Not sure what happened. This works in R 3.1.1 with VariantAnnotation_1.12.9. I'm getting an error that says that "keepNA" is missing when reading the header for this VCF file.

> library(VariantAnnotation)
> snpfile = "ftp://ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/mgp.v5.merged.snps_all.dbSNP142.vcf.gz"
> hdr = scanVcfHeader(file = snpfile)
Error in FUN(X[[i]], ...) :
  could not find symbol "keepNA" in environment of the generic function
>

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] VariantAnnotation_1.14.6 Rsamtools_1.20.4         Biostrings_2.36.1       
 [4] XVector_0.8.0            GenomicRanges_1.20.5     GenomeInfoDb_1.4.1      
 [7] IRanges_2.2.5            S4Vectors_0.6.1          BiocGenerics_0.14.0     
[10] BiocInstaller_1.18.3    

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.30.1    zlibbioc_1.14.0         GenomicAlignments_1.4.1
 [4] BiocParallel_1.2.7      BSgenome_1.36.2         tools_3.2.0            
 [7] Biobase_2.28.0          DBI_0.3.1               lambda.r_1.1.7         
[10] futile.logger_1.4.1     rtracklayer_1.28.6      futile.options_1.0.0   
[13] bitops_1.0-6            RCurl_1.95-4.7          biomaRt_2.24.0         
[16] RSQLite_1.0.0           GenomicFeatures_1.20.1  XML_3.98-1.3           
>

I can't reproduce this error in windows or unix.

> snpfile
[1] "ftp://ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/mgp.v5.merged.snps_all.dbSNP142.vcf
.gz"
> hdr = scanVcfHeader(snpfile)
> hdr
class: VCFHeader
samples(36): 129P2_OlaHsd 129S1_SvImJ ... WSB_EiJ ZALENDE_EiJ
meta(2): META contig
fixed(3): FILTER ALT QUAL
info(4): INDEL DP DP4 CSQ
geno(14): GT GQ ... PV4 FI

> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2008 R2 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages:
[1] VariantAnnotation_1.14.6 Rsamtools_1.20.4         Biostrings_2.36.1
[4] XVector_0.8.0            GenomicRanges_1.20.5     GenomeInfoDb_1.4.1
[7] IRanges_2.2.5            S4Vectors_0.6.1          BiocGenerics_0.14.0

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.30.1    zlibbioc_1.14.0         GenomicAlignments_1.4.1
 [4] BiocParallel_1.2.7      BSgenome_1.36.2         tools_3.2.1
 [7] Biobase_2.28.0          DBI_0.3.1               lambda.r_1.1.7
[10] futile.logger_1.4.1     rtracklayer_1.28.6      futile.options_1.0.0
[13] bitops_1.0-6            RCurl_1.95-4.7          biomaRt_2.24.0
[16] RSQLite_1.0.0           GenomicFeatures_1.20.1  XML_3.98-1.3
>

The only versions difference I see is R 3.2.0 vs 3.2.1. 'keepNA' is an Rboolean in Rinternals.h - looking at the svn logs it's tough to pinpoint anything obvious related to this. I'm assuming this is a reproducible error for you in a fresh R session?

Valerie

Yes, it's definitely reproducible.  However, I uninstalled R and Rtools and installed R 3.2.1 and Rtools 3.2.  Then I updated all of my Bioconductor packages and now the bug is gone.  Sorry for the false alarm. I didn't think that the minor R 3.2.1 release would make a difference.