Error with AnnotationTrack(gene, name = "Gene Model") part 3 in edX advanced bioconductor
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jt.cathey • 0
@bfcd9fcd
Last seen 21 months ago
Thailand

I get this error:

> atrack <- AnnotationTrack(gene, name = "Gene Model")

# Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function '.buildRange' for signature '"standardGeneric", "NULL", "NULL", "NULL"'
# searched google, can find anything on function  .buildRange

sessionInfo( )

R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.6

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

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      stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] Gviz_1.40.1          GenomicRanges_1.48.0 GenomeInfoDb_1.32.4  IRanges_2.30.1      
[5] S4Vectors_0.34.0     BiocGenerics_0.42.0 

loaded via a namespace (and not attached):
  [1] ProtGenerics_1.28.0         bitops_1.0-7                matrixStats_0.62.0         
  [4] bit64_4.0.5                 filelock_1.0.2              RColorBrewer_1.1-3         
  [7] progress_1.2.2              httr_1.4.4                  backports_1.4.1            
 [10] tools_4.2.1                 utf8_1.2.2                  R6_2.5.1                   
 [13] rpart_4.1.16                lazyeval_0.2.2              Hmisc_4.7-1                
 [16] DBI_1.1.3                   colorspace_2.0-3            nnet_7.3-18                
 [19] gridExtra_2.3               tidyselect_1.2.0            prettyunits_1.1.1          
 [22] bit_4.0.4                   curl_4.3.3                  compiler_4.2.1             
 [25] cli_3.4.1                   Biobase_2.56.0              htmlTable_2.4.1            
 [28] xml2_1.3.3                  DelayedArray_0.22.0         rtracklayer_1.56.1         
 [31] checkmate_2.1.0             scales_1.2.1                rappdirs_0.3.3             
 [34] stringr_1.4.1               digest_0.6.29               Rsamtools_2.12.0           
 [37] foreign_0.8-83              XVector_0.36.0              dichromat_2.0-0.1          
 [40] htmltools_0.5.3             base64enc_0.1-3             jpeg_0.1-9                 
 [43] pkgconfig_2.0.3             MatrixGenerics_1.8.1        ensembldb_2.20.2           
 [46] dbplyr_2.2.1                fastmap_1.1.0               BSgenome_1.64.0            
 [49] htmlwidgets_1.5.4           rlang_1.0.6                 rstudioapi_0.14            
 [52] RSQLite_2.2.18              BiocIO_1.6.0                generics_0.1.3             
 [55] BiocParallel_1.30.3         dplyr_1.0.10                VariantAnnotation_1.42.1   
 [58] RCurl_1.98-1.9              magrittr_2.0.3              GenomeInfoDbData_1.2.8     
 [61] Formula_1.2-4               interp_1.1-3                Matrix_1.5-1               
 [64] Rcpp_1.0.9                  munsell_0.5.0               fansi_1.0.3                
 [67] lifecycle_1.0.3             stringi_1.7.8               yaml_2.3.5                 
 [70] SummarizedExperiment_1.26.1 zlibbioc_1.42.0             BiocFileCache_2.4.0        
 [73] blob_1.2.3                  parallel_4.2.1              crayon_1.5.2               
 [76] deldir_1.0-6                lattice_0.20-45             Biostrings_2.64.1          
 [79] splines_4.2.1               GenomicFeatures_1.48.4      hms_1.1.2                  
 [82] KEGGREST_1.36.3             knitr_1.40                  pillar_1.8.1               
 [85] rjson_0.2.21                codetools_0.2-18            biomaRt_2.52.0             
 [88] XML_3.99-0.11               glue_1.6.2                  biovizBase_1.44.0          
 [91] latticeExtra_0.6-30         BiocManager_1.30.18         data.table_1.14.2          
 [94] png_0.1-7                   vctrs_0.4.2                 gtable_0.3.1               
 [97] purrr_0.3.5                 assertthat_0.2.1            cachem_1.0.6               
[100] ggplot2_3.3.6               xfun_0.33                   AnnotationFilter_1.20.0    
[103] restfulr_0.0.15             survival_3.4-0              tibble_3.1.8               
[106] GenomicAlignments_1.32.1    AnnotationDbi_1.58.0        memoise_2.0.1              
[109] cluster_2.1.4               ellipsis_0.3.2
annotationTools • 958 views
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How did you create gene ?

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Also test that you have the most recent versions of packages with BiocManager::valid() and BiocManager::install()

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@james-w-macdonald-5106
Last seen 1 day ago
United States

You cannot build an AnnotationTrack if you fail to provide the start and end of the range (and chromosome and genome, but those errors will come later) in your 'gene' object, then you will get the error you see. It's basically saying that you have not provided a start, end, or width argument.

See ?AnnotationTrack for examples of how you use this function.

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