[BioC] R crashes with GEOmetadb

[Sean Davis]

Hi, Guido.

The output of sessionInfo() might be helpful (or not).  It is
certainly possible that this is an issue with GEOmetadb, but the error
suggests that RSQLite might be to blame, also.  I'd suggest
reinstalling RSQLite as a start.  If you still have issues after doing
so, definitely include the output of sessionInfo().

Sean


On Wed, Jun 29, 2011 at 11:36 AM, Hooiveld, Guido <Guido.Hooiveld at wur.nl> wrote:
> 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 at wur.nl
> internet:   http://nutrigene.4t.com
> http://www.researcherid.com/rid/F-4912-2010
>
>
>        [[alternative HTML version deleted]]
>
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