Hi All,

I have tried to use import.gff3 from the rtracklayer package to import
annotation information for the mosquito genome (gff3 file here:
http://aaegypti.vectorbase.org/GetData/Downloads/) which is only 20 MB but
the memory usage has exceeded 100GB on one of our high memory servers. This
seems like far too much to just read in the file (which takes only 3 seconds
with read.delim) and convert to RangedData objects. Has anyone experienced
similar problems?

Here is my sessionInfo:
R version 2.13.0 (2011-04-13)
Platform: x86_64-redhat-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=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] biomaRt_2.8.0      rtracklayer_1.12.4 RCurl_1.5-0        bitops_1.0-4.1

loaded via a namespace (and not attached):
[1] Biostrings_2.20.0   BSgenome_1.20.0     GenomicRanges_1.4.1
[4] IRanges_1.10.0      tools_2.13.0        XML_3.2-0

-- 
Vince Buffalo
Statistical Programmer
Bioinformatics Core
UC Davis Genome Center
University of California, Davis

"There's real poetry in the real world. Science is the poetry of reality."
-Richard Dawkins

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