[BioC] GenomicFeatures: Unable to save TranscriptDb object

[Hervé Pagès]

Hi Paul,

Maybe you are trying to overwrite an SQLite file that is currently
in use? Something like:

   > saveFeatures(txdb1, "txdb1.sqlite")
   > txdb2 <- loadFeatures("txdb1.sqlite")
   > saveFeatures(txdb2, "txdb1.sqlite")
   Error in sqliteCopyDatabase(txdbConn(x), file) :
     RS-DBI driver: (database is locked)

Cheers,
H.


On 11-04-08 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
>
> 	[[alternative HTML version deleted]]
>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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