/guidoh/GEOmetadb.sqlite"
>
> con <- dbConnect(SQLite(), "GEOmetadb.sqlite")
> dbDisconnect(con)
[1] TRUE
>
> rs <- dbGetQuery(con,paste("select gsm,supplementary_file",
+                            "from gsm where gpl='GPL96'",
+                            "and supplementary_file like '%CEL.gz'"))

*** caught segfault ***
address 0x8, cause 'memory not mapped'

Traceback:
1: .Call("RS_SQLite_exec", conId, statement, bind.data, PACKAGE = .SQLitePkgName)
2: sqliteExecStatement(con, statement, bind.data)
3: sqliteQuickSQL(conn, statement, ...)
4: dbGetQuery(con, paste("select gsm,supplementary_file", "from gsm where gpl='GPL96'",     "and supplementary_file like '%CEL.gz'"))
5: dbGetQuery(con, paste("select gsm,supplementary_file", "from gsm where gpl='GPL96'",     "and supplementary_file like '%CEL.gz'"))

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: dim(rs)
Selection:


---------------------------------------------------------
Guido Hooiveld, PhD
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
Wageningen University
Biotechnion, Bomenweg 2
NL-6703 HD Wageningen
the Netherlands
tel: (+)31 317 485788
fax: (+)31 317 483342
email:      guido.hooiveld@wur.nl
internet:   http://nutrigene.4t.com
http://www.researcherid.com/rid/F-4912-2010


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