Hi,

I recently noticed that a script I have that uses ggbio stopped working. I wonder if there are any dependencies that are now incompatible?

The simplest case to reproduce the error:

library(ggbio)
library(GenomicRanges)
data(ideoCyto, package = "biovizBase")

autoplot(ideoCyto$hg19)

Error in FUN(X[[i]], ...) : object of type 'symbol' is not subsettable

sessionInfo( )

R version 3.6.1 (2019-07-05)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.2 (Maipo)

Matrix products: default
BLAS:   /sysapps/cluster/software/Anaconda2/5.3.0/lib/libblas.so.3.8.0
LAPACK: /sysapps/cluster/software/Anaconda2/5.3.0/lib/liblapack.so.3.8.0

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  grid     
[8] methods   base     

other attached packages:
[1] ggbio_1.32.0        ggplot2_3.3.2.9000  BiocGenerics_0.30.0

loaded via a namespace (and not attached):
 [1] ProtGenerics_1.16.0         bitops_1.0-6               
 [3] matrixStats_0.55.0          bit64_0.9-7                
 [5] RColorBrewer_1.1-2          progress_1.2.2             
 [7] httr_1.4.2                  GenomeInfoDb_1.20.0        
 [9] tools_3.6.1                 backports_1.1.5            
[11] R6_2.4.0                    rpart_4.1-15               
[13] Hmisc_4.2-0                 DBI_1.0.0                  
[15] lazyeval_0.2.2              colorspace_1.4-1           
[17] nnet_7.3-12                 withr_2.3.0                
[19] tidyselect_0.2.5            gridExtra_2.3              
[21] prettyunits_1.0.2           GGally_1.4.0               
[23] bit_1.1-14                  curl_4.2                   
[25] compiler_3.6.1              graph_1.62.0               
[27] Biobase_2.44.0              htmlTable_1.13.2           
[29] DelayedArray_0.10.0         rtracklayer_1.44.4         
[31] scales_1.0.0                checkmate_1.9.4            
[33] RBGL_1.60.0                 stringr_1.4.0              
[35] digest_0.6.21               Rsamtools_2.0.1            
[37] foreign_0.8-72              XVector_0.24.0             
[39] base64enc_0.1-3             dichromat_2.0-0            
[41] pkgconfig_2.0.3             htmltools_0.3.6            
[43] ensembldb_2.8.0             BSgenome_1.52.0            
[45] htmlwidgets_1.3             rlang_0.4.7                
[47] rstudioapi_0.10             RSQLite_2.1.2              
[49] BiocParallel_1.18.1         acepack_1.4.1              
[51] dplyr_0.8.3                 VariantAnnotation_1.30.1   
[53] RCurl_1.95-4.12             magrittr_1.5               
[55] GenomeInfoDbData_1.2.1      Formula_1.2-3              
[57] Matrix_1.2-17               Rcpp_1.0.2                 
[59] munsell_0.5.0               S4Vectors_0.22.1           
[61] stringi_1.4.6               SummarizedExperiment_1.14.1
[63] zlibbioc_1.30.0             plyr_1.8.4                 
[65] blob_1.2.0                  crayon_1.3.4               
[67] lattice_0.20-38             Biostrings_2.52.0          
[69] splines_3.6.1               GenomicFeatures_1.36.4     
[71] hms_0.5.1                   zeallot_0.1.0              
[73] knitr_1.25                  pillar_1.4.2               
[75] GenomicRanges_1.36.1        reshape2_1.4.3             
[77] biomaRt_2.40.5              stats4_3.6.1               
[79] XML_3.98-1.20               glue_1.3.1                 
[81] biovizBase_1.32.0           latticeExtra_0.6-28        
[83] data.table_1.12.4           BiocManager_1.30.4         
[85] vctrs_0.2.0                 gtable_0.3.0               
[87] purrr_0.3.2                 reshape_0.8.8              
[89] assertthat_0.2.1            xfun_0.10                  
[91] AnnotationFilter_1.8.0      survival_2.44-1.1          
[93] tibble_2.1.3                OrganismDbi_1.26.0         
[95] GenomicAlignments_1.20.1    AnnotationDbi_1.48.0       
[97] memoise_1.1.0               IRanges_2.18.3             
[99] cluster_2.1.0

I have a different system running an older version of R (i.e., version 3.6.0) with the same version of ggbio but slightly older versions of some of the Bioconductor dependency packages where this works fine, though I'm not exactly sure which one could be causing this issue. Any advice on which packages might need to be upgraded/downgraded, or how to get this working?

Thanks,

Andrew

The version of R/BioC that you are using are at least a year out of date. The first thing you should do is update to R-4.0.2 and the current release version of Bioconductor. That's what I am running, and your code works for me.