[BioC] ChiPpeakAnno: findOverlappingPeaks: running time

[George [guest]]

I am attempting to perform an overlap of 85,000 TFS peaks with 73,000 Dnase1 hypersensitivity sites.  The tool took probably 45 minutes.  As CisGenome is able to perform these overlaps very quickly, I am wondering if this time frame seems correct?  I also noticed that the annotation is taking much longer than CisGenome...
thanks, the ChiPpeakAnno software package looks very cool so far!

 -- output of sessionInfo(): 

>sessionInfo()
R version 2.10.1 (2009-12-14) 
x86_64-unknown-linux-gnu 

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] ChIPpeakAnno_1.2.15                 limma_3.2.3                        
 [3] org.Hs.eg.db_2.3.6                  GO.db_2.3.5                        
 [5] RSQLite_0.9-4                       DBI_0.2-5                          
 [7] AnnotationDbi_1.8.2                 BSgenome.Ecoli.NCBI.20080805_1.3.16
 [9] BSgenome_1.14.2                     Biostrings_2.14.12                 
[11] IRanges_1.4.16                      multtest_2.2.0                     
[13] Biobase_2.6.1                       biomaRt_2.2.0                      

loaded via a namespace (and not attached):
[1] MASS_7.3-4      RCurl_1.6-10    splines_2.10.1  survival_2.35-7
[5] tools_2.10.1    XML_3.4-2      
> 

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