Minimal reproducible example:

library(VariantAnnotation)
con <- url("https://raw.githubusercontent.com/timflutre/rutilstimflutre/master/inst/extdata/example.vcf")
vcf.txt <- readLines(con)
close(con)
vcf.file <- "example.vcf"
writeLines(vcf.txt, vcf.file)
vcf <- readVcf(vcf.file)
geno(vcf)$GT

which returns:

ind1 ind2 ind3
snp1   "0/0" "0/1" "1/1"
snp2   "0/1" "."   "."
indel1 "0/0" "0/1" "1/1"

However, "." should be "./.", as in the input file and in the VCF format specification. Or am I missing something?

ps: here is my sessionInfo()

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] 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
[8] methods   base     

other attached packages:
 [1] VariantAnnotation_1.20.2   Rsamtools_1.26.1          
 [3] Biostrings_2.42.0          XVector_0.14.0            
 [5] SummarizedExperiment_1.4.0 Biobase_2.34.0            
 [7] GenomicRanges_1.26.1       GenomeInfoDb_1.10.1       
 [9] IRanges_2.8.1              S4Vectors_0.12.0          
[11] BiocGenerics_0.20.0       

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.8              AnnotationDbi_1.36.0     GenomicAlignments_1.10.0
 [4] zlibbioc_1.20.0          BiocParallel_1.8.1       BSgenome_1.42.0         
 [7] lattice_0.20-34          tools_3.3.2              grid_3.3.2              
[10] DBI_0.5-1                digest_0.6.10            Matrix_1.2-8            
[13] rtracklayer_1.34.1       bitops_1.0-6             biomaRt_2.30.0          
[16] RCurl_1.95-4.8           memoise_1.0.0            RSQLite_1.1-2           
[19] compiler_3.3.2           GenomicFeatures_1.26.0   XML_3.98-1.5