[BioC] GenomicFeatures loadDb error

Linxzh [guest] guest at bioconductor.org
Fri Oct 11 04:52:59 CEST 2013


I made a db by GenomicFeatures:
    library(GenomicFeatures)
    chrominfo = data.frame(
        chrom=c('Chr1','Chr2','Chr3','Chr4','Chr5','Chr6','Chr7'),             length=c(29149675,23174626,39782674,23425844,28023477,29076228,19226500),
        is_circular=c(FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE))
    txdb = makeTranscriptDbFromGFF(file='Cucumber_no_Scaf.gff3',
        format='gff3',
        chrominfo=chrominfo,
        dataSource='SoLab',
        species='Cucumis sativus Linn')
    saveDb(txdb, file="Cu.sqlite")

below is the Rout message:

> chrominfo = data.frame(
+       chrom=c('Chr1','Chr2','Chr3','Chr4','Chr5','Chr6','Chr7'), 
+       length=c(29149675,23174626,39782674,23425844,28023477,29076228,19226500),
+       is_circular=c(FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE))
> 
> 
> txdb = makeTranscriptDbFromGFF(file='Cucumber_no_Scaf.gff3',
+       format='gff3',
+       chrominfo=chrominfo,
+       dataSource='SoLab',
+       species='Cucumis sativus Linn')
extracting transcript information
Extracting gene IDs
extracting transcript information
Processing splicing information for gff3 file.
Deducing exon rank from relative coordinates provided
Prepare the 'metadata' data frame ... metadata: OK
Warning message:
In .deduceExonRankings(exs, format = "gff") :
 that you have provided a valid attribute for exonRankAttributeName
> 
> saveDb(txdb, file="Cu.sqlite")
Error in sqliteCopyDatabase(dbConn(x), file) : 
  RS-DBI driver: (disk I/O error)
Calls: saveDb -> saveDb -> sqliteCopyDatabase -> .Call
Execution halted

how can i solve the error? thanks

 -- output of sessionInfo(): 

R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=zh_CN.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=zh_CN.UTF-8        LC_COLLATE=zh_CN.UTF-8    
 [5] LC_MONETARY=zh_CN.UTF-8    LC_MESSAGES=zh_CN.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] GenomicFeatures_1.12.3 AnnotationDbi_1.22.6   Biobase_2.20.1        
[4] GenomicRanges_1.12.5   IRanges_1.18.3         BiocGenerics_0.6.0    

loaded via a namespace (and not attached):
 [1] biomaRt_2.16.0     Biostrings_2.28.0  bitops_1.0-6       BSgenome_1.28.0   
 [5] DBI_0.2-7          RCurl_1.95-4.1     Rsamtools_1.12.4   RSQLite_0.11.4    
 [9] rtracklayer_1.20.4 stats4_3.0.1       tools_3.0.1        XML_3.98-1.1      
[13] zlibbioc_1.6.0

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