[BioC] R crashes with GEOmetadb
Hooiveld, Guido
Guido.Hooiveld at wur.nl
Wed Jun 29 20:01:25 CEST 2011
Hi Sean,
The reason i did not include the output of sessioninfo() was because my R session hangs. Anyway, below the output after loading GEOmetadb, but BEFORE running any other commands.
[below: output of sessioninfo]
> library(GEOmetadb)
Loading required package: GEOquery
Loading required package: Biobase
Setting options('download.file.method.GEOquery'='curl')
Loading required package: RSQLite
Loading required package: DBI
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] GEOmetadb_1.12.0 RSQLite_0.9-4 DBI_0.2-5 GEOquery_2.19.1
[5] Biobase_2.12.1
loaded via a namespace (and not attached):
[1] RCurl_1.5-0 tools_2.13.0 XML_3.4-0
>
To be sure, I also updated RSQLite, but the version that was already installed was up to date (v0.9.4).
Next I ran the sample script. Unfortunately, it again crashes... I did notice that the version of the SQLite database that was downloaded is the version of today (29 June). Earlier today it was from 18 June).
Taken together, despite updating RSQLite and the SQLite database, problem still persists.
Regards,
Guido
[below again lines of code that result into crash]
> 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"
>
> file.info("GEOmetadb.sqlite")
size isdir mode mtime ctime
GEOmetadb.sqlite 1565664256 FALSE 644 2011-06-29 19:48:53 2011-06-29 19:48:53
atime uid gid uname grname
GEOmetadb.sqlite 2011-06-29 19:49:14 1001 100 guidoh users
>
> 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:
-----Original Message-----
From: seandavi at gmail.com [mailto:seandavi at gmail.com] On Behalf Of Sean Davis
Sent: Wednesday, June 29, 2011 18:38
To: Hooiveld, Guido
Cc: bioconductor (bioconductor at stat.math.ethz.ch)
Subject: Re: [BioC] R crashes with GEOmetadb
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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