Hi,

Yesterday, I installed the package EBImage and updated other packages related to it but not Gviz and GenomicRanges.

But after that, I could not plot of annotation track from Gviz from BiomartGeneRegionTrack or AnnotationTrack

I have this error message

 plotTracks(biomTrack,from=start,to=end,showId=TRUE)
Error in queryHits(findOverlaps(feathers, resize(levels[[cur.level]],  :
  error in evaluating the argument 'x' in selecting a method for function 'queryHits': Error in findOverlaps(feathers, resize(levels[[cur.level]], width = width(levels[[cur.level]]) -  :
  error in evaluating the argument 'subject' in selecting a method for function 'findOverlaps': Error in resize(levels[[cur.level]], width = width(levels[[cur.level]]) -  :
  unused argument (width = width(levels[[cur.level]]) - 1)

To create biomTrack

end<- 139515750
start <- 139415251
gen<-"hg19"
chrom<-"chr7"

biomTrack <- BiomartGeneRegionTrack(genome = gen, biomart=martENSEMBL,
                                     chromosome = chrom, start = start,
                                     end = end,  name = "ENSEMBL",
                                     fontcolor="black")
 plotTracks(biomTrack,from=start,to=end,showId=TRUE)

Could you help me to solve it ?

Regards,

Tiphaine

sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] EBImage_4.6.0        BiocInstaller_1.14.3 XVector_0.4.0        coMET_0.99.4        
 [5] rtracklayer_1.24.2   GenomicRanges_1.16.4 GenomeInfoDb_1.0.2   IRanges_1.22.10     
 [9] Gviz_1.8.4           BiocGenerics_0.10.0  biomaRt_2.20.0      

loaded via a namespace (and not attached):
 [1] abind_1.4-0              acepack_1.3-3.3          AnnotationDbi_1.26.1     base64enc_0.1-2         
 [5] BatchJobs_1.5            BBmisc_1.8               Biobase_2.24.0           BiocParallel_0.6.1      
 [9] Biostrings_2.32.1        biovizBase_1.12.3        bitops_1.0-6             brew_1.0-6              
[13] BSgenome_1.32.0          checkmate_1.5.0          cluster_1.15.3           codetools_0.2-9         
[17] colorspace_1.2-4         colortools_0.1.5         DBI_0.3.1                dichromat_2.0-0         
[21] digest_0.6.4             fail_1.2                 foreach_1.4.2            foreign_0.8-61          
[25] Formula_1.1-2            GenomicAlignments_1.0.6  GenomicFeatures_1.16.3   ggbio_1.12.10           
[29] ggplot2_1.0.0            gridExtra_0.9.1          gtable_0.1.2             gWidgets_0.0-54         
[33] gWidgetstcltk_0.0-55     hash_2.2.6               Hmisc_3.14-5             iterators_1.0.7         
[37] jpeg_0.1-8               lattice_0.20-29          latticeExtra_0.6-26      locfit_1.5-9.1          
[41] MASS_7.3-34              matrixStats_0.10.3       munsell_0.4.2            nnet_7.3-8              
[45] pbapply_1.1-1            plyr_1.8.1               png_0.1-7                proto_0.3-10            
[49] RColorBrewer_1.0-5       Rcpp_0.11.3              RCurl_1.95-4.3           reshape2_1.4            
[53] R.methodsS3_1.6.1        rpart_4.1-8              Rsamtools_1.16.1         RSQLite_1.0.0           
[57] scales_0.2.4             sendmailR_1.2-1          splines_3.1.1            stats4_3.1.1            
[61] stringr_0.6.2            survival_2.37-7          tcltk_3.1.1              tiff_0.1-5              
[65] tools_3.1.1              trackViewer_1.0.2        VariantAnnotation_1.10.5 XML_3.98-1.1            
[69] zlibbioc_1.10.0        

Hi Tiphaine,

could you please include the code that creates the martENSEMBL object in order for me to reproduce this?

Thanks.