Dear developers,

I am trying to find my way to plot VCF objects nicely, and I cannot run code from the help page (a section of "code not run" which may not have been tested in a while). Any suggestion? Thank you!

> library(VariantAnnotation)
> vcffile <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
> vcf <- readVcf(vcffile, "hg19")
> ## default use type 'geno'
> ## default use genome position
> autoplot(vcf)
none geom is used
Error in data.frame(seqnames = as.factor(seqnames(x)), start = start(x),  :
  duplicate row.names: rs7410291, rs147922003, rs114143073, rs141778433, rs182170314, rs115145310, rs186769856, rs77627744, rs193230365, rs9627788, rs151129704, rs114659385, rs9627789, rs73443949, rs141100913, rs77481841, rs77619365, rs117571035, rs9616366, rs185633079, rs73443951, rs190097286, rs137922648, rs114335781, rs8135963, 22:50301488_C/T, 22:50301494_G/A, 22:50301584_C/T, 22:50301622_C/T, rs9627644, rs192916413, rs149477000, rs138658289, 22:50301957_C/CT, rs59612223, 22:50302021_CA/C, rs146271548, rs148469139, rs183994690, rs114727878, rs188676427, rs141791452, rs73181156, rs150605490, rs139702490, rs112796939, rs11702974, rs11703253, rs145507838, rs12166846, rs11704446, rs181416164, rs185259665, rs4075331, rs145358718, rs188399257, rs114264124, rs149209714, 22:50303006_A/G, rs76354698, rs75496139, rs182276967, rs143405289, rs56810176, rs115670095, rs187270471, rs4075330, rs80251032, rs150925909, rs9616367, rs9616204, rs9616368, 22:50303554_T/C, rs12167668, rs140835842

And the sessionInfo()

R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

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

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

other attached packages:
 [1] ggbio_1.20.1               ggplot2_2.1.0              BiocInstaller_1.22.2       VariantAnnotation_1.18.1   Rsamtools_1.24.0          
 [6] Biostrings_2.40.1          XVector_0.12.0             SummarizedExperiment_1.2.2 Biobase_2.32.0             GenomicRanges_1.24.0      
[11] GenomeInfoDb_1.8.1         IRanges_2.6.0              S4Vectors_0.10.1           BiocGenerics_0.18.0       

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.5                   biovizBase_1.20.0             lattice_0.20-33               digest_0.6.9                 
 [5] mime_0.4                      R6_2.1.2                      plyr_1.8.3                    chron_2.3-47                 
 [9] acepack_1.3-3.3               RSQLite_1.0.0                 httr_1.1.0                    zlibbioc_1.18.0              
[13] GenomicFeatures_1.24.2        data.table_1.9.6              rpart_4.1-10                  Matrix_1.2-6                 
[17] splines_3.3.0                 BiocParallel_1.6.2            AnnotationHub_2.4.2           stringr_1.0.0                
[21] foreign_0.8-66                RCurl_1.95-4.8                biomaRt_2.28.0                munsell_0.4.3                
[25] shiny_0.13.2                  httpuv_1.3.3                  rtracklayer_1.32.0            htmltools_0.3.5              
[29] nnet_7.3-12                   gridExtra_2.2.1               interactiveDisplayBase_1.10.3 Hmisc_3.17-4                 
[33] XML_3.98-1.4                  reshape_0.8.5                 GenomicAlignments_1.8.0       bitops_1.0-6                 
[37] grid_3.3.0                    RBGL_1.48.1                   xtable_1.8-2                  GGally_1.0.1                 
[41] gtable_0.2.0                  DBI_0.4-1                     magrittr_1.5                  scales_0.4.0                 
[45] graph_1.50.0                  stringi_1.1.1                 reshape2_1.4.1                latticeExtra_0.6-28          
[49] Formula_1.2-1                 RColorBrewer_1.1-2            ensembldb_1.4.3               tools_3.3.0                  
[53] dichromat_2.0-0               BSgenome_1.40.0               OrganismDbi_1.14.1            rsconnect_0.4.3              
[57] survival_2.39-4               AnnotationDbi_1.34.3          colorspace_1.2-6              cluster_2.0.4