writeVcf error with latest version 1.28.2

Hi,
the latest VariantAnnotation update in stable and devel somehow broke my package PureCN.
library(PureCN)
data(purecn.example.output)
purecnVcf <- predictSomatic(purecn.example.output, return.vcf=TRUE)
writeVcf(purecnVcf, file="Sample1_PureCN.vcf")
Error in if (idx != 1) { : argument is of length zero
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14.1

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

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] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] PureCN_1.13.5               DNAcopy_1.56.0             
 [3] VariantAnnotation_1.28.2    Rsamtools_1.34.0           
 [5] Biostrings_2.50.1           XVector_0.22.0             
 [7] SummarizedExperiment_1.12.0 DelayedArray_0.8.0         
 [9] BiocParallel_1.16.0         matrixStats_0.54.0         
[11] Biobase_2.42.0              GenomicRanges_1.34.0       
[13] GenomeInfoDb_1.18.1         IRanges_2.16.0             
[15] S4Vectors_0.20.1            BiocGenerics_0.28.0        

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0               lattice_0.20-38          prettyunits_1.0.2       
 [4] assertthat_0.2.0         digest_0.6.18            R6_2.3.0                
 [7] plyr_1.8.4               futile.options_1.0.1     RSQLite_2.1.1           
[10] httr_1.3.1               ggplot2_3.1.0            pillar_1.3.0            
[13] zlibbioc_1.28.0          rlang_0.3.0.1            GenomicFeatures_1.34.1  
[16] progress_1.2.0           lazyeval_0.2.1           data.table_1.11.8       
[19] blob_1.1.1               Matrix_1.2-15            splines_3.5.1           
[22] stringr_1.3.1            RCurl_1.95-4.11          bit_1.1-14              
[25] biomaRt_2.38.0           munsell_0.5.0            compiler_3.5.1          
[28] rtracklayer_1.42.0       pkgconfig_2.0.2          gridExtra_2.3           
[31] tibble_1.4.2             GenomeInfoDbData_1.2.0   XML_3.98-1.16           
[34] crayon_1.3.4             GenomicAlignments_1.18.0 bitops_1.0-6            
[37] grid_3.5.1               gtable_0.2.0             DBI_1.0.0               
[40] magrittr_1.5             formatR_1.5              scales_1.0.0            
[43] stringi_1.2.4            futile.logger_1.4.3      Rhdf5lib_1.4.0          
[46] lambda.r_1.2.3           RColorBrewer_1.1-2       tools_3.5.1             
[49] bit64_0.9-7              BSgenome_1.50.0          hms_0.4.2               
[52] rhdf5_2.26.0             AnnotationDbi_1.44.0     colorspace_1.3-2        
[55] BiocManager_1.30.4       memoise_1.1.0            VGAM_1.0-6
Bioconductor / VariantAnnotation

writeVcf error with latest version 1.28.2 #16
