I am seeing an error in the devel version of VariantAnnotation for VCF to VRanges conversion after this commit.

> library(VariantAnnotation)
> ​fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
> vcf <- readVcf(fl, "hg19")
> as(vcf, "VRanges")
Error in if allis.na(x)) || all(x == "PASS")) return(FilterMatrix(matrix(nrow = length(x),  : 
  missing value where TRUE/FALSE needed

> traceback()
3: parseFilterStrings(rd$FILTER)
2: asMethod(object)
1: as(vcf, "VRanges")

> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.5 (El Capitan)
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] VariantAnnotation_1.19.4   Rsamtools_1.25.0          
 [3] Biostrings_2.41.4          XVector_0.13.2            
 [5] SummarizedExperiment_1.3.6 Biobase_2.33.0            
 [7] GenomicRanges_1.25.8       GenomeInfoDb_1.9.1        
 [9] IRanges_2.7.11             S4Vectors_0.11.7          
[11] BiocGenerics_0.19.1       
loaded via a namespace (and not attached):
 [1] XML_3.98-1.4            GenomicAlignments_1.9.4 bitops_1.0-6           
 [4] DBI_0.4-1               RSQLite_1.0.0           GenomicFeatures_1.25.14
 [7] zlibbioc_1.19.0         BiocParallel_1.7.4      tools_3.3.0            
[10] BSgenome_1.41.2         biomaRt_2.29.2          RCurl_1.95-4.8         
[13] rtracklayer_1.33.8      AnnotationDbi_1.35.3  

Thanks, should be fixed in 1.19.5.