writeVcf: Error in recycleSingleBracketReplacementValue

Hi,

my package started to fail in devel because of an error in writeVcf. There are a couple of warnings where the genome version is ""hg19"" instead of "hg19". Not sure that's related and an error on my side.

Thanks, Markus

@vobencha

>library(PureCN)
>data(purecn.example.output)
>purecnVcf <- predictSomatic(purecn.example.output, return.vcf=TRUE)
>writeVcf(purecnVcf, file="Sample1_PureCN.vcf")
Error in recycleSingleBracketReplacementValue(value, x) : 
  replacement has length zero
>sessionInfo()
R Under development (unstable) (2019-03-18 r76245)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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_1.13.21              VariantAnnotation_1.29.23  
 [3] Rsamtools_1.99.3            Biostrings_2.51.5          
 [5] XVector_0.23.2              SummarizedExperiment_1.13.0
 [7] DelayedArray_0.9.8          BiocParallel_1.17.18       
 [9] matrixStats_0.54.0          Biobase_2.43.1             
[11] GenomicRanges_1.35.1        GenomeInfoDb_1.19.2        
[13] IRanges_2.17.4              S4Vectors_0.21.16          
[15] BiocGenerics_0.29.2         DNAcopy_1.57.0             

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0               lattice_0.20-38          prettyunits_1.0.2       
 [4] assertthat_0.2.1         digest_0.6.18            R6_2.4.0                
 [7] plyr_1.8.4               futile.options_1.0.1     RSQLite_2.1.1           
[10] httr_1.4.0               ggplot2_3.1.0            pillar_1.3.1            
[13] zlibbioc_1.29.0          rlang_0.3.1              GenomicFeatures_1.35.8  
[16] progress_1.2.0           lazyeval_0.2.1           data.table_1.12.0       
[19] blob_1.1.1               Matrix_1.2-17            splines_3.6.0           
[22] stringr_1.4.0            RCurl_1.95-4.12          bit_1.1-14              
[25] biomaRt_2.39.2           munsell_0.5.0            compiler_3.6.0          
[28] rtracklayer_1.43.3       pkgconfig_2.0.2          tibble_2.1.1            
[31] gridExtra_2.3            GenomeInfoDbData_1.2.0   XML_3.98-1.19           
[34] crayon_1.3.4             GenomicAlignments_1.19.1 bitops_1.0-6            
[37] grid_3.6.0               gtable_0.2.0             DBI_1.0.0               
[40] magrittr_1.5             formatR_1.6              scales_1.0.0            
[43] stringi_1.4.3            futile.logger_1.4.3      Rhdf5lib_1.5.1          
[46] lambda.r_1.2.3           RColorBrewer_1.1-2       tools_3.6.0             
[49] bit64_0.9-7              BSgenome_1.51.0          hms_0.4.2               
[52] rhdf5_2.27.15            AnnotationDbi_1.45.1     colorspace_1.4-0        
[55] memoise_1.1.0            VGAM_1.1-1

Bioconductor / VariantAnnotation

writeVcf: Error in recycleSingleBracketReplacementValue #26