Hello everything,

I have a question regarding the getTable function in the rtracklayer
package.  The code below used to work in previous R version, but it
doesn't for the current release. I can't figure out what the problem is.
Can anyone give some hint?  Thanks for your help!

 

Best,

 

Arthur Xuejun Li

City of Hope Comprehensive Cancer Center

Department of Information Science

1500 East Duarte Road

Duarte, CA 91010 - 3000

Ph:   (626) 256-4673 ext. 65121

Fax: (626) 471-7106

 

 

 

> session <- browserSession()

> genome(session) <- "mm9"

> foo <- trackNames(session)[trackNames(session) =="rmsk"]

> bar<- ucscTableQuery(session,  foo)

> bar1 <- getTable(bar)

Error in if (st[["status"]] == 100) { : 

  missing value where TRUE/FALSE needed

> 

> 

> sessionInfo()

R version 2.11.0 (2010-04-22) 

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] rtracklayer_1.8.1   RCurl_1.4-1         bitops_1.0-4.1     

[4] ShortRead_1.6.0     Rsamtools_1.0.0     lattice_0.18-5     

[7] Biostrings_2.16.0   GenomicRanges_1.0.1 IRanges_1.6.0      

 

loaded via a namespace (and not attached):

[1] Biobase_2.8.0   BSgenome_1.16.0 grid_2.11.0     hwriter_1.2    

[5] tools_2.11.0    XML_2.8-1      

 

 

 



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