Question: Setting up PLAYRDesign gives error on makeTxDbFromUCSC, error in tableNames
0
gravatar for songshan.guo
19 months ago by
songshan.guo0 wrote:

I'm trying to set up the software for the rapid design of PLAYR probes, as described in this paper: https://www.nature.com/articles/nmeth.3742#supplementary-information 

I'm using the GenomicFeatures library, but this line is giving me an error message. Here's the line, followed by the error message, followed by the output of traceback().

> txdb <- makeTxDbFromUCSC(genome = "hg19", tablename = "refGene")
Error in tableNames(ucscTableQuery(session, track = track)) :
  error in evaluating the argument 'object' in selecting a method for function 'tableNames': Error in normArgTrack(track, trackids) : Unknown track: RefSeq Genes

> traceback()
2: tableNames(ucscTableQuery(session, track = track))
1: makeTxDbFromUCSC(genome = "hg19", tablename = "refGene")

I've read the documentation of the makeTxDbFromUCSC function available here: https://bioconductor.org/packages/release/bioc/manuals/GenomicFeatures/man/GenomicFeatures.pdf, but I'm having a hard time understanding the error message.

As suggested by the Posting Guide, here's the output of sessionInfo(). Let me know if I need to provide any other information. 

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS

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] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] GenomicFeatures_1.22.13 AnnotationDbi_1.32.3    Biobase_2.30.0         
 [4] GenomicRanges_1.22.4    GenomeInfoDb_1.6.3      IRanges_2.4.8          
 [7] S4Vectors_0.8.11        BiocGenerics_0.16.1     PLAYRDesign_0.1        
[10] RSQLite_2.1.0           devtools_1.13.5         BiocInstaller_1.20.3   

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.16                      plyr_1.8.4                       
 [3] git2r_0.21.0                      futile.logger_1.4.3              
 [5] XVector_0.10.0                    AnnotationFuncs_1.20.0           
 [7] bitops_1.0-6                      futile.options_1.0.0             
 [9] tools_3.2.3                       zlibbioc_1.16.0                  
[11] biomaRt_2.26.1                    digest_0.6.15                    
[13] bit_1.1-12                        lattice_0.20-35                  
[15] memoise_1.1.0                     BSgenome_1.38.0                  
[17] pkgconfig_2.0.1                   shiny_1.0.5                      
[19] DBI_0.8                           curl_3.2                         
[21] stringr_1.3.0                     rtracklayer_1.30.4               
[23] withr_2.1.2                       httr_1.3.1                       
[25] Biostrings_2.38.4                 grid_3.2.3                       
[27] bit64_0.9-7                       R6_2.2.2                         
[29] BSgenome.Hsapiens.UCSC.hg19_1.4.0 tcltk_3.2.3                      
[31] XML_3.98-1.11                     BiocParallel_1.4.3               
[33] magrittr_1.5                      reshape2_1.4.3                   
[35] org.Hs.eg.db_3.2.3                lambda.r_1.2                     
[37] blob_1.1.1                        htmltools_0.3.6                  
[39] Rsamtools_1.22.0                  GenomicAlignments_1.6.3          
[41] SummarizedExperiment_1.0.2        xtable_1.8-2                     
[43] mime_0.5                          httpuv_1.3.6.2                   
[45] stringi_1.1.7                     RCurl_1.95-4.10                  
[47] zoo_1.8-1
 
genomicfeatures R • 326 views
ADD COMMENTlink modified 19 months ago • written 19 months ago by songshan.guo0

Your version of R, Bioconductor, and GenomicFeatures appears to be out-of-date.  Updgrading your version of R to the current release and following the instructions to update Bioconductor may solve the issue.

ADD REPLYlink written 19 months ago by daniel.vantwisk50
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