Error with BiomartGeneRegionTrack: could not find symbol "recursive"
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Entering edit mode
Diego Diez ▴ 760
@diego-diez-4520
Last seen 3.5 years ago
Japan

Since updating to R-3.3.3 yesterday (not clear if related) I get the following error when using BiomartGeneRegionTrack:

library(Gviz)
BiomartGeneRegionTrack(symbol = "Stat1", genome = "mm9")
Error in .Primitive("c")() : 
  could not find symbol "recursive" in environment of the generic function

EDIT: Just tested this with release_base2 docker image (that uses R-3.3.2) and installing Gviz package and it runs without problem.

Further information:

> traceback()
12: .Primitive("c")()
11: do.call(c, args)
10: do.call(c, args)
9: .local(x, ..., na.rm = na.rm)
8: range(, na.rm = FALSE)
7: range(, na.rm = FALSE)
6: .cacheMartData(.Object, chromosome, staged)
5: .local(.Object, ...)
4: initialize(value, ...)
3: initialize(value, ...)
2: new("BiomartGeneRegionTrack", start = start, end = end, chromosome = chromosome, 
       strand = strand, biomart = biomart, name = name, genome = genome, 
       stacking = stacking, filter = filters, featureMap = featureMap, 
       symbol = symbol, gene = gene, transcript = transcript, entrez = entrez, 
       ...)
1: BiomartGeneRegionTrack(symbol = "Stat1", genome = "mm9")
> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.3

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
 [1] grid      parallel  stats4    stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
[1] Gviz_1.18.1          GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 
[4] IRanges_2.8.1        S4Vectors_0.12.1     BiocGenerics_0.20.0 

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.9                   biovizBase_1.22.0            
 [3] lattice_0.20-34               Rsamtools_1.26.1             
 [5] Biostrings_2.42.1             assertthat_0.1               
 [7] digest_0.6.12                 mime_0.5                     
 [9] R6_2.2.0                      plyr_1.8.4                   
[11] backports_1.0.5               acepack_1.4.1                
[13] RSQLite_1.1-2                 BiocInstaller_1.24.0         
[15] httr_1.2.1                    ggplot2_2.2.1                
[17] zlibbioc_1.20.0               GenomicFeatures_1.26.3       
[19] lazyeval_0.2.0                data.table_1.10.4            
[21] rpart_4.1-10                  Matrix_1.2-8                 
[23] checkmate_1.8.2               splines_3.3.3                
[25] BiocParallel_1.8.1            AnnotationHub_2.6.4          
[27] stringr_1.2.0                 foreign_0.8-67               
[29] htmlwidgets_0.8               RCurl_1.95-4.8               
[31] biomaRt_2.30.0                munsell_0.4.3                
[33] shiny_1.0.0                   httpuv_1.3.3                 
[35] rtracklayer_1.34.2            base64enc_0.1-3              
[37] htmltools_0.3.5               nnet_7.3-12                  
[39] SummarizedExperiment_1.4.0    tibble_1.2                   
[41] gridExtra_2.2.1               htmlTable_1.9                
[43] interactiveDisplayBase_1.12.0 Hmisc_4.0-2                  
[45] matrixStats_0.51.0            XML_3.98-1.5                 
[47] GenomicAlignments_1.10.0      bitops_1.0-6                 
[49] xtable_1.8-2                  gtable_0.2.0                 
[51] DBI_0.5-1                     magrittr_1.5                 
[53] scales_0.4.1                  stringi_1.1.2                
[55] XVector_0.14.0                latticeExtra_0.6-28          
[57] Formula_1.2-1                 RColorBrewer_1.1-2           
[59] ensembldb_1.6.2               tools_3.3.3                  
[61] dichromat_2.0-0               BSgenome_1.42.0              
[63] Biobase_2.34.0                yaml_2.1.14                  
[65] survival_2.40-1               AnnotationDbi_1.36.2         
[67] colorspace_1.3-2              cluster_2.0.5                
[69] memoise_1.0.0                 VariantAnnotation_1.20.2     
[71] knitr_1.15.1     
gviz • 1.5k views
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Entering edit mode

This is fixed following A: Combining RangedData objects is broken (IRanges 2.8.1 with R version 3.3.3 RC) (setting type = "source" and installing GenomicRanges).

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