Question: Gviz error message after updating R
gravatar for ta_awwad
3.9 years ago by
Frankfurt am Main
ta_awwad280 wrote:

Hi everybody, I have actually weird situation. my Gviz script was working perfectly but after I updated my R version I am getting the following error message after running plotTracks:

> plotTracks(list(idxTrack, axTrack , cp, gc,gckd, ct, be, su, refGenes),
                from=from, to=to, showTitle=T,showId=T, scale=0.1)    
Error in (function (classes, fdef, mtable)  : 
      unable to find an inherited method for function 'displayPars<-' for signature '"character", "list"'

I changed nothing .. and I don't know what went wrong. does anyone have an experience with such error.

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)

[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     datasets 
 [9] methods   base     

other attached packages:
[1] lattice_0.20-34      Gviz_1.16.5          GenomicRanges_1.24.3 GenomeInfoDb_1.8.7  
[5] IRanges_2.6.1        S4Vectors_0.10.3     BiocGenerics_0.18.0  BiocInstaller_1.22.3

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.2.3    VariantAnnotation_1.18.7     
 [3] splines_3.3.1                 colorspace_1.2-6             
 [5] htmltools_0.3.5               rtracklayer_1.32.2           
 [7] GenomicFeatures_1.24.5        chron_2.3-47                 
 [9] interactiveDisplayBase_1.10.3 survival_2.39-5              
[11] XML_3.98-1.4                  foreign_0.8-67               
[13] DBI_0.5-1                     ensembldb_1.4.7              
[15] BiocParallel_1.6.6            RColorBrewer_1.1-2           
[17] matrixStats_0.50.2            plyr_1.8.4                   
[19] zlibbioc_1.18.0               Biostrings_2.40.2            
[21] munsell_0.4.3                 gtable_0.2.0                 
[23] latticeExtra_0.6-28           Biobase_2.32.0               
[25] biomaRt_2.28.0                httpuv_1.3.3                 
[27] AnnotationDbi_1.34.4          Rcpp_0.12.7                  
[29] xtable_1.8-2                  acepack_1.3-3.3              
[31] BSgenome_1.40.1               scales_0.4.0                 
[33] Hmisc_3.17-4                  XVector_0.12.1               
[35] mime_0.5                      Rsamtools_1.24.0             
[37] gridExtra_2.2.1               AnnotationHub_2.4.2          
[39] ggplot2_2.1.0                 digest_0.6.10                
[41] biovizBase_1.20.0             shiny_0.14                   
[43] tools_3.3.1                   bitops_1.0-6                 
[45] RCurl_1.95-4.8                RSQLite_1.0.0                
[47] dichromat_2.0-0               Formula_1.2-1                
[49] cluster_2.0.4                 Matrix_1.2-7.1               
[51] data.table_1.9.6              httr_1.2.1                   
[53] R6_2.1.3                      rpart_4.1-10                 
[55] GenomicAlignments_1.8.4       nnet_7.3-12
ADD COMMENTlink written 3.9 years ago by ta_awwad280

This error is usually seen when a function is called on the wrong type of object. Either you're calling the function incorrectly or the function definition has changed. This can also happen when there are two functions with the same name.

ADD REPLYlink written 3.9 years ago by Jean-Karim Heriche23k

ahhhhhh .. my mistake .. thanks for your reply

ADD REPLYlink written 3.9 years ago by ta_awwad280
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