Hi All,

I am analyzing some ChIP seq data using DESeq, reads have all been aligned and are in BAM format.
"aligned" in a names character vector containing the names of the bam files.
I'm trying to use the Genominator function importFromAlignedReads to read in the aligned data, but I get an error regarding the system.time function:

> aligned
  20417.6.bam   2041T.6.bam   305AG.8.bam   305D0.8.bam
"20417.6.bam" "2041T.6.bam" "305AG.8.bam" "305D0.8.bam"
> chroms
 [1] "chr1"  "chr2"  "chr3"  "chr4"  "chr5"  "chr6"  "chr7"  "chr8"  "chr9"
[10] "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17" "chr18"
[19] "chr19" "chr20" "chr21" "chrX"  "chrY"  "chrM"


> eData <- importFromAlignedReads(aligned, chrMap=chroms, dbFilename='test.db', tablename='raw', type="BAM", verbose=FALSE)
Error in system.time(exp) :
  Unable to write the table, delete table or specify overwrite.
In addition: Warning message:
In value[[3L]](cond) :
  RS-DBI driver: (error in statement: near "20417.6": syntax error)
Timing stopped at: 0.076 0 0.081
Timing stopped at: 12.851 0.74 13.631

Any idea what might be wrong, anyone seem a similar issue earlier? Seems to be the second call to system.time within importFromAlignedReads that breaks the function.


> sessionInfo()
R version 2.15.0 (2012-03-30)
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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
 [1] Genominator_1.10.0  GenomeGraphs_1.16.0 biomaRt_2.12.0
 [4] RSQLite_0.11.1      DBI_0.2-5           ShortRead_1.14.1
 [7] latticeExtra_0.6-19 RColorBrewer_1.0-5  Rsamtools_1.8.0
[10] lattice_0.20-6      Biostrings_2.24.1   GenomicRanges_1.8.3
[13] IRanges_1.14.2      DESeq_1.8.1         locfit_1.5-7
[16] Biobase_2.16.0      BiocGenerics_0.2.0  BiocInstaller_1.4.3

loaded via a namespace (and not attached):
 [1] annotate_1.34.0      AnnotationDbi_1.18.0 bitops_1.0-4.1
 [4] genefilter_1.38.0    geneplotter_1.34.0   hwriter_1.3
 [7] RCurl_1.91-1         splines_2.15.0       stats4_2.15.0
[10] survival_2.36-12     tools_2.15.0         XML_3.9-4
[13] xtable_1.7-0         zlibbioc_1.2.0


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