I made a db by GenomicFeatures: library(GenomicFeatures) chrominfo = data.frame( chrom=c('Chr1','Chr2','Chr3','Chr4','Chr5','Chr6','Chr7'), length=c(29149675,23174626,39782674,23425844,28023477,29076228,1922650 0), 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 -- Sent via the guest posting facility at bioconductor.org.