[BioC] rtracklayer error?

[Janet Young]

Hi there,

I was having some trouble using rtracklayer to obtain phyloP scores - I think maybe I have found a problem with rtracklayer. Is there a limit to the number of scores/positions it can get in a single query?

Hopefully the code and output below will explain all. I am using the devel version, and have included sessionInfo below.

thanks very much,

Janet Young

------------------------------------------------------------------- 

Dr. Janet Young 

Malik lab
http://research.fhcrc.org/malik/en.html

Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N., A2-025, 
P.O. Box 19024, Seattle, WA 98109-1024, USA.

tel: (206) 667 4512
email: jayoung  ...at...  fhcrc.org

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library(rtracklayer)
library(GenomicRanges)

session <- browserSession("UCSC")
genome(session) <- "hg19"


myRanges10k <- GRanges( seqnames=rep("chr1",10), ranges=IRanges(start=1:10*1000000,width=10000) )

query <- ucscTableQuery (session, "cons46way", range=myRanges10k)
tableName(query) <- "phyloP46wayPrimates"
scores <- track(query)
## fails with this error:

Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : 
  solving row 10001: range cannot be determined from the supplied arguments (too many NAs)
In addition: Warning messages:
1: In matrix(as.numeric(unlist(split_lines)), nrow = 2) :
  NAs introduced by coercion
2: In matrix(as.numeric(unlist(split_lines)), nrow = 2) :
  data length [20005] is not a sub-multiple or multiple of the number of rows [2]


## but both halves succeed:
query <- ucscTableQuery (session, "cons46way", range=myRanges10k[1:5])
tableName(query) <- "phyloP46wayPrimates"
scores <- track(query)
## works

query <- ucscTableQuery (session, "cons46way", range=myRanges10k[6:10])
tableName(query) <- "phyloP46wayPrimates"
scores <- track(query)
## works

sessionInfo()

R version 3.0.1 Patched (2013-07-29 r63455)
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=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] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] rtracklayer_1.21.9    GenomicRanges_1.13.35 XVector_0.1.0        
[4] IRanges_1.19.19       BiocGenerics_0.7.3   

loaded via a namespace (and not attached):
[1] Biostrings_2.29.14 bitops_1.0-5       BSgenome_1.29.1    RCurl_1.95-4.1    
[5] Rsamtools_1.13.26  stats4_3.0.1       tools_3.0.1        XML_3.98-1.1      
[9] zlibbioc_1.7.0