[BioC] GenomicFeatures: Unable to save TranscriptDb object

[Marc Carlson]

Hi Paul,

I am having trouble reproducing this error.  But when a SQLite database 
is locked it normally means that some other process is actively writing 
to it.  Can you update RSQLite using biocLite() and try again?  There 
are instructions on our website:

http://www.bioconductor.org/install/

Also, you version of R and Bioconductor is really pretty long in the 
tooth for using the GenomicFeatures (and related) packages.  You might 
want to update soon (R-2-13 will release imminently.

Hope this helps,


   Marc



On 04/08/2011 05:37 AM, KORIR, PAUL wrote:
> Hi,
>
> I've created a TranscriptDb object and would like to save it. I get an error that I'm unable to decode as shown below:
>
>> saveFeatures(txdb,file="../txdb.sqlite")
> Error in sqliteCopyDatabase(txdbConn(x), file) :
>    RS-DBI driver: (database is locked)
>
> Here's my sessionInfo() output:
>> sessionInfo()
> R version 2.11.0 (2010-04-22)
> x86_64-redhat-linux-gnu
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8
>   [8] LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GenomicFeatures_1.0.10 Rsamtools_1.0.8        Biostrings_2.16.9      GenomicRanges_1.0.9    IRanges_1.6.17         data.table_1.5.3
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.8.0     biomaRt_2.4.0     BSgenome_1.16.5   DBI_0.2-5         RCurl_1.4-3       RSQLite_0.9-2     rtracklayer_1.8.1 tools_2.11.0      XML_3.1-1
> Could someone please help?
>
> P. Kibet Korir
> Bioinformatics (PhD Student),
> NUI Galway
> +353 86 224 19 66
>
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>
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