greetings!  i'm using the development version of bioconductor with R-devel source from 3/23, rstudio 0.98.1103 running on ubuntu 14.04.

after converting a bed-bim-fam file set to vcf with the latest github pull of plink-ng (plink v1.90), i am getting this error using "readVcf("file.vcf", geno = "B36")" : 

"Error: scanVcf: _DNAencode(): key 73 not in lookup table"

originally i converted file.vcf to file.bcf using "bcftools view -O b -o file.bcf file.vcf" but both ReadVcf() and scanBcfHeader() crashed the R session!  scanVcfHeader() works and using "bcftools view -h" gives:

##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20150324
##source=PLINKv1.90
##contig=<ID=1,length=247189097>
##contig=<ID=2,length=242692821>
##contig=<ID=3,length=199318589>
##contig=<ID=4,length=191182473>
##contig=<ID=5,length=180642522>
##contig=<ID=6,length=170761396>
##contig=<ID=7,length=158812248>
##contig=<ID=8,length=146264219>
##contig=<ID=9,length=140147761>
##contig=<ID=10,length=135284294>
##contig=<ID=11,length=134445627>
##contig=<ID=12,length=132288870>
##contig=<ID=13,length=114109502>
##contig=<ID=14,length=106358709>
##contig=<ID=15,length=100217561>
##contig=<ID=16,length=88677424>
##contig=<ID=17,length=78653170>
##contig=<ID=18,length=76116153>
##contig=<ID=19,length=63785949>
##contig=<ID=20,length=62382908>
##contig=<ID=21,length=46919232>
##contig=<ID=22,length=49558259>
##contig=<ID=23,length=154582607>
##contig=<ID=24,length=27169977>
##contig=<ID=25,length=154908076>
##contig=<ID=26,length=16394>
##INFO=<ID=PR,Number=0,Type=Flag,Description="Provisional reference allele, may not be based on real reference genome">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##bcftools_viewVersion=1.2-5-g7fa0d25+htslib-1.2.1-29-gf83dfd2
##bcftools_viewCommand=view -O b -o file.bcf file.vcf
##bcftools_viewCommand=view -h -o w_header file.bcf
#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    BI0011_BI0011    BI0017_BI0017 ...

any info on what this error means and if/how the file can be repaired would be greatly appreciated.

> sessionInfo()
R Under development (unstable) (2015-03-23 r68069)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS

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

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

other attached packages:
 [1] VariantAnnotation_1.13.44 Rsamtools_1.19.47         Biostrings_2.35.11        XVector_0.7.4             rtracklayer_1.27.9        GenomicRanges_1.19.47    
 [7] GenomeInfoDb_1.3.15       IRanges_2.1.43            S4Vectors_0.5.22          BiocGenerics_0.13.8      

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.29.20    zlibbioc_1.13.3          GenomicAlignments_1.3.32 BiocParallel_1.1.21      BSgenome_1.35.19         tools_3.3.0             
 [7] Biobase_2.27.2           DBI_0.3.1                lambda.r_1.1.7           futile.logger_1.4        futile.options_1.0.0     bitops_1.0-6            
[13] RCurl_1.95-4.5           biomaRt_2.23.5           RSQLite_1.0.0            GenomicFeatures_1.19.33  XML_3.98-1.1